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This study sought to characterize and compare anti-inflammatory effects of twenty sorghum accessions with contrasting grain polyphenol concentrations but similar genetic backgrounds (based on a genomewide estimate of relatedness). Cell viability, tumor necrosis factor- (TNF-) α, and interleukin- (IL-) 6 were measured in RAW 264.7 macrophages treated with increasing doses (0, 15, 30, and 60 μg/mL) of sorghum ethanol extracts and stimulated with lipopolysaccharide (LPS). Extract dose had a significant effect on TNF-α and IL-6, with a trend of cytokines decreasing between 0 μg/mL and 15 μg/mL of sorghum extract. Genotype also had a significant effect on the cytokines, with extracts from four accessions significantly decreasing TNF-α and/or IL-6. Cells treated with 3-deoxyanthocyanidin-containing accessions had less cytokine production than non-3-deoxyanthocyanidin accessions, whereas cells treated with proanthocyanidin-containing accessions had more cytokine production than cells treated with nonproanthocyanidin accessions. Additionally, there was a significant effect of the Tannin1 allele on TNF-α and IL-6. Our results demonstrate that sorghum genotypes differentially modulate induction of inflammatory cytokine production in RAW 264.7 macrophages and that specialty grain has the potential to be tailored by controlling traits at the nucleotide level. This study adds to our knowledge of sorghum health effects and contributes to efforts aimed at developing health-promoting sorghum grain. [ABSTRACT FROM AUTHOR]

Maize genetic diversity has been used to understand the molecular basis of phenotypic variation and to improve agricultural efficiency and sustainability. We crossed 25 diverse inbred maize lines to the B73 reference line, capturing a total of 136,000 recombination events. Variation for recombination frequencies was observed among families, influenced by local (cis) genetic variation. We identified evidence for numerous minor single-locus effects but little two-locus linkage disequilibrium or segregation distortion, which indicated a limited role for genes with large effects and epistatic interactions on fitness. We observed excess residual heterozygosity in peticentromeric regions, which suggested that selection in inbred lines has been less efficient in these regions because of reduced recombination frequency. This implies that pericentromeric regions may contribute disproportionally to heterosis. [ABSTRACT FROM AUTHOR]

The genetic structures of the Iowa Corn Borer Synthetic #1 (CB) and Iowa Stiff Stalk Synthetic (SS) maize (Zea mays L.) populations are important because these populations serve as the model for development of modern commercial hybrids. In 1949, CB and SS were used to start a reciprocal recurrent selection (RRS) breeding program at Iowa State University. This study was conducted to analyze more thoroughly the genetic diversity within this RRS program and illustrate how the RRS program has changed over time at the molecular level. The progress of this program was measured by analyzing the variation at 86 SSR loci among 28 progenitor lines and 30 plants sampled from each of seven cycles (Cycle 0, Cycle 1, Cycle 3, Cycle 6, Cycle 9, Cycle 12, and Cycle 15) in each population. The progenitors of these populations show a high amount of variation on the basis of expected heterozygosity (0.557). As the RRS program proceeded, this variation decreased (Cycle 15, 0.245). In total, a larger amount of genetic variation was found among plants within cycles (66%) than among cycles (13%) or between populations (21%). The repartitioning of variation from within populations (96% in progenitors) to between populations (58% in Cycle 15) over time is consistent with theoretical expectations of divergence between the populations. By sampling intermediate time points, we gained a comprehensive genetic view of CB and SS permitting evaluation of the molecular-level changes occurring as a result of reciprocal recurrent selection. [ABSTRACT FROM AUTHOR]

ABSTRACT Phenotypic plasticity is the property of a genotype to produce different phenotypes under different environmental conditions. Understanding genetic and environmental factors behind phenotypic plasticity helps answer some longstanding biology questions and improve phenotype prediction. In this study, we investigated the phenotypic plasticity of flowering time and plant height with a set of diverse sorghum lines evaluated across 14 natural field environments. An environmental index was identified to quantitatively connect the environments. Reaction norms were then obtained with the identified indices for genetic dissection of phenotypic plasticity and performance prediction. Genome‐wide association studies (GWAS) detected different sets of loci for reaction‐norm parameters (intercept and slope), including 10 new genomic regions in addition to known maturity (Ma1) and dwarfing genes (Dw1, Dw2, Dw3, Dw4 and qHT7.1). Cross‐validations under multiple scenarios showed promising results in predicting diverse germplasm in dynamic environments. Additional experiments conducted at four new environments, including one from a site outside of the geographical region of the initial environments, further validated the predictions. Our findings indicate that identifying the environmental index enriches our understanding of gene‐environmental interplay underlying phenotypic plasticity, and that genomic prediction with the environmental dimension facilitates prediction‐guided breeding for future environments. [ABSTRACT FROM AUTHOR]

