Hemp Growing

Cattle are not affected by the toxins but humans may be severely impacted. Goats, sheep, feral pigs, and deer are also considered animals of significant risk for shedding E. coli O157:H7. Others, such as elk, coyotes, and raccoons, have also been shown to harbor this pathogen. Other wild animals, including birds, can acquire the bacteria from various sources, serve as a transient reservoir, or mechanically vector E. coli O157:H7 bacteria across a landscape. Although relatively limited in scope, studies assessing the seasonal association of E. coli O157:H7 in wildlife have generally concluded that the prevalence is very low or generally not detected in most regions studied . However, when there is a local potential source of E. coli O157:H7, such as a nearby dairy operation or feedlot, the prevalence can be much higher, and transmission between plant and animal agriculture may be demonstrated by genetic matches in isolates from the source and in associated rodents and birds visiting both areas . The two most common ways that E. coli O157:H7 can be spread from cattle into the environment and agricultural landscapes are through the land application of raw, uncomposted manure and through runoff of manure or lagoon water into streams and irrigation ditches. Bioaerosols of buoyant fine particulates have been suggested as another probable source of localized spread. Implementation of good agricultural practices as defined by the commodity specific food safety guidelines for the production and harvest of lettuce and leafy greens will help minimize risks of contamination of crops with E. coli O157:H7 . For hedgerows, the GAPs for leafy greens will likely require periodic monitoring of fields adjacent to wildlife habitat, cannabis drying system both for evidence of intrusion by animals of significant risk for carrying E. coli O157:H7 , as well as smaller known or potential vectors such as rodents and birds.

Presence of these smaller animals may also indicate the attraction of predators, such as coyotes, also shown to be potential vectors. If there is evidence of intrusion by animals, the production block must undergo a detailed food safety assessment by appropriately trained food safety personnel. The Salmonella spp. food safety issue is essentially the same as that for E. coli O157:H7, but the focus tends to turn to habitat for birds, reptiles, rodents, and amphibians. Apart from reptiles, in some areas, the prevalence and frequency of transmission again tends to be low except in association with significant point sources such as dairy, poultry, cattle, and swine production operations. However, Salmonella seems to have a much more prevalent environmental phase, so there is building evidence for a baseline that one is unlikely to escape. Hence, a mitigation treatment to reduce the threat of salmonellosis is needed if tolerated by the crop . Although much research remains to be done on the epidemiology of E. coli O157:H7, hedgerows around farms may actually help reduce the risk of E. coli O157:H7 by helping to trap and filter harmful pathogens in dust and irrigation or storm water runoff .Endemic and invasive weeds are important management concerns in California due to their direct and indirect costs to agriculture, the environment and society. Pimentel et al. estimated that weeds cost U.S. crop producers and pasture managers over $30 billion in control-related expenses and reduced productivity. Although specific data are not available for California’s portion of these losses, weed management costs for the state’s 40 million acres of crop and grazing lands, as well as the remaining 60 million acres of land area, amount, undoubtedly, to several billion dollars annually. In addition to the direct cost of weed control and lost agricultural productivity, weeds also affect ecosystem quality and function, reduce recreational access and degrade aesthetics in natural areas, change wild land fire regimes and severity, and impede water flow through rivers and canals, among other negative impacts.

Although crop weeds are seldom considered as being “invasive” in the traditional sense, novel biotypes can develop, spread and subsequently occupy a greater proportion of crop acreage than might normally be expected. For example, when a weed population evolves resistance to an herbicide or any other control measure, a “routine” pest can become a new and serious problem. The first case of an herbicide-resistant weed in California was reported in 1981 by UC scientists ; in recent years, additional species have evolved resistance to various herbicide chemistries used in some of California’s signature cropping systems, including flooded rice, orchards and vineyards as well as nearby non-crop areas.Environmental factors and production practices influence species composition at any location, a phenomenon known as selection pressure. Under constant conditions, the weed community will become dominated by species that thrive under those conditions. If this steady state is upset by a change in management practices, a weed shift may occur, resulting in a community dominated by different species adapted to the new conditions . This weed shift can be caused by agronomic and horticultural practices or by the use of herbicides, which are very strong selective agents. Some species will be less susceptible than others to any management practice, and repeated use of the same control strategy can shift weed populations to become dominated by naturally tolerant species . Herbicide resistance, on the other hand, implies that a genetic change has caused a formerly susceptible population of a species to become resistant to an herbicide. Herbicide resistance arises from the process of adaptive evolution, whereby mutations change the physiology of plants in such a way that the herbicide is less effective. Under the continued selection pressure exerted by the herbicide, resistant plants with the new genotype are not controlled, and their offspring build up in the population .

Depending on the initial frequency and genetic basis of resistance, the regularity and rate of herbicide applications, and the reproductive system of the weed, it may take from a few to many generations for resistance to become. The strongest selection pressure for herbicide-resistant weeds tends to be in modern, high-intensity agricultural cropping systems due to a high reliance on herbicides. According to the International Survey of Herbicide Resistant Weeds , since the first confirmed report of a resistant biotype in 1957, herbicide-resistant weed biotypes have been reported in at least 60 countries and include more than 400 unique species-herbicide group combinations . The United States has more herbicide-resistant biotypes than any other country , and California accounts for 21 of these . Worldwide, resistance to acetolactate synthase –inhibiting herbicides and photo system II –inhibiting herbicides are the most commonly occurring among weedy species. However, in recent years, glyphosate resistance and multiple resistances have also emerged as major problems in some cropping systems. Interestingly, while herbicide resistance in the United States as a whole is primarily found in broadleaf weeds, California has more herbicide-resistant grasses or sedges than broadleaf species . Due to the extensive use of preplant and in-season tillage in some agronomic crops in California, drying rack for weed along with the use of pre- and postemergence herbicides, herbicide resistance is not as widespread as it is in other parts of the country where no-till and minimum-till systems have been widely adopted. Reduced tillage systems are heavily reliant on a few herbicide modes of action and have correspondingly larger problems with herbicide resistance . In contrast to the rest of the United States, where herbicide resistance problems are centered on agronomic crops, the greatest problems with herbicide resistant weeds in California are in orchards, vineyards, flooded rice, roadsides and irrigation canal banks. Herbicideresistant weeds have become especially challenging problems in California’s signature cropping systems, which are characterized by little or no crop rotation due to soil limitations or long cropping cycles and relatively few opportunities for mechanical weed control. Although large by specialty crop standards, the approximately 3 million acres devoted to orchard, vineyard and rice production in California is a small market for herbicide manufacturers; thus, herbicide options are somewhat limited. Combined, these factors have led to a high degree of selection pressure for herbicide-resistant weed biotypes as well as weed population shifts to naturally tolerant species .In order to combat complex issues such as herbicide resistance, organized collaborations between weed scientists and other agricultural researchers with a wide array of expertise are required. This includes the activities of UC Cooperative Extension farm advisors and specialists, Agricultural Experiment Station faculty, support scientists, research staff and graduate students, as well as faculty from other universities and agricultural industry representatives .

Current herbicide-resistant weed management efforts range from applied research and extension efforts to basic plant biology and evolutionary ecology studies. Although the specifics vary, these efforts can be grouped into three general areas: applied management of herbicide-resistant plants, physiology and mechanisms of resistance and biology, ecology and evolution of herbicide resistance. Applied management of herbicide resistant plants. Many cases of herbicide resistance in weeds are identified after growers, land managers or pest control advisers observe weed control failures with treatments that were once effective. These weeds are generally brought to the attention of local or statewide Cooperative Extension personnel. If the herbicide application method is ruled out as the cause of poor weed control , researchers often conduct field or greenhouse tests to verify and quantify the level of resistance. Plants from the suspected herbicide-resistant population are treated with the herbicide of interest at rates ranging from below normal doses to doses well above those legally allowed in the field . The response of the putative resistant population is then compared with the response of the known susceptible, or wild-type, population. Resistance is confirmed if the herbicide affects the two populations of the same species in markedly different ways with respect to plant growth and survival. In many cases, an estimate of the level of resistance also is made from these data. For example, if the susceptible population is controlled at one-half the field rate, but the resistant population survives at twice the field rate, it would be described as having a fourfold level of resistance. Physiology and mechanisms of herbicide resistance. Identifying and verifying herbicide resistance and developing alternative management strategies provides short-term solutions for weed managers. Researchers often conduct further studies to determine the underlying molecular and physiological causes of resistance and to compare the biology, growth and competitive ability of herbicide-resistant species and biotypes. The mechanism and fitness costs of herbicide resistance can have important ramifications on the selection, spread and competitive ability of herbicide-resistant biotypes, in addition to directly impacting their management. The goal of these efforts is to help growers and pest control advisers recognize the importance of taking a proactive approach to preventing the evolution of a resistant population, rather than a reactive approach to managing herbicide resistance after it occurs. Target-site resistance occurs when the enzyme that is the target of the herbicide becomes less sensitive, or fully insensitive, to the herbicide, often due to a physical change in the target enzyme’s structure. These physical changes can impair the ability of the herbicide to attach to a specific binding site on the enzyme, thus reducing or eliminating herbicidal activity. Target-site resistance is sometimes evaluated at the tissue level using portions of plants such as leaves, leaf disks or roots . In some cases, a functioning target enzyme can be extracted and its function evaluated in laboratory in vitro experiments in the presence or absence of the herbicide. Recently, overproduction or enhanced activity of the target enzyme has been shown to confer herbicide resistance in certain cases . Several mechanisms of non-target-site resistance confer resistance to herbicides in plants without involving the target sites of the herbicides. This can result in unpredictable resistance to unrelated herbicides . Of these, the best-known cases involve resistance in which herbicide-resistant plants have an enhanced ability to metabolically degrade the herbicide to less- ornontoxic forms. Many processes can be involved in metabolic resistance, but the most well-understood cases are due to changes in three groups of isozymes and changes in ATP-binding cassette transporters . This type of resistance is most commonly evaluated using nonherbicidal inhibitors of the various isozymes in the presence or absence of the herbicide and comparing metabolic degradation of the herbicide in laboratory or greenhouse assays. Biology, ecology and evolution of herbicide resistance. 

The use of short-residual herbicides also reduces selection pressure for herbicide resistance. In addition, tank-mixing of herbicides with different modes of action can inhibit the evolution of resistance, but the combinations used should broaden the spectrum of weeds controlled along with controlling the weed species of major concern. If two herbicides have nearly the same weed control spectrum, you would do better to rotate between them rather than tank-mix the two compounds; little additional control will be achieved by adding the second material. Though unlikely, it is possible in theory that a weed population will simultaneously be selected for resistance to both herbicides. While weeds have traits that enhance their potential to evolve resistance, they also have traits that reduce that potential. Weed species with seeds that remain dormant in the soil for several years will maintain a population of susceptible plants within the seed bank. By maintaining susceptible plants in the population, a grower can dilute the resistance trait. If there is a fitness cost to resistance, removing the herbicide at some point in the crop rotation cycle will allow competition between the resistant and susceptible plants, further diluting the gene pool for the resistance trait. Besides the practice of crop rotation, certified seed, equipment sanitation, cultivation, and hand-weeding all impede resistance evolution. Resistance problems usually go undetected until land managers or farmers observe about 30 percent weed control failure for a particular species. If you can identify these resistant weed patches early, curing marijuana before their populations increase, you can employ management practices that prevent their spread.

If weed escapes appear in patterns such as distinct strips, or if several species normally controlled by the herbicide are present in these strips, the problem probably is associated with a calibration or application error. However, patches made up of only one escaped species and showing no distinctive pattern may indicate a herbicide-resistant population. Suspicious areas should be brought to the attention of a Farm Advisor or Extension Specialist, especially if weed populations reoccur in subsequent years after use of the same herbicide.However, weed species shifts and the selection for glyphosate-resistant weeds can result from the increased use of this technology if the crop is not managed properly from the outset. Aspects of the alfalfa production system both favor and discourage the occurrence of weed shifts and the evolution of resistant weeds. Alfalfa is a competitive perennial crop that is cut multiple times per year, making it difficult for most weeds to become established. On the other hand, the RR alfalfa system may be vulnerable to weed shifts and resistant weeds for several reasons: tillage typically only occurs between crops, alfalfa is produced over a wide geographical area and in large fields with a great diversity of weeds, and there is potential for long-term repeated use of a single herbicide because it is a perennial crop. In this publication we recommend an integrated weed management system designed to prevent the proliferation of tolerant or resistant weeds. Elements include crop rotation, rotations with herbicides of different modes of action , tank mixtures, and irrigation and harvest timing. Successful adaptation of these concepts into production systems would assure the long-term effectiveness and sustainability of the Roundup Ready system in alfalfa.

A preemptive approach is warranted; these strategies should be employed before weed shifts and weed resistance occur.Alfalfa, the queen of forages, is the principal forage crop in the United States and frequently the third most important crop in value. It is a vital component of the feed ration for dairy cows and is a principal feed for horses, beef cattle, sheep, and other livestock. Because animal performance depends upon the palatability and nutritional value of alfalfa, livestock managers, especially those in the dairy and horse industry, expect high-quality hay. Although many factors influence quality, the presence of grassy and broadleaf weeds plays a significant role in reducing the feeding value of hay throughout the United States. Weeds that accumulate nitrates or are poisonous to livestock are also a major concern in alfalfa, since poisonous weeds sicken or kill animals every year . Most livestock producers demand weed-free alfalfa for optimum quality and maximum animal performance. Weed-free alfalfa can be difficult to achieve, whether using non-chemical methods or conventional herbicides. Typically, no single herbicide controls all weeds present in a field, and some weeds—especially perennials—are not adequately controlled with any of the currently registered conventional herbicides. Cultural practices such as modifying harvest schedules, grazing, time of planting, and use of nurse crops such as oats help suppress weeds; however, these practices are almost never entirely effective and some of them suppress alfalfa seedling growth. In addition to being difficult to achieve, complete weed control in alfalfa is costly. Alfalfa growers continually seek ways to enhance the level of weed control while minimizing costs.Glyphosate is generally considered the most effective broad spectrum post-emergence herbicide available. The first commercially available glyphosate-resistant crops were soybean, canola, cotton, and corn, which were released in 1996, 1997, 1997, and 1998, respectively. Glyphosate-resistant or Roundup Ready alfalfa was developed through biotechnology in late 1997 and became commercially available in the fall of 2005.

