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.