Focuses on Limonium dufourii (Plumbaginaceae), a triploid species with obligate apomictic reproduction endemic to the East Mediterranean coast of Spain, where it is present in only six populations, most of which have a very low number of individuals. How genetic variation and population structure in this species was studied using amplified fragment length polymorphisms (AFLPs) as markers; Comparative analyses of data from AFLPs with those from a previous study using random amplified polymorphic DNA (RAPD); Results suggesting relationships among the different AFLP patterns and the estimates of population genetic parameters obtained with this evolutionary distance are in good agreement with previous results; What these analyses show with respect to genetic variability and differentiation among populations of L. dufourii; Reasons making AFLPs a much better DNA fingerprinting technique.

Focuses on genotyping plant genetic resources by multiplex polymerase chain reaction and fluorescence-based, semi-automated allele sizing technology. Observed fragment sizes; Primer labeling and DNA extraction; Inheritance and linkage data; Amplification protocols; Flanking sequences.

The chemical composition of grain stalks has been extensively studied and has long been assumed to have a major influence on stalk lodging. However, much less attention has been given to the influence of stalk architecture (i.e. physical features of anatomy and morphology). We show in this study that stalk architecture is far more influential on stalk bending strength (a common measure of lodging resistance) than chemical composition. This insight was obtained through the novel combination of structural engineering principles and a plant-by-plant experimental design using two major grain species (maize and sorghum). Lodging resistance was quantified using stalk bending strength which provides plant-specific data while also removing dependence on weather events. Stalk anatomy and morphology as and chemical composition of the stalk were also measured for each specimen in this study. Statistical results indicate that (a) the quantification of stem architecture via engineering beam theory is four times more predictive of stalk bending strength than composition, and (b) stalk architecture and chemical composition are interrelated. These results explain why previous studies attempting to link chemistry and lodging have been inconsistent. Furthermore, these results indicate that future studies aimed at studying lodging must not overlook the dominant influence of stalk architecture. • Architectural, chemical composition, and bending strength measured for each specimen. • Stalk architecture (anatomy/morphology) was highly predictive of bending strength. • Chemical composition was weakly related to bending strength. • Stalk architecture and chemistry are interrelated. • Future studies should control for the powerful influence of stalk architecture. [ABSTRACT FROM AUTHOR]

Sorghum [Sorghum bicolor (L.) Moench] is a potential crop for organic production that could help meet the demand increase in organic food products and feed grains, but no efforts have been made to improve sorghum breeding tools, techniques, and methods for this cropping system. Based on revelations in other crops, focal traits and their prioritization to optimize sorghum for organic use likely differs from conventional sorghum breeding targets. This study evaluated yield performance, agronomic characteristics, and biotic stress resistance under certified organic practices in a range of grain sorghum genotypes that included 70 hybrids, 72 advanced breeding lines, and 43 diverse accessions, as well as 10 sweet sorghum cultivars and four commercial maize hybrids. Multiyear, multilocation trial data demonstrated that sorghum can be effectively produced using sustainable and organic inputs, but hybrid or cultivar selection is extremely important for success as entry means for grain yield ranged from 26 to 5,970 kg ha−1. Yields of top sorghum entries rivaled commercially available maize (Zea mays) hybrids. Overall, hybrids significantly outperformed inbred lines as heterosis proved beneficial for influential agronomic traits, although a Clemson F6 advanced breeding line, PV20_0426, ranked second in yield. Sugarcane aphid tolerance, increased canopy closure, and grain mold resistance were positively correlated with grain yield and should be considered target traits for breeding sorghum hybrids and cultivars for organic use. Depending on possible seed production constraints, developing pure line cultivars with the proper trait package may be effective to diminish this potential obstacle for the organic sorghum market. Core Ideas: Sorghum can be effectively produced using sustainable and organic inputs.Sorghum hybrid or cultivar selection is extremely important for success.Yields of top grain sorghum entries rivaled commercially available organic maize hybrids.Hybrids significantly outperformed inbred lines as heterosis was evident for multiple traits.Increased canopy closure along with sugarcane aphid and grain mold resistance serve as target traits. [ABSTRACT FROM AUTHOR]