This technology imparts genetic resistance to glyphosate by inserting a single gene from a soil bacterium into alfalfa. These biotechnology-derived alfalfa plants have an altered enzyme that allows them to tolerate a glyphosate application while susceptible weeds are killed. Glyphosate resistance is the first commercially available, genetically engineered trait in alfalfa. This technology was a major development in alfalfa weed control, providing growers with a useful weed management tool and a means to deal with some of the most difficult-to-control weed species. Researchers have evaluated its effectiveness as a weed control strategy . The advantages and disadvantages of this technology have been reviewed . Glyphosate was found to be especially effective for weed control in seeding alfalfa . Glyphosate typically causes no perceptible crop injury, is much more flexible and less restrictive in application, and provides superior weed control across a range of weed species when compared with other currently used herbicides. One of the greatest advantages of this technology is that it provides a tool for suppressing perennial weeds such as dandelion , yellow nutsedge , bermudagrass Pers., and quackgrass Nevski that have not been adequately controlled with conventional practices. After deregulation of this trait in 2005, over 300,000 acres of RR alfalfa were planted in the United States, about 1.4 percent of U.S. acreage. However, in the spring of 2007, further plantings were suspended pending the outcome of a legal challenge and further environmental analysis by the U.S. Department of Agriculture’s Animal and Plant Health Inspection Service . There were two key issues in this process: the possibility of contamination of organic and conventional alfalfa through the adventitious presence of the gene, and the possibility of a greater level of weed resistance due to the adoption of the Roundup Ready technology in alfalfa . Grower experience in commercial fields following deregulation confirmed many of the benefits that early research had suggested in terms of the efficacy and safety of the RR system . Growers have generally found that this technology is easy to use and provides superior weed control and improved forage quality in many cases compared with conventional herbicides. However, no new technology is a panacea, and, pipp mobile storage like other weed control strategies, RR alfalfa has its limitations. An important limitation of this new weed-management system is the potential for weed shifts and weed resistance. This publication discusses techniques that are available to manage the possibility of weed shifts and weed resistance occurring in Roundup Ready alfalfa weed control systems.Change in weed populations as a result of repeated use of a single herbicide is not a new phenomenon. Such changes result from shifts in the weeds present from susceptible to tolerant species, or conversion of a population within a species to resistant individuals, as a consequence of selection pressure .In the case of chemical weed control, no single herbicide controls all weeds, as weeds differ in their susceptibility to an herbicide. This allows inherently tolerant weed species to remain, which often thrive and proliferate with the reduced competition. As a result, there is a gradual shift to tolerant weed species when practices are continuously used that are not effective against those species.

A weed shift does not necessarily have to be a shift to a different species. For example, with a foliar herbicide without residual activity like glyphosate, there could also be a shift within a weed species to a late-emerging biotype that emerges after application. In the case of weed shifts, the total population of weeds does not necessarily change as a result of an herbicide or an agronomic practice; these practices simply favor one species over another.In contrast to a weed shift, weed resistance is a change in the population of weeds that were previously susceptible to an herbicide, turning them into a population of the same species that is no longer controlled by that herbicide .While weed shifts can occur with any agronomic practice , the evolution of weed resistance is only the result of continued herbicide application. The use of a single class of herbicides continually over time creates selection pressure so that resistant individuals of a species survive and reproduce, while susceptible ones are killed.A weed species shift is far more common than weed resistance, and ordinarily takes less time to develop. If an herbicide does not control all the weeds, the tendency is to quickly jump to the conclusion that resistance has occurred. However, a weed shift is a far more likely explanation for weed escapes following an application of glyphosate. See table 1 for a list of weeds sometimes found in alfalfa fields that are tolerant to or difficult to control with glyphosate.A common misconception is that weed resistance is intrinsically linked to genetically engineered crops. However, this is not correct. The occurrence of weed shifts and weed resistance is not unique to genetically engineered crops. Weed shifts and resistance are caused by the practices that may accompany a GE crop , not the GE crop itself. Similarly, some people believe that herbicide resistance is transferred from the GE crop to weed species. However, unless a crop is genetically very closely related to a naturally-occurring weed, weed resistance cannot be transferred from crop to weed. In the case of alfalfa, there are no known wild plants that cross with alfalfa, so direct transfer of herbicide resistance through gene flow to weedy species will not occur. However, the glyphosate-tolerant genes from RR alfalfa can be transferred to feral alfalfa plants if cross pollination occurs.resistance is transferred from the GE crop to weed species. However, unless a crop is genetically very closely related to a naturally-occurring weed, weed resistance cannot be transferred from crop to weed. In the case of alfalfa, there are no known wild plants that cross with alfalfa, so direct transfer of herbicide resistance through gene flow to weedy species will not occur. However, the glyphosate-tolerant genes from RR alfalfa can be transferred to feral alfalfa plants if cross pollination occurs.Transgenic herbicide-resistant crops do, nonetheless, have greater potential to foster weed shifts and resistant weeds since a grower is more likely to use a single herbicide repeatedly in herbicide-resistant crops such as RR alfalfa. Additionally, the accumulation of acreage of different RR crops could increase the potential for weed shifts or weed resistance in cropping systems utilizing RR crops. This is because the probability of repeated use of the same herbicide is higher and the potential applied acreage is greater. Fortunately, there are simple methods available to prevent weed shifts and weed resistance from occurring. In studies conducted in San Joaquin County, California, weeds shifts were found to occur during the first few years of use when glyphosate-tolerant weeds were present . Annual bluegrass and shepherd’s purse were adequately controlled with glyphosate, whereas chickweed control was about 80 percent and burning nettle andannual sowthistle were not adequately controlled with any of the glyphosate rates . During the 3 years of this field trial, when glyphosate was used repeatedly, there was a gradual weed species shift away from annual bluegrass and shepherd’s purse to higher populations of burning nettle and annual sowthistle .

Intriguing differeIntriguing differentially expressed genes located within likelihood intervals of rhizome related quantitative trait loci include an auxilin/cyclin G-associated kinase , tandemly duplicated ethylene responsive transcription factors , and a Ca2 + /calmodulindependent protein kinase, EF-Hand protein superfamily gene . Both polyploidy and interspecific hybridity appear to contribute to the ‘mosaic’ nature of rhizome gene expression, with over expression of some homoeologs from rhizomatous S. propinquum and others from non-rhizomatous S. bicolor . For example, different calmodulin family members have evolved specificity to rhizome buds and shoot buds . Tandem duplicated ethylene responsive transcription factors within a rhizome-related QTL are both overexpressed in S. halepense rhizome buds, although the sequence of Sb07g006195 closely resembles S. propinquum and adjacent Sb07g006200 is identical to S. bicolor . The Teosinte-branched 1 growth repressor gene implicated in apical dominance of maize shoots has two family members with enriched expression in rhizome buds , ironically both completely matching the non-rhizomatous S. bicolor progenitor sequences .Introgression is suggested in a general sense by S. bicolor enriched allele composition of the S. halepense draft genome , and for specific genes by S. halepense SNP distribution patterns matching the S. bicolor reference genome of an elite breeding line , but differing from both several wild S. bicolors and each of two outgroups . Seven ‘hotspots’ for introgression of sorghum alleles in five geographically diverse US S. halepense populations , show non-random correspondence with published sorghum QTLs conferring variation in rhizome growth, curing cannabis seed size, and lutein content . While sorghum lacks rhizomes and has large seeds, rhizome growth-related alleles masked in domesticated sorghum genotypes by a lack of rhizomes may be unmasked in interspecific crosses with rhizomatous S. halepense.

Particularly intriguing among S. halepense introgression hotspots are those that correspond with 3 of 4 QTL likelihood intervals spanning 4.9% of the genome that account for variation in seed content of the carotenoid lutein . Sorghum leaf photosynthetic capacity is susceptible to damage under low-temperature but high-light conditions when electron transport exceeds the capacity of carbon fixation to utilize available energy . Such conditions are infrequent in the tropics where Sorghum originated but common in the temperate springtime. Spring regrowth of S. halepense starts about 4 weeks before cultivated sorghum is seeded at 38.7◦ N . Xanthophyll carotenoids such as lutein are most abundant in plant leaves, modulating light energy and performing non-photochemical quenching of excited ‘triplet’ chlorophyll which is overproduced at very high light levels during photosynthesis . Ironically, Sb01g030050 and Sb01g048860 related to lutein biosynthesis, are close to the only lutein QTL not near an introgression hotspot . Within the lutein QTL likelihood intervals, and homozygous in the Gypsum 9E , are also loss of function mutations in Sb01g013520, 9-cis epoxycarotenoid dioxygenase. This enzyme cleaves xanthophylls to xanthoxin, a precursor of the plant hormone abscisic acid  that plays a central role in regulating plant tissue quiescence. Also in the lutein QTL likelihood intervals are nonsynonymous SNPs inferred to have striking functional effects on Sb02g026600, a cytochrome P450 performing a key step of ABA catabolism . A hypothesis for investigation is whether modified alleles at these loci degrade ABA to release S. halepense seeds from dormancy early and/or increase seedling vigor under cold conditions.Synergy between gene duplication and interspecific hybridity may add an important element to the classical notion that polyploids adapt better than their diploid progenitors to environmental extremes .

Evidence is growing that polyploidy is an important contributor to biological invasions . Genome duplication facilitates the evolution of genes with new or modified functions such as we report, permitting a nascent polyploid to adapt to environments beyond the reach of its progenitors. Hybridity preserves novel alleles such as many recruited into S. halepense rhizome-enriched gene expression from non-rhizomatous S. bicolor, putatively contributing to the transgressive rhizome growth and ability of S. halepense but not rhizomatous S. propinquum derived progeny to overwinter in the temperate United States. Several lines of evidence point to a richness of DNA-level variation in S. halepense, including an abundance of novel coding sequences, much richer diversity of neutral DNA markers than its progenitors, and novel gene expression patterns exemplified by rhizome-enriched expression of some alleles from its nonrhizomatous S. bicolor progenitor. The spread of invasive taxa is much more rapid than migration in native taxa, and may require more genetic variation to sustain . Although there is somewhat less variation near the invasion front than the center of its US distribution , rich S. halepense diversity may support its projected 200–600 km northward spread in the coming century . Rich genetic variation in S. halepense offers not only challenges but also opportunities. Long under selection for weediness related attributes that enhance its competitiveness with crops, some US S. halepense genotypes have transitioned to nonagricultural niches and may also experience selection favoring alleles that could improve sorghum and other crops, e.g., for cold tolerance, rapid vegetative development and flowering, disease and pest resistance, and ratooning . Sorghum bicolor can routinely serve as the pollen parent of triploid and tetraploid and under some circumstances diploid , interspecific hybrids with Sh, offering the opportunity to test S. halepense alleles in sorghum.

As the first surviving polyploid in its lineage in ∼96 million years , S. halepense may open new doors to sorghum improvement, with synergy between gene duplication and interspecific hybridity nurturing the evolution of genes with new or modified functions . Already, genetic novelty from S. halepense is being used in efforts to breed ratooning/perennial sorghums that better protect ‘ecological capital’ such as topsoil and organic matter . Attributes of S. halepensesuch as endophytic nitrogen fixation , if transferred to sorghum, could help to narrow a ‘yield gap’ reflected by 1961–2012 yield gains in the U.S. of only 61% for sorghum versus 323% for maize2 . Likewise, its perenniality may have resulted in selection for ‘durable’ biotic stress resistance mechanisms that are absent from, but of importance to the improvement of, sorghum and other crops.The temperate region summer annual weed EchinochloaoryzicolaVasing. is a morphological mimic of rice that can germinate and initiate shoot growth under hypoxia in flooded paddies and causes up to 50% rice yield losses in California if not controlled. Decades of heavy reliance on herbicides for E. oryzicola control have resulted in the widespread occurrence of populations with simultaneous resistance to most available grass herbicides for selective use in rice.Successful control of herbicide-resistant E. oryzicola now hinges on maximizing weed seedling recruitment in order to eliminate such seedlings prior to planting the crop.The stale seedbed approach entails recruiting and treating weeds prior to planting rice with a mechanical method or a broad spectrum herbicide for which resistance does not exist in these weeds. The effectiveness of this approach would be optimized if the timing of weed seedling emergence under varying temperatures and irrigation regimes could be accurately predicted and if the conditions for maximizing emergence rate and synchrony could be identified. Population-based threshold models have been developed to describe germination responses to temperature, water potential and oxygen, and have been used to predict crop seedling emergence. For non-dormant E. oryzicola seed, the PBTM approach predicted with useful accuracy the germination responses of seeds to shifting temperature and water availability and their subsequent emergence from field soils. However, Poaceae seeds typically possess non-deep physiological dormancy , which indicates that seed dormancy release and increases in germination rates vary along a continuum of time and environmental conditions. NDPD may be released by stratification, after-ripening, scarification, excision of the embryo or addition of gibberellin and by various environmental signals including light, fluctuating temperatures and soil nitrate. In addition, the environmental requirements for dormancy alleviation are often population- rather than species specific, thus requiring analysis at the population level. While non-dormant seeds of selected herbicide-resistant and herbicide-susceptible populations of E. oryzicola germinated similarly, information on differences in seed dormancy between R and S populations is lacking. Herbicide-resistant E.oryzicola populations trace their origin to a single introduced biotype dispersed throughout California rice fields suggesting that R populations may respond similarly to environmental variables affecting germination and dormancy. As in many summer annual species with NDPD, innate dormancy of E. oryzicola seed populations that emerge in spring is alleviated by cold stratification when exposed to a period of moisture at wintertime temperatures in California. Thus,hydration and dark storage at 3uC alleviated dormancy of most seeds in this species. In California, yearly wintertime variation in field temperatures may be less than year-to-year variation in moisture levels, which may range from sporadic rain to prolonged periods of flooding. Adaptation to these conditions would suggest that stratification moisture levels may influence the magnitude of E. oryzicola seed dormancy release and that dormancy levels could perhaps be manipulated using wintertime irrigation to increase the rate of springtime germination and weed seedling recruitment. The median base water potential estimated using hydrotime germination models is often a measure of the relative dormancy status of a seed population, and because dormancy removal enables E. oryzicola seeds to transition from aerobic respiration to anaerobic alcoholic fermentation, oxygen-time germination models might also provide a means of assessing dormancy levels in seeds of this species. To understand the environmental requirements for E. oryzicola seed dormancy alleviation, we sought here to: 1) quantify stratification effects upon germination of seeds of R and S populations of E. Oryzicola across a range of moisture and oxygen levels; and 2) ascertain the relative contributions of alternating temperatures and of stratification temperature, water potential and duration towards dormancy release in R and S E. oryzicola populations. This knowledge will contribute towards the accuracy of germination-based predictions of seedling emergence as affected by the dormancy status of the seed and thus improve the timing and efficacy of weed control programs.E. oryzicola seeds of four populations representing the range of phenotypic variability previously reported in California were mass collected from Sacramento Valley, California, rice fields between 1997 and 2002 [16] and used in all experiments of this study. Populations CR and HR were subsequently classified as herbicide-susceptible and populations KS and SW as herbicide-resistant. In the summers of 2007 and 2009, 38 plants from each population were placed in separate greenhouses for seed multiplication at the University of California, Davis. Plants were grown in 2-L pots filled with soil placed in flooded basins under conditions set to approximate mid-springtime field conditions in the Sacramento Valley: 28/14uC day/ night temperatures, 50% relative humidity;natural light was supplemented by 900 mmol m22 s 21 of photosynthetic photon flux density from metal halide and high pressure sodium lamps to maintain a 16-h day length; soluble fertilizer was applied through irrigation as needed. Seeds were harvested from panicles at the time of seed shattering in early fall, stored at 20uC for 3 weeks to approximate typical early autumn temperatures and thereafter stored at 3uC, approximating mid-winter temperatures. Water content of seeds kept in dry storage was 7 to 9% .Tillage has long been an essential component of traditional agricultural systems. Broadly defined, tillage is the mechanical manipulation of the soil and plant residues to prepare a seedbed for crop planting. The benefits of tillage are many: it loosens soil, enhances the release of nutrients from the soil for crop growth, kills weeds, and regulates the circulation of water and air within the soil . In some cases, however, intensive tillage has been found to adversely affect soil structure and cause excessive breakdown of aggregates, leading to soil erosion in higher-rainfall areas. Intensive tillage can also have a negative impact on environmental quality by accelerating soil carbon loss and greenhouse gas emissions . Further, tillage operations account for more than 25 percent of agricultural production costs . With recent increases in fuel prices, tillage now accounts for a higher proportion of production costs than harvesting does . Such concerns have fueled interest in finding tillage systems that minimize negative impacts to the environment while sustaining economic crop productivity. The tillage systems being developed and studied to address these concerns can broadly be termed conservation tillage . In California, conventional tillage practices face additional challenges as population centers expand into farming areas and new residents raise serious concerns about the air quality effects of smog and dust emissions from farm machinery and vehicle use. Growers in California are looking at CT as a possible way to reduce their operating costs. Estimates from the Conservation Technology Information Center showed that by switching to CT, a U.S. grower can save as much as 225 labor hours and 1750 gallons of fuel per year on just 500 acres.ntially expressed genes located within likelihood intervals of rhizome related quantitative trait loci include an auxilin/cyclin G-associated kinase , tandemly duplicated ethylene responsive transcription factors , and a Ca2 + /calmodulindependent protein kinase, EF-Hand protein superfamily gene . Both polyploidy and interspecific hybridity appear to contribute to the ‘mosaic’ nature of rhizome gene expression, with over expression of some homoeologs from rhizomatous S. propinquum and others from non-rhizomatous S. bicolor . For example, different calmodulin family members have evolved specificity to rhizome buds and shoot buds . Tandem duplicated ethylene responsive transcription factors within a rhizome-related QTL are both overexpressed in S. halepense rhizome buds, although the sequence of Sb07g006195 closely resembles S. propinquum and adjacent Sb07g006200 is identical to S. bicolor .

The Teosinte-branched 1 growth repressor gene implicated in apical dominance of maize shoots has two family members with enriched expression in rhizome buds , ironically both completely matching the non-rhizomatous S. bicolor progenitor sequences .Introgression is suggested in a general sense by S. bicolor enriched allele composition of the S. halepense draft genome , and for specific genes by S. halepense SNP distribution patterns matching the S. bicolor reference genome of an elite breeding line , but differing from both several wild S. bicolors and each of two outgroups . Seven ‘hotspots’ for introgression of sorghum alleles in five geographically diverse US S. halepense populations , show non-random correspondence with published sorghum QTLs conferring variation in rhizome growth, seed size, and lutein content . While sorghum lacks rhizomes and has large seeds, rhizome growth-related alleles masked in domesticated sorghum genotypes by a lack of rhizomes may be unmasked in interspecific crosses with rhizomatous S. halepense. Particularly intriguing among S. halepense introgression hotspots are those that correspond with 3 of 4 QTL likelihood intervals spanning 4.9% of the genome that account for variation in seed content of the carotenoid lutein . Sorghum leaf photosynthetic capacity is susceptible to damage under low-temperature but high-light conditions when electron transport exceeds the capacity of carbon fixation to utilize available energy . Such conditions are infrequent in the tropics where Sorghum originated but common in the temperate springtime. Spring regrowth of S. halepense starts about 4 weeks before cultivated sorghum is seeded at 38.7◦ N . Xanthophyll carotenoids such as lutein are most abundant in plant leaves, weed dryer modulating light energy and performing non-photochemical quenching of excited ‘triplet’ chlorophyll which is overproduced at very high light levels during photosynthesis . Ironically, Sb01g030050 and Sb01g048860 related to lutein biosynthesis, are close to the only lutein QTL not near an introgression hotspot . Within the lutein QTL likelihood intervals, and homozygous in the Gypsum 9E , are also loss of function mutations in Sb01g013520, 9-cis epoxycarotenoid dioxygenase. This enzyme cleaves xanthophylls to xanthoxin, a precursor of the plant hormone abscisic acid  that plays a central role in regulating plant tissue quiescence. Also in the lutein QTL likelihood intervals are nonsynonymous SNPs inferred to have striking functional effects on Sb02g026600, a cytochrome P450 performing a key step of ABA catabolism . A hypothesis for investigation is whether modified alleles at these loci degrade ABA to release S. halepense seeds from dormancy early and/or increase seedling vigor under cold conditions.Synergy between gene duplication and interspecific hybridity may add an important element to the classical notion that polyploids adapt better than their diploid progenitors to environmental extremes . Genome duplication facilitates the evolution of genes with new or modified functions such as we report, permitting a nascent polyploid to adapt to environments beyond the reach of its progenitors. Hybridity preserves novel alleles such as many recruited into S. halepense rhizome-enriched gene expression from non-rhizomatous S. bicolor, putatively contributing to the transgressive rhizome growth and ability of S. halepense but not rhizomatous S. propinquum derived progeny to overwinter in the temperate United States. Several lines of evidence point to a richness of DNA-level variation in S. halepense, including an abundance of novel coding sequences, much richer diversity of neutral DNA markers than its progenitors, and novel gene expression patterns exemplified by rhizome-enriched expression of some alleles from its nonrhizomatous S. bicolor progenitor. The spread of invasive taxa is much more rapid than migration in native taxa, and may require more genetic variation to sustain . Although there is somewhat less variation near the invasion front than the center of its US distribution , rich S. halepense diversity may support its projected 200–600 km northward spread in the coming century . Rich genetic variation in S. halepense offers not only challenges but also opportunities. Long under selection for weediness related attributes that enhance its competitiveness with crops, some US S. halepense genotypes have transitioned to nonagricultural niches and may also experience selection favoring alleles that could improve sorghum and other crops, e.g., for cold tolerance, rapid vegetative development and flowering, disease and pest resistance, and ratooning . Sorghum bicolor can routinely serve as the pollen parent of triploid and tetraploid and under some circumstances diploid , interspecific hybrids with Sh, offering the opportunity to test S. halepense alleles in sorghum. As the first surviving polyploid in its lineage in ∼96 million years , S. halepense may open new doors to sorghum improvement, with synergy between gene duplication and interspecific hybridity nurturing the evolution of genes with new or modified functions . Already, genetic novelty from S. halepense is being used in efforts to breed ratooning/perennial sorghums that better protect ‘ecological capital’ such as topsoil and organic matter . Attributes of S. halepensesuch as endophytic nitrogen fixation , if transferred to sorghum, could help to narrow a ‘yield gap’ reflected by 1961–2012 yield gains in the U.S. of only 61% for sorghum versus 323% for maize2 . Likewise, its perenniality may have resulted in selection for ‘durable’ biotic stress resistance mechanisms that are absent from, but of importance to the improvement of, sorghum and other crops.The temperate region summer annual weed EchinochloaoryzicolaVasing. is a morphological mimic of rice that can germinate and initiate shoot growth under hypoxia in flooded paddies and causes up to 50% rice yield losses in California if not controlled. Decades of heavy reliance on herbicides for E. oryzicola control have resulted in the widespread occurrence of populations with simultaneous resistance to most available grass herbicides for selective use in rice.Successful control of herbicide-resistant E. oryzicola now hinges on maximizing weed seedling recruitment in order to eliminate such seedlings prior to planting the crop.The stale seedbed approach entails recruiting and treating weeds prior to planting rice with a mechanical method or a broad spectrum herbicide for which resistance does not exist in these weeds. The effectiveness of this approach would be optimized if the timing of weed seedling emergence under varying temperatures and irrigation regimes could be accurately predicted and if the conditions for maximizing emergence rate and synchrony could be identified. Population-based threshold models have been developed to describe germination responses to temperature, water potential and oxygen, and have been used to predict crop seedling emergence. For non-dormant E. oryzicola seed, the PBTM approach predicted with useful accuracy the germination responses of seeds to shifting temperature and water availability and their subsequent emergence from field soils. However, Poaceae seeds typically possess non-deep physiological dormancy , which indicates that seed dormancy release and increases in germination rates vary along a continuum of time and environmental conditions. NDPD may be released by stratification, after-ripening, scarification, excision of the embryo or addition of gibberellin and by various environmental signals including light, fluctuating temperatures and soil nitrate. In addition, the environmental requirements for dormancy alleviation are often population- rather than species specific, thus requiring analysis at the population level. While non-dormant seeds of selected herbicide-resistant and herbicide-susceptible populations of E. oryzicola germinated similarly, information on differences in seed dormancy between R and S populations is lacking. Herbicide-resistant E.oryzicola populations trace their origin to a single introduced biotype dispersed throughout California rice fields suggesting that R populations may respond similarly to environmental variables affecting germination and dormancy. As in many summer annual species with NDPD, innate dormancy of E. oryzicola seed populations that emerge in spring is alleviated by cold stratification when exposed to a period of moisture at wintertime temperatures in California. Thus,hydration and dark storage at 3uC alleviated dormancy of most seeds in this species. In California, yearly wintertime variation in field temperatures may be less than year-to-year variation in moisture levels, which may range from sporadic rain to prolonged periods of flooding. Adaptation to these conditions would suggest that stratification moisture levels may influence the magnitude of E. oryzicola seed dormancy release and that dormancy levels could perhaps be manipulated using wintertime irrigation to increase the rate of springtime germination and weed seedling recruitment. The median base water potential estimated using hydrotime germination models is often a measure of the relative dormancy status of a seed population, and because dormancy removal enables E. oryzicola seeds to transition from aerobic respiration to anaerobic alcoholic fermentation, oxygen-time germination models might also provide a means of assessing dormancy levels in seeds of this species. To understand the environmental requirements for E. oryzicola seed dormancy alleviation, we sought here to: 1) quantify stratification effects upon germination of seeds of R and S populations of E. Oryzicola across a range of moisture and oxygen levels; and 2) ascertain the relative contributions of alternating temperatures and of stratification temperature, water potential and duration towards dormancy release in R and S E. oryzicola populations. This knowledge will contribute towards the accuracy of germination-based predictions of seedling emergence as affected by the dormancy status of the seed and thus improve the timing and efficacy of weed control programs.E. oryzicola seeds of four populations representing the range of phenotypic variability previously reported in California were mass collected from Sacramento Valley, California, rice fields between 1997 and 2002 [16] and used in all experiments of this study. Populations CR and HR were subsequently classified as herbicide-susceptible and populations KS and SW as herbicide-resistant. In the summers of 2007 and 2009, 38 plants from each population were placed in separate greenhouses for seed multiplication at the University of California, Davis. Plants were grown in 2-L pots filled with soil placed in flooded basins under conditions set to approximate mid-springtime field conditions in the Sacramento Valley: 28/14uC day/ night temperatures, 50% relative humidity;natural light was supplemented by 900 mmol m22 s 21 of photosynthetic photon flux density from metal halide and high pressure sodium lamps to maintain a 16-h day length; soluble fertilizer was applied through irrigation as needed. Seeds were harvested from panicles at the time of seed shattering in early fall, stored at 20uC for 3 weeks to approximate typical early autumn temperatures and thereafter stored at 3uC, approximating mid-winter temperatures. Water content of seeds kept in dry storage was 7 to 9% .Tillage has long been an essential component of traditional agricultural systems. Broadly defined, tillage is the mechanical manipulation of the soil and plant residues to prepare a seedbed for crop planting. The benefits of tillage are many: it loosens soil, enhances the release of nutrients from the soil for crop growth, kills weeds, and regulates the circulation of water and air within the soil . In some cases, however, intensive tillage has been found to adversely affect soil structure and cause excessive breakdown of aggregates, leading to soil erosion in higher-rainfall areas. Intensive tillage can also have a negative impact on environmental quality by accelerating soil carbon loss and greenhouse gas emissions . Further, tillage operations account for more than 25 percent of agricultural production costs . With recent increases in fuel prices, tillage now accounts for a higher proportion of production costs than harvesting does . Such concerns have fueled interest in finding tillage systems that minimize negative impacts to the environment while sustaining economic crop productivity. The tillage systems being developed and studied to address these concerns can broadly be termed conservation tillage . In California, conventional tillage practices face additional challenges as population centers expand into farming areas and new residents raise serious concerns about the air quality effects of smog and dust emissions from farm machinery and vehicle use. Growers in California are looking at CT as a possible way to reduce their operating costs. Estimates from the Conservation Technology Information Center showed that by switching to CT, a U.S. grower can save as much as 225 labor hours and 1750 gallons of fuel per year on just 500 acres.