Summary: With the recent development of genomic resources and high‐throughput phenotyping platforms, the 21st century is primed for major breakthroughs in the discovery, understanding and utilization of plant genetic variation. Significant advances in agriculture remain at the forefront to increase crop production and quality to satisfy the global food demand in a changing climate all while reducing the environmental impacts of the world's food production. Sorghum, a resilient C4 grain and grass important for food and energy production, is being extensively dissected genetically and phenomically to help connect the relationship between genetic and phenotypic variation. Unlike genetically modified crops such as corn or soybean, sorghum improvement has relied heavily on public research; thus, many of the genetic resources serve a dual purpose for both academic and commercial pursuits. Genetic and genomic resources not only provide the foundation to identify and understand the genes underlying variation, but also serve as novel sources of genetic and phenotypic diversity in plant breeding programs. To better disseminate the collective information of this community, we discuss: (i) the genomic resources of sorghum that are at the disposal of the research community; (ii) the suite of sorghum traits as potential targets for increasing productivity in contrasting environments; and (iii) the prospective approaches and technologies that will help to dissect the genotype–phenotype relationship as well as those that will apply foundational knowledge for sorghum improvement. Significance statement: Using genetic and genomic resources efficiently and appropriately is critical to advance our understanding of biology and advance crop improvement. We review the myriad genomic resources available and currently in development for the sorghum community. [ABSTRACT FROM AUTHOR]

Multiparent advanced eneration inter-cross (MAGIC) populations improve the precision of quantitative trait loci (QTL) mapping over biparental populations by incorporating increased diversity and opportunities to reduce linkage disequilibrium among variants. Here, we describe the development of a MAGIC B-Line (MBL) population from an inter-cross among 4 diverse founders of grain sorghum [Sorghum bicolor (L.) Moench] across different races (kafir, guinea, durra, and caudatum). These founders were selected based on genetic uniqueness and several distinct qualitative features including panicle architecture, plant color, seed color, endosperm texture, and awns. A whole set of MBL (708 F6) recombinant inbred lines along with their founders were genotyped using Diversity Arrays Technology (DArTseq) and 5,683 single-nucleotide polymorphisms (SNPs) were generated. A genetic linkage map was constructed using a set of polymorphic, quality-filtered markers (2,728 SNPs) for QTL interval-mapping. For population validation, 3 traits (seed color, plant color, and awns) were used for QTL mapping and genome-wide association study (GWAS). QTL mapping and GWAS identified 4 major genomic regions located across 3 chromosomes (Chr1, Chr3, and Chr6) that correspond to known genetic loci for the targeted traits. Founders of this population consist of the fertility maintainer (A/B line) gene pool and derived MBL lines could serve as female/seed parents in the cytoplasmic male sterility breeding system. The MBL population will serve as a unique genetic and genomic resource to better characterize the genetics of complex traits and potentially identify superior alleles for crop improvement efforts to enrich the seed parent gene pool. [ABSTRACT FROM AUTHOR]

Hybrid breeding in sorghum [Sorghum bicolor (L.) Moench] utilizes the cytoplasmic-nuclear male sterility (CMS) system for seed production and subsequently harnesses heterosis. Since the cost of developing and evaluating inbred and hybrid lines in the CMS system is costly and time-consuming, genomic prediction of parental lines and hybrids is based on genetic data genotype. We generated 602 hybrids by crossing two female (A) lines with 301 diverse and elite male (R) lines from the sorghum association panel and collected phenotypic data for agronomic traits over two years. We genotyped the inbred parents using whole genome resequencing and used 2,687,342 high quality (minor allele frequency > 2%) single nucleotide polymorphisms for genomic prediction. For grain yield, the experimental hybrids exhibited an average mid-parent heterosis of 40%. Genomic best linear unbiased prediction (GBLUP) for hybrid performance yielded an average prediction accuracy of 0.76-0.93 under the prediction scenario where both parental lines in validation sets were included in the training sets (T2). However, when only female tester was shared between training and validation sets (T1F), prediction accuracies declined by 12-90%, with plant height showing the greatest decline. Mean accuracies for predicting the general combining ability of male parents ranged from 0.33 to 0.62 for all traits. Our results showed hybrid performance for agronomic traits can be predicted with high accuracy, and optimizing genomic relationship is essential for optimal training population design for genomic selection in sorghum breeding. [ABSTRACT FROM AUTHOR]