Once isolated, high-value unknowns can then be synthesized to determine their direct biological activities and mobility. Additionally, they can be more finely monitored to discern their spatial distributions. There will be several translational opportunities stemming from these efforts. Biosynthetic pathways could be engineered to produce new bioactive metabolites into plants or other organisms; these could be useful beyond plant health applications. Furthermore, for pathogen/pest-derived chemicals, a next step will be to develop strategies such as HIGS to abrogate pest/microbe chemical effectors. As noted above, chemical immunomodulators could be applied in the field or plants with altered chemistry could be bred/engineered as part of a disease control strategy. Knowledge of the chemical repertoires of plants and their associated microbes/pests could allow the design of sensitive metabolite biosensors that would act as sentinels for perturbations.Diverse pathogens, pests, parasites, and symbionts deploy large repertoires of secreted proteins known as effectors to modify host processes for their benefit. Effector activities range from the suppression of plant immunity to the manipulation of host biochemical and developmental processes. In addition to these virulence activities, effectors can trigger immunity following recognition by cognate receptors, often NLR proteins . Effectors are thus central in dictating the outcomes of plant immunity and disease development. Comprehensive characterization of effector repertoires and determination of their modes of action should therefore be a high priority. Understanding effector biology offers several opportunities for disease control, pipp horticulture as well as tools for manipulating plant biochemistry and development in the absence of disease. Effectors that trigger immunity can expedite the discovery of R genes .

Selection of breeding material with individual effectors is an informative alternative to marker-assisted selection that can facilitate pyramiding multiple R genes, each of which confers resistance to most or all strains of a pathogen by allowing selection of each R gene individually. Effectors have been effectively used in resistance breeding to control diseases caused by diverse classes of pathogen . Effector directed breeding also provides the possibility of identifying and prioritizing R genes that recognize core effectors that are broadly conserved within the species and play important roles in virulence. R genes that recognize core effectors are potentially more durable to pathogen co-evolution, because deletion or silencing of the effector would impose a fitness penalty on the pathogen; however, the caveats regarding possible second site compensating mutations and redundancy in effector function need to be considered . In addition, effector-based screens can be used to identify sources of resistance in plants that are non-hosts for the pathogen of interest. Effectors are also needed for comparative functional studies of the biophysical/biochemical basis of immune-receptor activation . This will address how many ways there are to activate NLRs and how receptor complexes are impacted biochemically and biophysically by immune modulating effectors. Having this information will provide opportunities to re-wire activation mechanisms to facilitate resistance.Diverse pathogens, pests, parasites, and symbionts deploy large repertoires of secreted proteins known as effectors to modify host processes for their benefit. Effector activities range from the suppression of plant immunity to the manipulation of host biochemical and developmental processes.

In addition to these virulence activities, effectors can trigger immunity following recognition by cognate receptors, often NLR proteins . Effectors are thus central in dictating the outcomes of plant immunity and disease development. Comprehensive characterization of effector repertoires and determination of their modes of action should therefore be a high priority. Understanding effector biology offers several opportunities for disease control, as well as tools for manipulating plant biochemistry and development in the absence of disease. Effectors that trigger immunity can expedite the discovery of R genes . Selection of breeding material with individual effectors is an informative alternative to marker-assisted selection that can facilitate pyramiding multiple R genes, each of which confers resistance to most or all strains of a pathogen by allowing selection of each R gene individually. Effectors have been effectively used in resistance breeding to control diseases caused by diverse classes of pathogen . Effector directed breeding also provides the possibility of identifying and prioritizing R genes that recognize core effectors that are broadly conserved within the species and play important roles in virulence. R genes that recognize core effectors are potentially more durable to pathogen co-evolution, because deletion or silencing of the effector would impose a fitness penalty on the pathogen; however, the caveats regarding possible second site compensating mutations and redundancy in effector function need to be considered . In addition, effector-based screens can be used to identify sources of resistance in plants that are non-hosts for the pathogen of interest. Effectors are also needed for comparative functional studies of the biophysical/biochemical basis of immune-receptor activation .

This will address how many ways there are to activate NLRs and how receptor complexes are impacted biochemically and biophysically by immune modulating effectors. Having this information will provide opportunities to re-wire activation mechanisms to facilitate resistance.In addition to improving genetics of a crop itself to enhance resistance against deleterious organisms, there are multiple opportunities to use beneficial plant-associated organisms as allies . These include many types of microbes, arthropod predators and 12 / Molecular Plant-Microbe Interactionsparasitoids, companion crops, and other organisms. Beneficial microorganisms play a central role in maintaining plant health in terms of both nutrition and defense. For example, arbuscular mycorrhizal fungi and plant growth-promoting rhizobacteria not only enhance plant nutrient capture but also can directly modulate plant defenses . The advent of high throughput DNA and RNA sequencing technologies and increased capacity for characterizing small molecules from soil samples have driven a rapid expansion in environmental genomics directly germane to plant productivity . However, virtually nothing is known of the principles of evolution and biochemistries that determine the composition of plant-associated microbiota above and below ground. Robust experimental systems are crucially needed to investigate principles of microbiota structure and function, from reductionist settings, through increasingly complex ecological settings, to deployment. Most crops have been bred independently of many of their rhizosphere- and phyllosphere associated organisms, potentially due to loss of microbe diversity and intensity in agricultural ecosystems as a result of tillage and chemical inputs . Traditional breeding programs may have inadvertently selected against beneficial microbial associations due to their use of high nutrient conditions and pesticides, which decrease opportunities for microbial benefits. For example, under ample soil nutrient conditions, the carbon drain of AMF can present a fitness cost, potentially selecting against traits favoring mycorrhizal associations. Research is required to evaluate the performance of different crop genotypes under low input conditions, including their ability to attract and sustain beneficial microorganisms. There is a dearth of knowledge as to how intra- or inter-specific plant genetic variation impacts the plant-associated microbiota. Current results support the existence of a core microbiome that may be tuned by specific plant genotype x microbiome and genotype x environment interactions . For example, plant root exudates contain signaling chemicals that influence the species composition of the rhizosphere but little is known of natural genetic variation influencing the support of beneficial rhizosphere microbes. Harnessing beneficial microbes will be increasingly important as low-till, low-input agricultural systems are adopted . Foundational research is also needed to identify appropriate combinations of beneficial organisms that can be used to develop cocktails of plant growth promoting or bio-control organisms. Addressing this difficult challenge is dependent on deriving associations of microbes that provide diverse benefits to plants and are also able to invade and persist as complex microbial communities in the target environment, vertical growing weed potentially in a co-dependent manner. Research is needed to investigate trade-offs involved in hosting potentially beneficial microorganisms. Priming is a long-lasting memory that provides potentiation of faster and stronger defense responses . Beneficial microorganisms have been demonstrated to induce defense; well-studied examples include root-colonizing bacteria that promote plant growth and provide enhanced broad spectrum resistance to several types of pathogens . Pathogens can also activate resistance distant from the site of infection . Some signaling components are involved in both of these long-distance responses. The challenge is to ensure that plants have the capacity to be well-colonized with ISR-promoting microbes and also capable of adequately activating these signaling pathways for resistance.

Priming or induction of plant defenses, particularly SAR, may incur a yield penalty, which is yet to be fully understood. Germplasm should therefore be screened to find genotypes amenable to beneficial colonization. Plant genes that regulate responses to different microbial populations should also be characterized to identify input genotypes for breeding programs to enhance beneficial associations. Progress towards implementing these strategies will require extensive sequencing for microbial characterization, high resolution metabolomics, the ability to culture and maintain promising organisms, and the ability to assess many plants rapidly for a variety of responses. It is important to develop interventions for improving plant health that go beyond altering crop genetics. Small molecule signals generated in response to beneficial microorganisms could be commercialized for external application, in a similar manner to chemicals inducing SAR. Both biological control and bio-pesticides have much scope for development. There are multiple approaches to improving biological control by boosting populations of natural enemies of pests, pathogens, and weeds. Classical bio-control involves recruiting biological control agents from the areas of origin of invasive pests and weeds and introducing them to the areas where they have invaded. This approach has had several impressive successes as well as some inconsistent results. It requires long-term research efforts to find candidates, determine likely effectiveness, and verify safety. Conservation bio-control involves exploiting resident populations of natural enemies of pests, weeds and pathogens as an ecosystem service; interventions to improve the effectiveness of conservation bio-control are required to support natural populations. Again, the new tools for determining microbial community structure and identifying insect pest population structure help to build mechanistic understanding of the ecosystems, leading to more reliable predictions. This requires food resources and suitable habitat. Considerable progress has been made with field margins to support populations of natural enemies of insect pests; however, there is often insufficient movement of beneficials into the crop where they are needed. Lure and reward strategies to attract beneficials with semiochemicals coupled with food rewards that enhance their fitness and performance are required . A greater foundational understanding of the ecology of tritrophic interactions and signaling is needed to enable better recruitment of natural enemies of pests , perhaps by breeding. Companion cropping can both repel pests and attract their natural enemies; a successful example of this is the push-pull system in Kenya . The development of biopesticides involves formulation of living organisms, for example an entomopathogenic fungus or a virus that affects insects, can kill the pest target and can be sprayed or applied like a pesticide. Research priorities include discovery of new agents, development of new biopesticide delivery methods, and approaches in which a killing agent is formulated with an attractant semiochemical.Because viruses are obligate intra-cellular pathogens with small genomes, they are completely dependent on cellular host factors to complete their life cycle and on vectors such as insects, nematodes, or plasmodiophorids for dissemination. Plant viruses are comprised of either RNA or DNA genomes, which typically encode only four to ten proteins and differ in replication strategies . Several aspects of viral biology remain insufficiently characterized. The last decade has seen major advances in characterization of host factors involved in replication and movement and virus manipulation of host gene regulation . Viruses also modify host and insect vector behaviors . However, the knowledge of the underlying mechanisms is still lacking. In addition, virus-plant and virus-vector interactions as well as regulatory host small RNAs are affected by environmental factors such as temperature and light . The basis of virus specificity for certain cell types and tissues and why some viruses have wide or narrow host ranges are also not understood. It is known that hormone and defense pathways are affected by viruses, but information on spatial and temporal restriction of viruses at the cellular level is lacking. Discovery of the underlying reasons may enable the development of novel strategies that restrict virus infection. The drivers of virus evolution and the mechanisms by which vector population complexity influences viral population composition and transmission remain incompletely known. Multiple studies are needed to address these gaps in our knowledge. Single-cell genomics and transcriptional profiling may reveal molecular details of viral restriction, cell autonomous and nonautonomous virus responses, basis of seed transmission, and the influence of environmental factors and host developmental stage on virus infection. Development of anti-viral peptides targeting key components is needed to determine the basis of host and tissue specificity.

The global population is projected to reach 9.7 billion by 2050, and traditional farming methods are struggling to keep up with the rising demand for food. At the same time, urbanization and climate change are shrinking arable land, forcing innovators to rethink agriculture. Enter vertical farming and hydroponics—two technologies that promise to revolutionize food production. But can they work together? Specifically, can vertical grow racks be used for hydroponics?

This article explores the synergy between vertical grow racks and hydroponic systems, analyzing their compatibility, benefits, challenges, pipp racking and real-world applications. By the end, you’ll understand why this combination is not just possible but a game-changer for sustainable agriculture.

Section 1: Understanding Vertical Grow Racks and Hydroponics

What Are Vertical Grow Racks?

Vertical grow racks are multi-tiered structures designed to maximize growing space by stacking plants vertically. These systems are commonly made of metal or plastic and can be adjusted to accommodate different plant heights. Key features include:

• Space efficiency: Grow upward instead of outward.
• Modularity: Customizable layouts for crops like leafy greens, herbs, or strawberries.
• Climate control integration: Compatible with LED lighting, irrigation, and ventilation systems.

Vertical farming is ideal for urban environments, warehouses, or regions with limited land.

What Is Hydroponics?

Hydroponics is a soil-free farming method where plants grow in nutrient-rich water solutions. Roots are supported by inert media like perlite, clay pellets, or rockwool. Benefits include:

• Faster growth rates: Direct access to nutrients accelerates plant development.
• Water conservation: Uses up to 90% less water than soil farming.
• Year-round production: Controlled environments eliminate seasonal limitations.