Reports on the teamup of Pioneer Hi-Bred International with the US Agricultural Research Service (ARS) to find genetic markers called sequence repeats for finger printing corn and other crops. Use of sequence repeats for germplasm curators.

SUMMARY: Association mapping panels represent foundational resources for understanding the genetic basis of phenotypic diversity and serve to advance plant breeding by exploring genetic variation across diverse accessions. We report the whole‐genome sequencing (WGS) of 400 sorghum (Sorghum bicolor (L.) Moench) accessions from the Sorghum Association Panel (SAP) at an average coverage of 38× (25–72×), enabling the development of a high‐density genomic marker set of 43 983 694 variants including single‐nucleotide polymorphisms (approximately 38 million), insertions/deletions (indels) (approximately 5 million), and copy number variants (CNVs) (approximately 170 000). We observe slightly more deletions among indels and a much higher prevalence of deletions among CNVs compared to insertions. This new marker set enabled the identification of several novel putative genomic associations for plant height and tannin content, which were not identified when using previous lower‐density marker sets. WGS identified and scored variants in 5‐kb bins where available genotyping‐by‐sequencing (GBS) data captured no variants, with half of all bins in the genome falling into this category. The predictive ability of genomic best unbiased linear predictor (GBLUP) models was increased by an average of 30% by using WGS markers rather than GBS markers. We identified 18 selection peaks across subpopulations that formed due to evolutionary divergence during domestication, and we found six Fst peaks resulting from comparisons between converted lines and breeding lines within the SAP that were distinct from the peaks associated with historic selection. This population has served and continues to serve as a significant public resource for sorghum research and demonstrates the value of improving upon existing genomic resources. Significance Statement: The whole‐genome sequencing of the sorghum association panel, which represents the most heavily utilized panel in sorghum breeding, will serve as a pivotal resource in the sorghum community to provide improved genotype‐to‐phenotype associations, genomic prediction, and pan‐genome graph construction as demonstrated here. These data will support ongoing and future research focused on gene discovery and trait introgression in the sorghum community and further provide insights into the historic selection and domestication of this multi‐purpose crop. [ABSTRACT FROM AUTHOR]

Root exudation is one of the primary processes that mediate interactions between plant roots, microorganisms, and the soil matrix, yet the mechanisms by which exudation alters microbial metabolism in soils have been challenging to unravel. Here, utilizing distinct sorghum genotypes, we characterized the chemical heterogeneity between root exudates and the effects of that variability on soil microbial membership and metabolism. Distinct exudate chemical profiles were quantified and used to formulate synthetic root exudate treatments: a high-organic-acid treatment (HOT) and a highsugar treatment (HST). To parse the response of the soil microbiome to different exudate regimens, laboratory soil reactors were amended with these root exudate treatments as well as a nonexudate control. Amplicon sequencing of the 16S rRNA gene illustrated distinct microbial diversity patterns and membership in response to HST, HOT, or control amendments. Exometabolite changes reflected these microbial community changes, and we observed enrichment of organic and amino acids, as well as possible phytohormones in the HST relative to the HOT and control. Linking the metabolic capacity of metagenome-assembled genomes in the HST to the exometabolite patterns, we identified microorganisms that could produce these phytohormones. Our findings emphasize the tractability of high-resolution multiomics tools to investigate soil microbiomes, opening the possibility of manipulating native microbial communities to improve specific soil microbial functions and enhance crop production. [ABSTRACT FROM AUTHOR]

The classification of domesticated sorghum [Sorghum bicolor (L.) Moench] into five major races is based on phenotypic characteristics of the spikelet and panicle. Presumably, this classification also reflects genetic relatedness. In this study, we apply both model-based (STRUCTURE) and model-free (principal components analysis) approaches to a genetic data set of 434 single nucleotide polymorphisms and simple sequence repeat alleles in a panel of 216 exotic sorghum lines to study the congruence between genetic relatedness and phenotype- based racial classification. Both model-based and model-free approaches clearly identify genetic groups that correspond closely to the caudatum, durra, kafir, and guinea races of sorghum. Genetic groups differ from racial groups in several significant ways, including the classification of the West African Kaura group with guineas rather than with caudatums, and the identification of a novel genetic group affiliated with both kafirs and guineas. These results highlight that high-throughput genotyping now provides curators with an additional, critical tool to better characterize and quantity diversity found in collections. Because of technological advances and associated cost reductions of unit assays, high-throughput genotyping is now applicable to all crop species. [ABSTRACT FROM AUTHOR]

To assess the usefulness of linkage disequilibrium mapping in an autogamous, domesticated species, we have characterized linkage disequilibrium in the candidate region for xa5, a recessive gene conferring race-specific resistance to bacterial blight in rice. This trait and locus have good mapping information, a tractable phenotype, and available sequence data, but no cloned gene. We sampled 13 short segments from the 70-kb candidate region in 114 accessions of Oryza sativa. Five additional segments were sequenced from the adjacent 45-kb region in resistant accessions to estimate the distance at which linkage disequilibrium decays. The data show significant linkage disequilibrium between sites 100 kb apart. The presence of the xa5 resistant reaction in two ecotypes and in accessions with different haplotypes in the candidate region may indicate multiple origins or genetic heterogeneity for resistance. In addition, genetic differentiation between ecotypes emphasizes the need for controlling for population structure in the design of linkage disequilibrium studies in rice. [ABSTRACT FROM AUTHOR]

Community association populations are composed of phenotypically and genetically diverse accessions. Once these populations are genotyped, the resulting marker data can be reused by different groups investigating the genetic basis of different traits. Because the same genotypes are observed and scored for a wide range of traits in different environments, these populations represent a unique resource to investigate pleiotropy. Here, we assembled a set of 234 separate trait datasets for the Sorghum Association Panel, a group of 406 sorghum genotypes widely employed by the sorghum genetics community. Comparison of genome-wide association studies (GWAS) conducted with two independently generated marker sets for this population demonstrate that existing genetic marker sets do not saturate the genome and likely capture only 35-43% of potentially detectable loci controlling variation for traits scored in this population. While limited evidence for pleiotropy was apparent in cross-GWAS comparisons, a multivariate adaptive shrinkage approach recovered both known pleiotropic effects of existing loci and new pleiotropic effects, particularly significant impacts of known dwarfing genes on root architecture. In addition, we identified new loci with pleiotropic effects consistent with known trade-offs in sorghum development. These results demonstrate the potential for mining existing trait datasets from widely used community association populations to enable new discoveries from existing trait datasets as new, denser genetic marker datasets are generated for existing community association populations. [ABSTRACT FROM AUTHOR]

Genomic structural mutations, especially deletions, are an important source of variation in many species and can play key roles in phenotypic diversification and evolution. Previous work in many plant species has identified multiple instances of structural variations (SVs) occurring in or near genes related to stress response and disease resistance, suggesting a possible role for SVs in local adaptation. Sorghum [Sorghum bicolor (L.) Moench] is one of the most widely grown cereal crops in the world. It has been adapted to an array of different climates as well as bred for multiple purposes, resulting in a striking phenotypic diversity. In this study, we identified genome-wide SVs in the Biomass Association Panel, a collection of 347 diverse sorghum genotypes collected from multiple countries and continents. Using Illumina-based, short-read whole-genome resequencing data from every genotype, we found a total of 24,648 SVs, including 22,359 deletions. The global site frequency spectrum of deletions and other types of SVs fit a model of neutral evolution, suggesting that the majority of these mutations were not under any types of selection. Clustering results based on single nucleotide polymorphisms separated the genotypes into eight clusters which largely corresponded with geographic origins, with many of the large deletions we uncovered being unique to a single cluster. Even though most deletions appeared to be neutral, a handful of cluster-specific deletions were found in genes related to biotic and abiotic stress responses, supporting the possibility that at least some of these deletions contribute to local adaptation in sorghum. [ABSTRACT FROM AUTHOR]