Common hydroponic systems include Nutrient Film Technique (NFT), Deep Water Culture (DWC), and Aeroponics.

Section 2: The Marriage of Vertical Grow Racks and Hydroponics

Technical Compatibility

Vertical grow racks and hydroponics are a natural fit. Here’s why:

1. Modular Design Alignment
   • Hydroponic systems can be scaled vertically using racks. For example, NFT channels or DWC troughs can be installed on each tier.
   • Automated pumps distribute nutrient solutions evenly across tiers.
2. Lighting Optimization
   • LED grow lights can be mounted at each level, ensuring uniform light distribution.
   • Adjustable spectrum LEDs cater to specific crop needs (e.g., blue light for leafy greens, red for fruiting plants).
3. Climate Control Synergy
   • Vertical racks allow precise control of temperature, humidity, and CO2 levels per tier.
   • Closed-loop hydroponic systems minimize water loss through evaporation.

Case Study: Bowery Farming

Bowery Farming, a U.S.-based vertical farming company, uses hydroponic vertical racks to grow over 50 varieties of greens and herbs. Their system integrates:

• Proprietary software to monitor plant health.
• Stacked grow trays with recirculating nutrient solutions.
• Energy-efficient LEDs tailored to each crop’s growth stage.

Result: 100x higher yield per square foot compared to traditional farms.

Section 3: Advantages of Vertical Hydroponic Systems

1. Space Efficiency and Scalability

Vertical hydroponics transforms underutilized spaces (e.g., abandoned warehouses, rooftops) into productive farms. For example:

• Singapore’s Sky Greens: A 9-meter-tall vertical hydroponic farm producing 1 ton of vegetables daily on 0.5 hectares.

2. Resource Conservation

• Water: Closed-loop systems recycle nutrients and water.
• Land: A 10-tier vertical farm can produce the equivalent of 1 acre of farmland.

3. Higher Yields and Faster Harvests

• Lettuce: Grown in 30 days vs. 60 days in soil.
• Strawberries: Year-round production with vertical NFT systems.

4. Reduced Pest and Disease Risk

• Soil-free environments eliminate root rot and soil-borne pathogens.
• Isolated tiers prevent cross-contamination.

Section 4: Challenges and Solutions

1. High Initial Costs

• Setup expenses: Vertical racks, LEDs, and hydroponic infrastructure require significant investment.
  • Solution: Governments (e.g., Japan, Netherlands) subsidize vertical farms to boost food security.

2. Energy Consumption

• LED lighting accounts for ~60% of operational costs.
  • Solution: Solar panels and energy-efficient LEDs (e.g., Philips GreenPower).

3. Technical Expertise

• Maintaining pH, nutrient balance, pipp racks and lighting schedules demands skill.
  • Solution: AI-driven platforms like Plenty Ag automate monitoring and adjustments.

Section 5: Future Trends and Innovations

1. AI and IoT Integration

• Sensors track plant health in real time, adjusting nutrients and light automatically.

2. Hybrid Systems

• Combining hydroponics with aquaponics (fish waste as fertilizer) for closed-loop ecosystems.

3. Urban Farming Expansion

• Companies like Infarm install modular vertical hydroponic units in supermarkets and restaurants.

Conclusion

Vertical grow racks and hydroponics are not just compatible—they’re a powerful duo reshaping agriculture. By merging space-efficient vertical farming with hydroponics’ resource-saving benefits, this technology addresses critical challenges like food security, water scarcity, and urbanization. While hurdles like upfront costs remain, advancements in automation and renewable energy are making vertical hydroponic systems increasingly accessible.

From skyscraper farms in Singapore to modular units in Berlin grocery stores, the future of farming is undeniably upward.

Analysis was con‐ ducted with correlated allele frequencies and an admixture model for K values ranging from 1 to 20. Each run was conducted with a burn‐in period of 100,000 steps followed by 100,000 Monte Carlo Markov Chain replicates. To further assess the relationships of rice samples without assumptions of specific relationship or population models, a principal component analysis of all samples was conducted in DARwin software using 99 genetic markers. In order to examine the level of differences or genetic relatedness among weedy rice biotypes and other rice groups as a whole, we looked at the pairwise fixation index among clusters of wild rice, cultivated, and weedy rice biotypes.The 99 markers used in this study covered the 12 chromosomes of rice with an average of 8 markers per chromosome and a mean interval distance of 4.43 Mb between markers. The markers showed high polymorphism with an average of 5 alleles and a mean polymorphism information content value of 0.61 per marker. In total, 508 different alleles were scored among 96 rice genotypes using the 99 markers . The presence or ab‐ sence of a 14‐basepair deletion at the Rc gene correlated with red or white pericarp in rice individuals . All weedy rice individuals had the wild‐type allele lacking the deletion, demonstrating the effectiveness of this marker for genetic identification of red pericarp in California weedy rice . In the neighbor‐joining phylogenetic analysis, individuals largely clustered by rice type . While bootstrap support for many basal branches of the tree is low, the grouping of most rice individuals into clusters by rice type is well‐supported. The cultivated japonica rice varieties were separated from indica and all other rice groups with the exception of one red‐pericarped temperate japonica variety, bud curing indicating the effectiveness of SSR markers in differentiating the two main subspecies of rice. Moreover, the tropical and temperate japonica rice varieties are well separated.

The indica rice samples, however, were not placed together, with IR29, IR64, and Milagrosa clustered together separately from red‐pericarped Pokkali landrace rice. Basmati rice, which is an aromatic rice be‐ longing to group V rice, clustered with aus rice varieties with high bootstrap support. The wild rice species samples were scattered throughout the tree as expected by the wide diversity in their genomes. The wild rice O. officinalis samples, which have a CC genome type, clustered together. The southern United States weedy rice individuals were grouped into two separate clusters, with strawhull weedy rice clustered together with high bootstrap support, while blackhull weedy rice grouped together with less support. The California weedy rice samples were grouped into four clusters, which correspond to five distinct biotypes categorized by hull color, grain type, and presence of awn . The first cluster grouped all the short grain , strawhull, awn‐ less individuals . While high bootstrap values support the grouping of Type 1 individuals, the cluster is grouped near an O. nivara individual and one temperate japonica variety as well as aus and Basmati rice with low statistical sup‐ port. The second California weedy rice cluster included all the medium grain , bronzehull, and awnless weedy rice individuals , placed near southern SH weedy rice and some wild rice. A third cluster grouped all the MG, strawhull with long awn . The single SG blackhull with long awn individual closely grouped together with the strawhull Type 3 weedy rice. The fourth weedy rice cluster grouped together some MG and long grain strawhull weedy rice accessions with variable awn length . Type 5 weedy rice was placed with high bootstrap support near the japonica rice varieties, and these two groups were placed with low support near Type 3 and Type 4 weedy rice.

The clustering of California weedy rice by grain attributes validates the division of weedy rice samples by phenotypic similarities. Two noncertified introduced cultivated red‐pericarped specialty rice varieties grown in California, , clustered with California weedy rice. These red‐pericarped cultivated rice varieties have not gone through California’s third‐party variety certification and inspection process and have been previously implicated in rice contamination . RR125 clustered within Type 2 weedy rice and RR126 clustered within MG Type 5 weedy rice, indicating that these red‐peri‐ carped specialty rice varieties are related to California weedy rices. It is unclear from this analysis, however, whether the California weedy rice could be derived directly from these noncertified varieties or whether their relationship is the result of gene flow from these varieties or their ancestors into another population. Since California weedy rice individuals clustered into distinct biotypes, genetic differences among groups of weedy rice were examined in more detail. Analysis of molecular variance indicated that California weedy rice collections are very diverse, with the majority of the variation due to differences among groups while 40% is due to variation among individuals, and differences within group or biotype account for only 5% of genetic variation . Each weedy rice biotype is genetically distinct from the others with an overall FST value of 0.548 among biotypes. Comparison of genetic diversity patterns among the four major biotypes indicate that Type 5 is the most diverse group with the highest number of alleles detected per locus , highest percentage of poly‐ morphicloci , and most heterozygous alleles . In contrast, Type 3 weedy rice has the lowest number of alleles detected per locus , lowest Shannon diversity index within group , and lowest number of heterozygotes. Type 2, which was found in four counties , is also diverse but has the highest inbreeding coefficient estimate of 0.90, indicating homozygosity of individuals in this group .

Overall, California weedy rice biotypes are genetically diverse but with a high frequency of homozygous alleles at 99 loci as indicated by high mean FIS estimate for each group or biotype as well as the overall estimates of FIS and FIT , as would be expected for a species such as rice that reproduces primarily by self‐fertilization. To investigate the relationships among rice individuals while allowing for gene flow and admixture, unlike phylogenetic analysis, STRUCTURE analysis was used to assign each individual’s genotype to genetic clusters or populations. The largest increase in data probability was observed at K = 6 , and this model distinguishes the major biotype groups fairly well . The STRUCTURE grouping of California weedy rice individuals and all other rice samples is consistent with their group membership from phylogenetic analysis . The majority of individuals assign to a single cluster with high probability, and most individuals of the same biotype assign to the same genetic cluster . However, the majority of indica rice and wild rice individuals assign to multiple clusters, indicating higher background genetic diversity or admixture between clusters. Some weedy rice individuals also assign to multiple clusters, indicating hybridization with or evo‐ lutionary origin from other rice groups. The cluster that all Type 1 individuals assign to also has minor genetic contributions from O. nivara, one indica rice variety, and some Type 2 weedy rice individuals. Some Type 2 individuals show admixture with strawhull weedy rice from the southern United States, indica rice, or wild rice species. Type 3 and Type 4 rice individuals all assign highly to a cluster that also has minor contributions from wild rice. A principal component analysis was used to assess genetic similarities among individuals without assuming spe‐ cific relationship or population models . The first three axes account for 22.9%, 11.6%, curing weed and 10.2% of genetic variation present. As in previous analyses, most rice individuals cluster together by rice type, and were spatially well differentiated on the first two axes . Type 1 rice clustered closely with aus rice, Basmati, the single temperate japonica individual that clustered separately from the others in phylogenetic analysis , and BH southern weedy rice. Type 2 weedy rice individuals clustered with SH southern weedy rice and indica rice. Type 3 and Type 4 rice clustered closely together, well differentiated on axis 2 from all other rice samples. Type 5 clus‐ tered together with temperate and tropical japonica rices. The wild rice samples did not cluster together closely, but were distributed mostly in the lower right corner. Genetic differentiation between biotypes was assessed for all weedy, wild, and culti‐ vated rice biotypes. Most estimates of pairwise FST were high, ranging from 0.177 to 0.696 . The very high pairwise FST values between the single Type 4 individual and all other groups indicate genetic differentiation but are likely artificially high due to the sample size of 1. The majority of California weedy rice biotypes, with the exception of Type 5, show high genetic differentiation from the temperate japonica rice cultivars grown in California .

In contrast, low pairwise FST between a weedy rice biotype and another rice type can indicate more shared genetic content. For example, Type 2 shows low differentiation from indica cultivars and from wild rice , indicating less differentiation between these groups and possible relatedness.The increasing spread of weedy rice in California and the recent report of weedy rice originating from cultivated California rice varieties raised questions about the origin of California weedy rice and its management. For this reason, we conducted a genetic study to understand the relationships be‐ tween existing weedy rice in California and to investigate their possible origins. In the phylogenetic analysis, weedy rice individu‐ als clustered together by biotype, indicating that for California weedy rice biotypes, samples can be easily classified by phenotype into groups that are biologically and genetically meaningful . The five biotypes of California weedy rice clustered within multiple larger genetic groups of weedy, wild, and cultivated rice . This division of weedy rice into separate clusters most likely indicates at least four separate evolutionary origins of California weedy rice from diverse lineages of cultivated, weedy, and wild rice. In fact, the four major groups of weedy rice are quite divergent from each other based on principal component analysis . Population structure analysis gives more insight into relationships of individuals and biotypes, revealing close correspondence between genetic populations and rice types . However, some rice groups, especially wild rice and indica rice, are more genetically heterogeneous, with genotypes assigning to multiple genetic clusters. STRUCTURE analysis also identified admixed individuals, indicating hybridization of weedy rice both with other weedy rice biotypes and with wild and cultivated rice , despite the fact that rice is primarily self‐fertilizing with generally low outcrossing rates . Individual and biotype differentiation analyses provide insights into the relationships of California weedy rice biotypes. The high pairwise FST values between most California weedy rice biotypes, with the exception of Type 5, and the temperate japonica cultivars widely grown in California, indicates high genetic differentiation between California weedy rice and California cultivated rice and their relatively low shared genetic content , suggesting that most weedy rice did not evolve from the cultivated rice varieties widely grown in California. The observed FST levels do not necessarily exclude the possibility of infrequent hybridization with cultivated rice within California. One Type 1 individual and one Type 2 individual showed over 10% genetic assignment to the genetic cluster containing Type 5 and japonica rices in STRUCTURE analysis . However, the majority of California weedy rice biotypes have a high inbreeding coefficient and low level of hetero‐ zygosity at 99 loci . Therefore, it is likely that hybridization between rice groups happened many years or generations ago. Type 5 weedy rice was shown in phylogenetic, STRUCTURE, and PCA analyses to be closely related to japonica cultivars, raising questions of whether it is derived directly from the temperate japonica cultivars grown in California or from tropical japonica cultivars outside California and imported. The high inbreeding coefficient of Type 5 weedy rice and moderate genetic differentiation from temperate japonica rice make it likely that its evolutionary origin significantly predates its recent detection, although it is possible that a small weedy rice population could have been present unnoticed for some time prior to detection. Another possibility for the origin and spread of California weedy rice is from the cultivation of red‐pericarped specialty rice varieties. While the majority of rice‐growing acreage in California is devoted to non-colored pericarp rice production, some specialty colored pericarp rice varieties are also grown at a commercial scale.