Sorghum bicolor, a photosynthetically efficient C4 grass, represents an important source of grain, forage, fermentable sugars, and cellulosic fibers that can be utilized in myriad applications ranging from bioenergy to bioindustrial feedstocks. Sorghum’s efficient fixation of carbon per unit time per unit area per unit input has led to its classification as a preferred biomass crop highlighted by its designation as an advanced biofuel by the U.S. Department of Energy. Due to its extensive genetic diversity and worldwide colonization, sorghum has considerable diversity for a range of phenotypes influencing productivity, composition, and sink/source dynamics. To dissect the genetic basis of these key traits, we present a sorghum carbon-partitioning nested association mapping (NAM) population generated by crossing 11 diverse founder lines with Grassl as the single recurrent female. By exploiting existing variation among cellulosic, forage, sweet, and grain sorghum carbon partitioning regimes, the sorghum carbon-partitioning NAM population will allow the identification of important biomassassociated traits, elucidate the genetic architecture underlying carbon partitioning and improve our understanding of the genetic determinants affecting unique phenotypes within Poaceae. We contrast this NAM population with an existing grain population generated using Tx430 as the recurrent female. Genotypic data are assessed for quality by examining variant density, nucleotide diversity, linkage decay, and are validated using pericarp and testa phenotypes to map known genes affecting these phenotypes. We release the 11-family NAM population along with corresponding genomic data for use in genetic, genomic, and agronomic studies with a focus on carbonpartitioning regimes. [ABSTRACT FROM AUTHOR]

Sorghum [Sorghum bicolor (L.) Moench] is a common feed grain globally with vast genetic and phytochemical diversity that may provide numerous health benefits, including its aptitude as an antimicrobial feed grain. This study highlights the antimicrobial potential of a collection of 384 diverse sorghum accessions against two prominent foodborne pathogens, Clostridium perfringens and Salmonella enterica. Following extensive screening, we determined that sorghum grain extract is more efficient at inhibiting C. perfringens than S. enterica. Antimicrobial activity observed against C. perfringens was not significantly correlated with either total phenols (r = 0.12) or tannin concentration (r = 0.12). Moreover, we mapped loci associated with antimicrobial activity to C. perfringens that are independent of loci associated with total phenols and tannins. The two most significant associations were determined to have an epistatic interaction and 20 candidate genes were identified. By sequence homology studies, we found the potential functions of these candidates to include plant stress response (Sobic.002G083600) and phenol metabolism regulation (Sobic.010G222600). Additionally, we noted no relationship between antimicrobial activity and either grain yield or composition. These results highlight significant heritable variation of antimicrobial activity in sorghum that may be useful for breeding to improve its value as a feed source by incorporating grain‐based antibiotics in animal production. [ABSTRACT FROM AUTHOR]

Sorghum is a climate resilient grain cereal crop originating from Africa that has traditionally been used to make a variety of fermented beverages such as pito and baijiu. In Western markets, the use of sorghum to produce beers and beverages has recently risen due to the visibility of a gluten sensitive/intolerant market and a growing interest in unique inputs for beverage production. As such, there is a developing body of research on sorghum as a malted input into beverages. A major limitation to the wider adoption of sorghum as a substrate in mashing is its low activity of amylolytic enzymes, either the result of insufficient activity or inhibition by endogenous compounds. A collection of 42 diverse accessions representing the grain sorghum diversity panel, was evaluated for associations between alpha and beta amylase content, race, origin, and seed colour as well as two classes of amylase inhibitors, phenols and tannins. Among these accessions are several commonly used genetic resources, including reference line BTx623. Notable findings include accessions with high alpha amylase content, sources that may harbour additional high amylase sorghums, associations with grain colour, and populations which may be used to genetically map the trait. © 2020 The Authors. Journal of the Institute of Brewing published by John Wiley & Sons Ltd on behalf of The Institute of Brewing & Distilling [ABSTRACT FROM AUTHOR]