Lower rates seldom yield adequate forage production to justify the expense.Traditionally, nitrogen applications have been made in the fall near the time of the first rains. In regions of high rainfall and where heavy winter grazing has occurred, the forage may become extremely nitrogen deficient in the spring, even though nitrogen was applied the previous fall. Under these circumstances, spring applications of nitrogen fertilizer may be beneficial, but this practice has not been adequately evaluated on annual rangelands. Where rainfall is not great enough to leach all of the fertilizer nitrogen out of the soil, and plant nitrogen uptake is insufficient to use all of the fertilizer nitrogen, there may be a carryover response to nitrogen fertilization during the next growing season. In the 1950s, many grazing trials were conducted to demonstrate the response of range livestock gains to rangenitrogen fertilization. Carryover effects were assessed in 13 of the tests. In all but one test there was an appreciable carryover effect from fertilization, the additional gain being equivalent to about 50 percent of the first-year effects on the average. Part of the gains in these studies should be credited to the phosphorus and sulfur also applied, but the amount of credit to be given cannot be determined with the available data. Without applied nitrogen or a good stand of legumes, there is usually no response to phosphorus or sulfur on annual rangelands of California.Fertilizer can be applied from the ground or by aircraft. Large, inaccessible, rough, cannabis racks and rocky ranges are usually fertilized by aircraft. Fertilizer application equipment and tractors are usually restricted to use on rangeland where slopes are less than 20 to 30 percent and the surface is relatively free of rocks or other obstructions to the equipment.

The analysis of range sites on a given ranch during a range management planning process will help to identify those areas that can be treated from the ground and those that must be treated from the air.Fall nitrogen fertilization generally increases the protein content in annual grasses and broad-leaved forbs early in the growing season. However, an increase in protein in winter is not beneficial, since there is typically adequate protein for animal needs in unfertilized pasture at that time of year. The primary benefit from nitrogen in the early part of the season is an increase in dry matter production. As the season advances, the protein levels may decrease more rapidly in plants fertilized at moderate nitrogen levels than in those not fertilized. As a result, at the end of the growing season fertilized plants are often lower in protein than are unfertilized plants. Exceptions may occur in very dry spring seasons when moisture becomes limiting and plants are unable to grow to their full potential, thus drying up before growth dilutes the nitrogen to a low level. Yearly application of nitrogen generally increases the percentage of grasses and forbs. The particular grasses or forbs that increase will depend upon the grazing or clipping management of the pasture in question. For example, slender wild oats or ripgut brome often become dominant where nitrogen fertilizer is applied to ungrazed plots. In similarly treated plots that are heavily grazed, soft chess may become dominant. This is due to the greater tillering ability of soft chess when grazed as compared to wild oats or ripgut, which tiller poorly. Moderate to heavy grazing pressure tends to reduce the impact of fertilizer on botanical composition.Invasive species have a multitude of ecological and socio-economic effects, and can play a strong role in ecosystem functioning .

However, eradication of invasive species is expensive and difficult: globally, only ~50% of eradication attempts are successful, and success rates are substantially lower in semi-natural habitats relative to man-made environments such as greenhouses . Additionally, invasive species can become community mainstays and assume novel ecological roles in the environments they invade . In some cases, reducing invasive species can have strong habitat implications for native species of conservation concern. Therefore, if the invading species is eradicated without other restoration activities, native organisms may experience negative consequences . Scenarios like these are increasingly common around the world and present an urgent dilemma: how can natural resource managers minimize negative effects of invasive species without depleting native taxa that have come to rely on them? We address this question through our case study in the Sacramento–San Joaquin River Delta.In this case study, we examined whether water hyacinth management activities influence invertebrate communities that may support fishes of the Sacramento–San Joaquin River Delta . The Delta is part of the largest estuary on the Pacific Coast of the Americas, and serves as a critical link between California’s water supply, aquatic species, and human populations. The Delta faces many challengesthat have been described extensively by natural resources agencies and researchers . Aquatic invasive species are of great concern in the Delta because they can affect ecological communities, water distribution, commerce, recreation, and other human industries . For these and other reasons, the Delta is an ecosystem with novel features—“abiotic, biotic, and social components that, by virtue of human influence, differs from those that prevailed historically, having a tendency to self-organize and manifest novel qualities without intensive human management” .

Water hyacinth is one of the most visible invaders in the Delta, because it is a floating aquatic weed and is found nearly Delta-wide. Historically, much of the Delta, including our study location, was characterized by freshwater emergent wetlands . Vegetated littoral zones like these are important for producing invertebrate biomass as food for threatened and endangered juvenile salmonids and other fishes that forage on insects and zooplankton . However, only a small proportion of historic Delta freshwater wetlands remain today . In the absence of the once-abundant Delta littoral native plant communities, invertebrates must use available habitats. Today, the littoral habitat includes water hyacinth throughout the Delta.Water hyacinth is a floating aquatic macrophyte native to the Amazon basin. It has invaded aquatic ecosystems around the world, affecting human endeavors as well as abiotic and biotic ecosystem elements. For example, Water hyacinth can block sunlight and alter turbidity levels; decrease phytoplankton production, dissolved oxygen , and nutrient levels; and influence heavy metal concentrations . Water hyacinth can also clog navigable water ways, displace native vegetation, alter nutrient cycling, and change sediment dynamics . There is limited research that describes the role of water hyacinth in structuring and sustaining invertebrate communities. However, Villamagna et al. determined that, in general, water hyacinth increases habitat complexity but decreases food availability for invertebrates. Toft et al. demonstrated that—compared to a native macrophyte —water hyacinth had lower macroinvertebrate densities, and that the invertebrates found on water hyacinth were less prevalent in fish diets. Even so, water hyacinth has been a feature of the Delta for ~70 years, is widely dispersed, extremely abundant, and provides complex habitat for invertebrates. Given that water hyacinth is a major physical and biological feature of the Delta and serves as habitat for invertebrates that are common in the diets of some Delta fishes , it is incumbent upon Delta managers to consider the implications of water hyacinth management on the species that use it as habitat.In accordance with the Harbors and Navigation Code , the California Parks Division of Boating and Waterways is the lead agency responsible for cooperating with state, local, and federal agencies in “identifying, detecting, controlling, and administering programs to manage invasive aquatic plants in the Sacramento–San Joaquin Delta, its tributaries, and the Suisun Marsh.” In cooperation with the California Department of Fish and Wildlife, CDBW is tasked with evaluating the threat of aquatic invasive species to the environment, economy, and human health. Consequently, CDBW has undertaken programs to control water hyacinth, Brazilian waterweed , indoor grow rack and South American sponge plant in the Delta. The CDBW uses several techniques in its water hyacinth control program, including the use of herbicides . Though it is imperative that water hyacinth in the Delta be managed—given its wide distribution, ability to block navigation, rapid growth rate, and sheer abundance—weed management activities in other ecosystems demonstrate that such actions may also alter habitat, hydrology, water quality, and food resources for aquatic invertebrates that are associated with invasive macrophytes . The CDBW prepares biological assessments of their management activities—including justification of the amount of herbicide applied—for regulatory review. In an effort to reduce the environmental effects of their operations over time, they also provide logistical support for on-going research as part of their adaptive management process. Widespread herbicide application in the Delta creates a mosaic of living and decaying water hyacinth that can persist for at least 4 weeks before the decaying material dissipates.

Little is known about the macroinvertebrate communities within these decaying water hyacinth mats. It is difficult to predict how management will affect macroinvertebrates because decaying water hyacinth releases nutrients and organic particles that support the food web, but also feed bacterial communities that may drive DO down and subsequently negatively affect macroinvertabrates and zooplankton . We hypothesized that herbicide applications under current management protocols would reduce the abundance and diversity of aquatic invertebrates because they would alter structural and biological habitat.This study provides valuable information for the “evaluate and respond” component of the Delta Water Hyacinth Control Program , which employs adaptive management: a systematic approach for improving resource management by learning from management outcomes . This study also serves as a case study example for generating experimentally derived evidence to support adaptive management programs in other systems where water hyacinth is present . To ensure best practices in their management and policy operations, the CDBW has employed this work in their Section7 Biological Assessment with the United States Fish and Wildlife Service. This case study is also pertinent to management of novel ecosystems, where even non-native species can have important ecological roles . Since water hyacinth is intensively managed with herbicides on a global scale, this work has broad applicability and provides an example for future hypothesis-driven adaptive management efforts involving invasive plants’ roles in ecosystem functioning.Experimental sites were in the central Delta, California , in water hyacinth mats that surround Bacon Island . We chose to focus our study on sites that surrounded Bacon Island because they had predictable herbicide treatment dates. Other site-selection criteria included: mats of floating water hyacinth that were likely to remain in place for the study’s duration; mats at control sites that would remain untreated with herbicide; habitat characteristics similar enough to be comparable between and among treatment and control sites; and no other management activities by the CDBW.Using a Before, After, Control, Intervention experimental design, we established five sampling sites to receive herbicide treatment with glyphosate, each paired with a control site that would not receive any herbicide treatment. CDBW applied glyphosate treatments along with AgriDex at treatment locations. Treatment dates varied among sites during spring and summer 2015 . During herbicide application, the CDBW left untreated buffer strips to comply with the agency’s fish passage protocols that protect migrating and resident fish . However, for treated sites, we assumed that treatment effects would be detected throughout the site, across treated and untreated strips. To ensure this assumption matched reality, we randomly sampled across the entire spatial extent of mats at both treatment and control sites.At each site, we sampled approximately 1 month before the herbicide treatment to ensure that we had pre-treatment data. We sampled each location again approximately 4 weeks post-treatment. We used this post-treatment lag-time to ensure that herbicide effects were as uniform as possible at each of the treatment sites. Since the control locations did not receive any herbicide treatment, we describe them in terms of before and after the treatment date to indicate the point in time when herbicides were applied at comparable treatment locations. CDBW staff collected water-quality measures throughout the treatment season in accordance with National Pollution Discharge Elimination System permitting requirements using a Hach HQ30 meter and Luminescent Dissolved Oxygen probe for DO measures on the periphery of water hyacinth mats. For each sampling event, we used a numbered grid overlaid on a graphical representation of each weed mat, and a random number generator to select four portions of the mat to sample.

Fertilizer should be applied evenly over the top surface followed by a thorough irrigation to move the material into the bale . Since nitrogen levels are the limiting factor in the preconditioning process, one should select a water-soluble fertilizer high in nitrogen. As an alternative to the schedules shown in tables 1 and 2, Wilson recommended a constant liquid feed with 250 parts per million of nitrogen be used with frequent but small additions until the bales are saturated. At that point the bales are planted and liquid feed continues at every watering; 1.5 teaspoons of 24-8-16 in 5 gallons of water will approximate his method. Either organic or synthetic materials will work, but organic materials such as fish emulsion will be more expensive. Products such as fish emulsion produce a strong, disagreeable odor as the bale composts. In urban settings, this odor may be strong enough to be noticed by neighbors. Fish emulsion and other products with a similar odor can attract wildlife—particularly skunks and raccoons—that can damage the bale. Some dogs may be attracted to these bales as well and should be supervised during the conditioning process if fish emulsion is used. Figure 2 shows a bale treated with fish emulsion damaged during the night by a raccoon. Flies may also be attracted to fish emulsion when used in conditioning the bale. If animal damage occurs, replace the loose straw back into the bale firmly as soon as possible.To prepare the bale for planting, vertical growing weed apply either the full rate or half rate of the fertilizer used as determined by the preconditioning schedule you selected. Rates to use of common materials are shown in table 3. Enough variability exists between bales and gardeners’ watering practices that exact accuracy is unnecessary.

After the first 9 days of preparing the bales, once they have cooled down internally below 99°F , the conditioning process has progressed enough to plant; however, bales may not appear visually different than when the process began. A thermometer inserted into the side of the bale can be used to monitor the temperature. It is normal for this process to take 9 to 14 days. Continue to keep bales moist during this time. Figure 3 shows the recorded temperatures of two bales conditioned with 24-8-16. The composting process continues after the initial 9-day conditioning period but at a slower pace with lower temperatures than during the initial phase. Past studies of intensive wheat straw composting show this second phase can last from 20 to 37 days, after which temperatures return to ambient . It is common for mushrooms to emerge from the bale after conditioning. This is normal and is a sign of active decomposition in the bales. These mushrooms should be considered toxic and should not be eaten. Their presence will not affect your plants, but their emergence can disrupt the seed bed, interfering with germination. In low desert basins with highly saline soils, salts may be drawn upward into the bale when bales are set directly on the ground. An air gap formed by locating bales on coarse gravel or similar material will interrupt this process. Alternatively, bales can placed atop an impermeable surface such as concrete or plastic sheeting. Once the conditioning process begins, the bales should not be moved.The process of raising crops in straw bales is very similar to that used in raised bed gardening. Gardening guides such as the California Master Gardener Handbook provide cultural information for many crops; however, growing in straw bales deviates from traditional gardening in two important aspects: planting and nutrient management. Bales are usually good for only one growing season.

After that they can be used as mulch or added to a compost pile.For plants usually grown from seeds such as lettuce, squash, and carrots, an effective method of planting is to cover the surface with 2 to 3 inches of a soilless potting mix or media suitable for growth. This allows seeds to germinate in a finer-textured medium than straw. Seed planted in this prepared surface can be planted in the same manner as one would plant a traditional garden in soil or a raised bed. This method is also suitable for small transplants An alternative to starting seeds in the bale is to remove some of the bale to make a small hole. Fill this hole with a potting mix and plant seeds into the prepared area. This technique is appropriate for vegetables that form large plants, such as squash. As with any garden, plants should be spaced with enough room for them to grow. Planting suggestions for common warm-season vegetables are provided in table 4. For other crops, follow space recommendations printed on seed packets or consult a garden reference to guide you.For plants grown as transplants, remove some straw or pry apart the straw “flakes” with a garden trowel and set the transplant and its soil into the opening. Add additional potting soil to fill any gaps. Water immediately after transplanting, ensuring that both the potting soil and bale are well irrigated. Any trellises or supports should be anchored directly into the ground. As a bale decomposes, its ability to provide support diminishes, and the trellis may fall over. Bales aligned in a row with a single T-post at each end as an anchor are a good option for support and will provide additional support for the bales on the ends as they decompose. When planting bales, be sure to give consideration to how you will irrigate your crop.

Soaker hoses and drip emitters are common methods of providing water slowly to each bale. New transplants set into straw bales may dry out quickly until their roots move into the bale. Expect to water frequently while bales are still fresh. As the bales age and plants’ roots spread throughout the bale, the frequency of irrigation will diminish.Management of vegetation with fire, heavy equipment, herbicides, improved forage plants, and fertilizer played an important role in range improvement following World War II until the late 1970s. Increased fuel and fertilizer costs following the energy crisis of the mid-1970s, low prices for livestock in the 1980s and ’90s, increased liability associated with prescribed burning, the ban from the Environmental Protection Agency on the use of 2,4,5-T for brush control, requirements for environmental impact statements, and other economic and policy changes all conspired to reduce the economic return from many range improvement practices. In addition, low grazing land rental rates often made it more cost effective to rent another acre than to improve an acre. While these forces may have reduced the application of range improvement practices on California’s rangelands for the past 30 years, vegetation management remains the only practical way to increase carrying capacity or to improve wildlife habitat. Current trends of higher lease rates and limited availability of rental property due to conversion to other uses may rejuvenate interest in these practices. Vegetation management has been a continuing theme of research at the University of California since the late 1880s . Prior to the 1970s, the focus was primarily to increase carrying capacity by growing more forage and improving animal performance by increasing forage quality. Following federal and state environmental legislation in the 1970s, management for water quality, air quality, and threatened and endangered species became important management objectives on California’s and the nation’s rangelands. While increasing carrying capacity by producing more forage remains an important objective, ranchers and public agencies also manage for fire hazard reduction, improved water quality, air quality, and biodiversity. Suppressing introduced species and restoring native species has become a major theme among conservation organizations and some government agencies. In this publication, we will first identify practices that reduce seasonal gaps in forage availability and quality. Then we will discuss the economics of vegetation management. Finally, we will review brush and weed control,rangeland seeding, and rangeland fertilization practices, growing rack emphasizing the findings and recommendations of the University of California and other researchers as they have been the main source of what is known about rangeland improvement on annual rangelands.Most ranches in California combine irrigated and dryland hay and pasture with the rangeland forage base in an integrated forage system.

These additional forages are complementary to the rangeland forage base, and they increase the carrying capacity of the ranch or improve forage quality. Annual rangeland ranches depend on numerous complementary forages and feed sources to provide adequate nutrients for beef cattle and sheep production enterprises. Several common and uncommon sources of feed and forage are described below for different seasons of the year. The productive potential and feasibility of each of these sources must be adapted to the forage plant and livestock requirements, and these are dependent on the ranch’s natural, managerial, and financial resources.In this section, we will discuss the influence of vegetation management practices on seasonal forage production, forage quality, and animal performance. The range improvement practice alternatives are often applied in combination with weed and brush control to increase carrying capacity while mitigating seasonal forage gaps. For a thorough discussion of seasonal forage productivity including examples of seasonal and annual production, see the first publication in this series, “Mediterranean Climate,” and Becchetti et al. . The seventh publication in this series, “Livestock Production,” discusses seasonal forage quality and animal performance. The annual range forage year has been divided into seasons to reflect variations in productivity, quality, and animal performance. Bentley and Talbot segregated the seasons into the inadequate-green season, adequate-green season, and inadequate-dry season. George et al. and Becchetti et al. defined four seasons: fall onset of growth, winter slow growth, rapid spring growth, and summer dry. Each of these seasons has characteristic productivity limitations. The fall season is the period between the first germinating rains and the onset of cool winter temperatures. This season can be quite short to several weeks long, depending on the timing of fall precipitation and the onset of cool temperatures. During this period, the dry residual forage that was produced the previous season provides low-quality dry matter for grazing. As germination and seedling establishment progresses, the amount of new green forage increases. This new forage is high in protein and energy, but high water content may limit nutrient intake. During winter, new forage continues to grow slowly, and residual dry forage disappears due to grazing and decomposition. During the fall-winter period, low forage levels can limit intake of dry matter, energy, protein, and other nutrients. Supplementation, seeding, and fertilization can improve animal performance during the fall and winter period. Rapid spring growth begins with rising spring temperatures. During this portion of the growing season, forage quantity and quality are usually adequate for rapid livestock gains. Forage level increases rapidly and frequently outproduces the livestock’s ability to consume it. Unused forage at the end of this season remains as low-quality dry residue. Forage production and quality during this period are increased by seeding legumes and fertilization. Although not common, excess forage can be conserved as high-quality hay for future use if properly timed. Conservation of forage avoids risk associated with uncertain weather conditions, and it may increase market flexibility. However, required equipment increases overhead costs. Standing dry forage gradually shatters and decomposes, resulting in continued decline in forage quality through the summer season. This forage provides energy to grazing stock but frequently is of inadequate quality to meet other nutrient requirements. Intake of this forage is limited by its quality. It is common practice to move stock to higher elevations and irrigated pasture or provide protein and mineral supplements during this season. Strategic use of appropriate legumes can increase the quality of this dry forage. The following seasonal forage and grazing management practices can provide solutions to limitations in forage production, quality, and utilization that are manifested as inadequate animal production per acre. Controlling medusahead, goatgrass, yellow starthistle and other weeds, in combination with the seeding and fertilization that may be desirable during this season, can increase carrying capacity of annual rangeland and forage quality.In California the cost of improving an acre of rangeland has always had to compete with the cost of renting an acre of grazing land. Often it has been cheaper to increase carrying capacity by renting another acre rather than paying the per-acre cost of range improvement. However, as it becomes harder to find grazing land to lease, range improvement may become more important.

Three crop safety studies and two supplemental dose-response evaluations were conducted in 2019 and 2020 to evaluate the crop safety of the Israeli-developed PICKIT decision support system on California processing tomatoes. These studies were conducted at the UC Davis Plant Sciences Field Research Facility near Davis, California . The soil composition at this site was 41% sand, 34% silt, and 25% clay with 2.1% OM, 6.98 pH, and estimated CEC of 18.2 cmolc/kg of soil. The site did not contain broomrape; this protocol focused on crop safety of 1X and 2X rates of herbicides used in the PICKIT system that are not currently registered for use in tomato in the United States. Plots were 12 m long on 1.5 m beds with one plant line in the center of the bed. Cultivar ‘Heinz 1662’ processing tomato transplants were planted at 30.5 cm spacing. Each bed had two 15.9 mm drip lines buried at 30.5 cm with 0.6 L/hr emitters spaced every 30.5 cm; one line ran the full length of the beds and was used for crop irrigation and fertigation, the second line was terminated at the end of each plot and connected to an above-ground manifold system which was used to apply the experimental chemigation herbicide treatments. Plots were arranged in a randomized complete block design with four replications per treatment. In 2019, two experiments were conducted to represent twoplanting dates, April 25 and May 30; a single experiment was conducted in 2020 with an April 22 planting date. Pre-plant incorporated applications of sulfosulfuron were made one day before transplanting on April 24 and May 29, 2019 in the early- and late-planted experiments respectively, and on the day of planting, April 22, 2020 . PPI herbicides were applied using a backpack sprayer and three-nozzle boom delivering 280.5 L/ha with AIXR 11003 nozzles at 28 pounds per square inch .

PPI treatments were mechanically incorporated to 7.6 cm after application, commercial grow racks after which tomatoes were mechanically transplanted with a three-row transplanter on April 25, 2019 , May 30, 2019 , and April 22, 2020. The PICKIT system’s thermal time model is based on growing degree days , with applications at 400, 500, 600, 700, and 800 GDD after transplanting depending on treatment regimes . The PICKIT program has various regimes depending on level of infestation, with each calling for different application types and total number of applications . In 2019, chemigation applications were made through the terminated irrigation line using a 20.8 L/min 12-volt electric pump and 113.5 L tank. Treatments were applied to four plots at once, with a total carrier volume of 96.1 L per treatment resulting in approximately 15.9 L per plot . In 2020, chemigation applications were made using CO2 to inject a chemigation mix into a distribution manifold with valved connections at each plot . Treatments were applied to two replicate plots at once with separate injection ports for replicates 1 and 2 and replicates 3 and 4 to reduce the system volume receiving herbicide treated water. Herbicides were diluted in 11 L of water and this solution was injected into the already-running irrigation system over approximately 15 minutes, followed by 20 minutes ofwater to flush the distribution lines. Foliar imazapic treatments were made on July 16, 2019, August 15, 2019, and June 12, 2020 and approximately 21 days later with a backpack sprayer and two-nozzle boom delivering 280.5 L/ha with AIXR 11005 nozzles at 20 PSI. These applications were made at estimated broomrape emergence and approximately 21 days later, as these studies occurred in uninfested fields. Phytotoxicity was recorded in all three studies and representative plant height was recorded in the 2020 study. All fruit from one-meter square sections of row were harvested on September 4, 2019, September 19, 2019, and September 3, 2020 at commercial maturity and fresh weights were recorded .

Phytotoxicity, height, and yield data were analyzed using a one-way analysis of variance followed by a Tukey-HSD test using the agricolae package in R version 1.2.5033 . Two supplemental crop safety trials were conducted to evaluate increasing rates of foliar applied imazapic, which is not currently registered on processing tomatoes in California. These studies were conducted at the UC Davis Plant Sciences Field Facility near Davis, CA, . Cultivar ‘Heinz 1662’ tomatoes were transplanted on April 22, 2020 in a single plant line on a 1.5 m bed with 30.5 cm spacing. Imazapic was applied late in the growing season to simulate a rescue application in a PICKIT program. Applications were made on July 7, 2020, 73 days after transplant in the first experiment and on July 21, 2020, 87 days after transplant in the second experiment at 280.5 L/ha using a two-nozzle boom with AIXR 11003 nozzles at 28 PSI. Five rates were applied in a dose response style experiment with a 0.25% v/v nonionic surfactant . Applications were made at full fruit set . Each treatment was replicated four times in a single guard row of an existing processing tomato experiment. Visual crop injury ratings were taken 3, 7, and 14 days after treatment . Phytotoxicity means were analyzed using a one-way analysis of variance followed by a Tukey-HSD test using the agricolae package in R version 1.2.5033 .A two-year study was conducted from spring 2019 to fall 2020 to evaluate rotational crop-safety of the Israeli-developed PICKIT decision support system. This field experiment included a 2019 tomato crop treated with PICKIT herbicides followed by a planting of six common rotational crops in 2020. The study was conducted at the UC Davis Department of Plant Sciences Field Research Facility near Davis, California . The site did not contain broomrape; this experiment focused on crop safety of sulfosulfuron, imazapic, and 2X rates of imazamox, imazapyr, and imazethapyr, none of which are currently registered for use in tomato in the United States.

The 2019 tomato main plots were 54.8 m long on 1.5 m beds with one plant line in the center of the bed. Each bed had one 15.9 mm drip line at a depth of 30.5 cm with 0.6 L/hr emitters spaced every 30.5 cm. This drip line was used for crop irrigation and fertigation as well as chemigation of PICKIT treatments. For the 2019 tomato crop, main plots were arranged as whole rows in a randomized complete block design with four replications. PPI applications of sulfosulfuron were made on May 29, 2019 one day before transplanting tomatoes. PPI herbicides were applied using a backpack sprayer and three-nozzle boom delivering 280.5 L/ha with AIXR 11003 nozzles at 28 PSI. PPI treatments were mechanically incorporated to 7.6 cm after application. Tomato cultivar ‘DRI 319’ transplants were planted at a 30.5 cm spacing with a three-row transplanter on May 30, 2019. At each growing degree day target chemigation applications were made through the drip line using a Venturi-style injection system attached to a cone tank over the course of 45 minutes, with treatments applied to four replicate plots at once . A single one-meter square section of each plot was harvested on September 19, 2019 and total weight of all fruit were recorded . Following the tomato harvest in 2019, the tomato crop was destroyed in place with a flail mower. After the crop residue dried, beds were lightly cultivated to reshape beds but minimize soil mixing. The 54.9 m long tomato main plots were split into six 9.1 m subplots for the 2020 rotational crops in a split plot design. The six rotational crops including wheat, corn, safflower, sunflower, beans and melons were randomly assigned to a subplot such that the 2020 experimental design was a randomized split plot with four replications. On November 22, 2019, wheat subplots were planted with a grain drill. Visual wheat injury measurements were recorded during the winter of 2019 and spring of 2020. In mid-April 2020, vertical grow weed all beds were treated with glyphosate to terminate the wheat and control winter weeds in all plots and lightly cultivated to prepare a seedbed. On April 17, 2020, corn , safflower , sunflower , beans , and melons were planted using an Earthway precision garden seeder .

Plant height and fresh weight biomass were recorded nine weeks after planting on June 23, 2020; the experiment was subsequently terminated without being taken to maturity. Height and fresh biomass data were analyzed using a one-way analysis of variance followed by a Tukey-HSD test with the agricolae package in R version 1.2.5033 .A study was conducted in a commercial tomato field in Yolo County, CA, that had been reported as infested with branched broomrape in 2019 and a portion of the crop was destroyed under CDFA quarantine provisions. The infested area was prepared for planting by the grower and used for a 2020 experiment to test the efficacy of the PICKIT protocol on branched broomrape in California tomato systems. The soil composition at this site was 25% sand, 42% silt, and 33% clay with 2.7% OM, 7.2 pH, and estimated CEC of 23.6 . Plots were 30.5 m long on 1.5 m beds with two drip lines: one 22.2 mm drip line buried at 25.4 cm and one 25.4 mm drip line buried at 30.5 cm in the center of the bed. The 22.2 mm drip line was terminated at the ends of each plot serving as the dedicated chemigation line with 0.6 L/hr emitters at 30.5 cm spacing. The 25.4 mm line was used for crop irrigation and fertigation of the entire experimental area. Plots were arranged in a randomized complete block design with four replications. PPI applications of sulfosulfuron were made on March 27, 2020 . Sulfosulfuron was applied using a backpack sprayer and three-nozzle boom delivering 280.5 L/ha with AIXR 11003 nozzles at 28 PSI. PPI treatments were mechanically incorporated to 7.6 cm after application on the same day. In addition to the experimental treatments, the entire plot area was treated with the grower’s preplant incorporated tank mix, which consisted of S-metolachlor , pendimethalin , metribuzin , and diazinon on March 27, 2020. Cultivar ‘BQ271’were mechanically transplanted using a two-row transplanter on March 30, 2020 with two plant lines in each row with plants spaced 30.5 cm apart within and between lines. A routine foliar application of 7.2 g ai/ha rimsulfuron was made by the grower to the entire experimental area after transplanting.Chemigation applications were made using CO2 to inject the chemigation mix into 50.8 mm lay flat hose connected to valved 22.2 mm chemigation lines in each plot . Treatments were applied to two replicate plots at once; plots of the same treatment in replications 1 and 2 and replications 3 and 4 were treated together. Herbicide treatments were mixed in 11 L of solution which was injected into the already-running irrigation system over approximately 15 minutes, followed by 20 minutes of water to flush the lines. Chemigation applications were made according to a modified version of the PICKIT protocol . Foliar imazapic treatments were made with a 2-nozzle backpack sprayer delivering 280.5 L/ha with AIXR 11003 nozzles at 28 PSI. Broomrape scouting was done 3 times weekly for seven weeks, followed by 1 time per week for 3 weeks starting on June 1, 2020. At each rating, individual clusters of shoots were marked with wire construction flags, with different colors representing each week’s emergence . Broomrape shoot clusters were counted and recorded weekly. Total broomrape cluster numbers were analyzed using a one-way analysis of variance followed by a Tukey-HSD test in the agricolae package in R . Broomrape emergence over time was analyzed with a 3-parameter log-logistic function in the drc package in R version 1.2.5033 . Before the trial was terminated and after the final broomrape cluster count, locations of individual clusters marked by flags were recorded with a GPS device . A Trimble Handheld GPS device was placed at each flag, the coordinate was recorded in the FarmWorksMobile application , and the color of the corresponding flag was recorded. This data was entered into ArcGIS online , and a color coordinated map was created .After two field seasons and three studies, crop safety for the imidazolinone and sulfonylurea herbicides utilized in the PICKIT system appears acceptable at both the proposed rate structure and two times the proposed rate structure in California processing tomato. These results confirm the crop safety reported for the PICKIT program in Israel.

M-209 T50 was affected by planting depth in 2019, at 79 DAP and 80 DAP for 3 cm and 6 cm planting depths, respectively. Full-season plant heights were not affected by PPB treatment, cultivar or planting depth either year .In 2018 there were no harvestable panicles or yield component analysis in UTC plots. Rice yield components in weed-free plots were significantly affected by cultivar in 2018 ; all measured yield components were greater for M-209 at either planting depth. M-209 averaged 26 more florets per panicle , and 19 more filled grains than M-206 in 2018. Percent unfilled grains was 1.6-fold greater in M-209 . Although not significant, panicle yield, 1000-grain weight, total florets per panicle, and filled florets per panicle were generally greater for rice seeded at the 6 cm planting depth for both cultivars in 2018. In 2019 yield components were significantly reduced in UTC plots. Averaged across planting depth and cultivar, panicle grain yield, florets per panicle, filled grains per panicle, and 1000-grain weight decreased 47%, 31%, 37%, and 15%, respectively . M-209 planted at the 6 cm depth had the greatest reductions in yield components in 2019 UTC plots, with nearly 30% lower 1000-grain weight and 50% blanking when seeded to that depth. In 2019 weed-free plots, cultivar differences in yield components varied. Averaged across planting depths, M-206 had greater panicle grain yield and 1000-grain weight , vertical grow racks while M-209 had greater florets per panicle . M-209 blanking percentage averaged 1.7-fold greater than M-206 in 2019.Weed group composition in untreated plots did not vary between years, however weed group densities varied greatly.

Aquatic broad leaves and algae were not observed in either year, which is in agreement with previous research on DS rice using early-season flush irrigation, orfull-season alternate wetting and drying . As aquatic weeds and algae can inhibit rice growth via shading and physical barrier in water-seeded systems, the potential suppressive benefit of early-season flushing in DS rice is clear. This can be a useful component of the stale-drill method as a measure for herbicide resistance management, as algae and broad leaf suppression can occur without any additional resistance selection pressure. Grass densities were high in both study years, however Echinochloa densities were lower in 2019, allowing L. fusca and sedges to become more competitive. It is interesting that all three major weed groups were present in roughly equal numbers early in 2019 , yet Echinochloa and sedge densities decreased dramatically by 45 DAP, while L. fusca densities increased. In 2018, extreme relative density allowed Echinochloa grasses to easily out-compete other weeds and rice in UTC plots, whereas in 2019 reduced Echinochloa density allowed L. fusca to out-compete other weeds. Emergence of L. fusca is discontinuous throughout the season , and the lack of suppressive competition -particularly from Echinochloa spp.- appeared to allow later-emerging L. fusca to freely establish.Drilling rice seed at 3cm and 6 cm depths delayed rice emergence and successfully permitted the use of a postplant burndown herbicide treatment just as rice was beginning to emerge. Using flush-irrigation to prime weed seed resulted in timed emergence of the majority of observed grasses, and glyphosate use alone reduced combined grasses by more than 50% in both study years .

Although L. fusca emergence appeared to continue after PPB treatment, this was not observed with Echinochloa or sedges. Echinochloa spp. emergence is also known to be discontinuous in rice systems , however our results suggest that shallow flushing may have inhibited Echinochloa emergence from heavy soil as it dried and crusted over. Previous research showed a weed control benefit to applying pendimethalin at rice emergence, as a part of a PPB treatment . As there were no differences in further weed control between the subsequent treatments in the present study , it appears that there were no added late-season benefits of applying pendimethalin or clomazone at the 3-leaf stage. Using the stale-drill method with PPB can achieve the dual cultural-chemical effects suppressing aquatic species and shifting the weed spectrum, as well as allowing novel modes of action to be used to control grasses and sedges. Both of these effects could reduce the spread of herbicide resistance, if stale-drill is used in rotation with other rice establishment methods.Previous research found that M-206 emergence in the field was delayed by up to three extra days by planting to 5.1 cm, compared to 1.3 cm . However, emergence in that study was likely slowed by unseasonably cool temperatures immediately following planting. A related greenhouse study comparing the relative vigor four California cultivars found that M-206 planted to 5.1 cm and 6.4 cm had time to 50% emergence of 9.4 and 14.0 days, respectively. In contrast, M-209 had T50 of 8.3 and 9.4 days at the same respective planting depths . Based on these prior findings, we expected shallower-sown rice to emerge earlier, and expected M-209 to emerge before M-206. However, although there were minor differences in emerged seedling length, we found no differences in emergence date between cultivars or planting depths. The soil at the study site is a Vertisol, characterized by shrinking and cracking as it dries .

We observed that soil cracking in hot weather after the initial flushing event followed the lines of furrows left by the seeding drill. This cracking likely exposed elongating seedlings to light and oxygen, hastening emergence . Taken together, our findings support the hypothesis that California cultivars have sufficient vigor to emerge rapidly and evenly from these depths, however the increased vigor of M-209 may provide an emergence advantage if planted in cooler than normal conditions. The stand reductions at 6 cm planting depth observed in 2018 were not repeated in 2019. It is possible that physical or allelopathic effects of the much higher weed density that year inhibited some rice from establishing. The relative competitiveness of rice and Echinochloa spp. is well documented, and recent research suggests that root exudates from E. crus-galli and E. colona may have inhibitory effects on rice germination and emergence. Alternatively, growing degree day accumulation was more rapid in 2019 due to the later planting date, which may have minimized stand reductions due to deeper seeding. Nevertheless, increased tillering in M-206 compensated for stand reductions in 2018. In a related study we found increased tillering with increasing soil crown depth in these cultivars , although the opposite has been observed previously in small-seeded cereals . In addition, M-209 planted at a depth of 6 cm reached heading later than the more shallow seeding in 2019, which resulted in fewer filled grains at time of harvest.Applying glyphosate to just-emerged rice resulted in tip die-back, but no other symptoms developed. Glyphosate is a systemic herbicide, and needs to be translocated to the crown of a graminid species in order to fatally inhibit the 5-enolpyruvlyshikimate-3-phosphate synthase enzyme . Although the emerged rice seedlings were green at the time of PPB application, the lack of secondary symptoms could be evidence that seedlings were not yet translocating, and therefore still using seed reserves for growth. In addition, glyphosate in solution is anionic, and readily binds to clay soil particles, especially in lower pH soils such as found in rice systems . It is also possible that soil particles attached to the coleoptile below the emerged leaf may have protected the rice somehwat by binding glyphosate molecules. Al-Khatib et al. found that foliar uptake of glyphosate bound to particles of silt loam with 6.6 pH was less than 1% each in alfalfa and pea , and 3% in grape , compared to roughly 50% uptake of aqueous glyphosate in the same species. Grains with starchy reserves such as rice tend to tolerate anaerobic environments well , and this fact is certainly a major factor in the ability of rice organs to elongate vigorously through heavy soils or floodwaters. Alpi and Beevers found that a vigorous japonica cultivar was able to continue coleoptile elongation for up to two weeks before exhausting seed reserves. The cellular machinery in rice that is optimized for fermentative anaerobiosis also appears to provide an emergence benefit for rice grown aerobically in deep soil. Rapid and even stand emergence is key to timing a PPB treatment in deep-sown rice, and good field scouting is essential to determining emergence.

Although application of a non-selective herbicide directly to emerged rice seedlings would not be recommended, growing tables the continued reliance of just-emerged seedlings on seed reserves can provide a fail-safe against application of a normally-lethal herbicide as a burndown treatment.Differential cultivar responses to seasonal variability were apparent in this study. Trials were planted later in 2019, for a 129-day growing season versus 139 days in 2018. Although both cultivars have nominal season durations of about 140 days , M-209 is slower to mature than M-206, reaching 50% heading about six days later in traditional WS rice culture. M- 209 reached 50% heading eight days later than M-206 in 2018, but only 3-4 days later in 2019, reflecting a T50 shift of 3-4 DAP in 2019 . As the rice was planted later in the summer, growing degree day accumulation would be expected to be greater early in the season, resulting in panicle initiation occurring earlier than expected in M-209. This possibility, along with the shortened season duration, may explain why M-209 appeared to have higher sensitivity to seasonal fluctuations than M-206.We find that the present study serves as a successful proof-of-concept for the stale-drill method as a new strategy for rice production and weed management. This work agrees with previous studies that suggested that California semidwarf rice cultivars possessed suitable vigor to emerge evenly from seeding depths up to 6 cm, and that a PPB application of a non-selective herbicide could be safely administered to emerging rice without causing sustained crop injury. Aquatic weeds were suppressed by water management, and the PPB treatment reduced overall weed density by more than 50% in both years, regardless of planting depth or cultivar used. Variability in observed effects of deeper planting on rice growth and development do not support planting rice deeper than 3 cm, however. Although the two cultivars used in this study have varying levels of observed responses to seasonal variability, adequate field preparation, irrigation management, variety selection, and scouting can help to ensure healthy and economically competitive stands. In order to validate our confidence in this method, field-scale trials analyzing the logistical and economic parameters of implementing this program across soil and climate types are necessary. In addition, further refinements to herbicide programs emphasizing reduced input costs, and the potential of reducing seedbanks of weedy rice and herbicide-resistant weeds, would help to more adequately assess the flexibility and potential utility of this method.Glyphosate-resistant crops, also known as “Roundup Ready” , have become an important part of cropping systems in the United States. In 2004, approximately 13 percent of corn, 85 percent of soybean, and 60 percent of cotton acreage was occupied by RR varieties. Alfalfa is the nation’s third most important crop in economic value, and it occupies more than 22 million acres in the United States . It is considered the premier forage crop. It is the primary feed for dairy production, and is commonly fed to beef cattle, sheep, and horses. Alfalfa is also used for green chop and silage in many areas. California is the leading producer of alfalfa hay in the United States, followed by Wisconsin, South Dakota, Minnesota, and Idaho. Roundup Ready technology has been successfully incorporated into alfalfa and is scheduled for commercial release in 2005. This publication reviews the important attributes and issues pertaining to RR technology as applied to alfalfa and the potential impacts of this technology on production systems and markets.Roundup is a broad-spectrum herbicide that kills a wide range of plants. It is not normally applied directly to crops. The RR technology incorporates genetic resistance to glyphosate into crop plants by inserting a single bacterial gene that modifies 5-enolpyruvylshikimate-3-phosphate synthase, an enzyme essential for plant growth. Monsanto has used this technology to develop several RR crops . Specifically, these new varieties will allow glyphosate to be applied over the top of the entire crop to control a wide spectrum of annual and perennial weeds commonly found in alfalfa. Several of these weeds, especially perennials, are difficult to control using conventional herbicides or non-herbicide weed control methods.