Simple sugars are the essential foundation to plant life, and thus, their production, utilization, and storage are highly regulated processes with many complex genetic controls. Despite their importance, many of the genetic and biochemical mechanisms remain unknown or uncharacterized. Sorghum, a highly productive, diverse C4 grass important for both industrial and subsistence agricultural systems, has considerable phenotypic diversity in the accumulation of nonstructural sugars in the stem. We use this crop species to examine the genetic controls of high levels of sugar accumulation, identify genetic mechanisms for the accumulation of nonstructural sugars, and link carbon allocation with iron transport. We identify a speciesspecific tandem duplication event controlling sugar accumulation using genome-wide association analysis, characterize multiple allelic variants causing increased sugar content, and provide further evidence of a putative neofunctionalization event conferring adaptability in Sorghum bicolor. Comparative genomics indicate that this event is unique to sorghum which may further elucidate evolutionary mechanisms for adaptation and divergence within the Poaceae. Furthermore, the identification and characterization of this event was only possible with the continued advancement and improvement of the reference genome. The characterization of this region and the process in which it was discovered serve as a reminder that any reference genome is imperfect and is in need of continual improvement. [ABSTRACT FROM AUTHOR]

Population structure is an important factor that affects the accuracy of estimated breeding values in genomic prediction. Natural sorghum [Sorghum bicolor (L.) Moench] populations exhibit population structure resulting from genetic and morphological differentiation due to evolutionary divergence. To study the impact of sorghum racial structure and diversity in genomic prediction, we conducted two cross‐validation (CV) experiments: CV1, proportional sampling from races; and CV2, sampling from across race (AR) or within race (WR). A diversity panel with 389 individuals with 224,007 single nucleotide polymorphisms was used for genomic prediction. Genomic heritabilities for traits were positively correlated (0.63) with their mean prediction accuracy (r) from CV1, and within‐subpopulation variance accounted for ∼80% of total genetic variance. The CV1 prediction accuracy ranged from 0.52–0.69, but r declined by 39 and 54% on average for WR and AR methods, respectively. As a predictor, race explained 30–50% of covariance for grain and panicle traits, but race was a bad predictor of plant height, as expected. Grain weight was consistently the best predicted trait across CV1 and CV2 methods except in AR. Difference in average r for WR and AR was greater in durra and caudatum, small in kafir, and nonexistent in guinea and mixed subgroups. We observed higher prevalence of minor alleles among guinea and mixed subgroups, highlighting contribution of allelic diversity towards prediction accuracy. Genomic prediction in sorghum will benefit from utilization of interracial diversity, and we emphasize the need for further investigations into the role of racial structure in genomic prediction. [ABSTRACT FROM AUTHOR]

The animal industry is a major sector of agriculture in the southeastern United States, but a large deficit exists in regional feed grains needed to support the industry. An increase in production of sorghum [Sorghum bicolor (L.) Moench], a water- and nutrient-use-efficient cereal, on marginal lands could lead to an alternative crop option for growers and reduce the current grain deficit. Quantitative trait locus (QTL) mapping of grain yield components in two sorghum biparental recombinant inbred line (RIL) populations was performed to better understand the genetic basis of grain yield and characterize these traits in a marginal environment. A more robust knowledge of the genetics underlying these complex traits could provide insights into molecular breeding strategies that aim to increase genetic gain. Specific yield traits investigated were grain number per primary panicle (GNP), 1000-grain weight (TGW), and grain yield per primary panicle (YPP). Two-year phenotyping in the South Carolina coastal plain revealed greater than threefold variation for both GNP and YPP, whereas TGW variation was just above twofold in both RIL families. There were 16 total yield trait QTL identified across both populations. Of the 16, eight QTL colocated with previously published QTL for yield-related traits, including a QTL on chromosome 1 that was significant for all three grain yield components. A novel QTL for TGW was identified on chromosome 5 that explained >21% of the phenotypic variance observed in one RIL population. This QTL and the seven additional novel QTL identified in this study provide new targets for grain yield improvement in sorghum. [ABSTRACT FROM AUTHOR]

Key message: Coordinated association and linkage mapping identified 25 grain quality QTLs in multiple environments, and fine mapping of the Wx locus supports the use of high-density genetic markers in linkage mapping. Abstract: There is a wide range of end-use products made from cereal grains, and these products often demand different grain characteristics. Fortunately, cereal crop species including sorghum [ Sorghum bicolor (L.) Moench] contain high phenotypic variation for traits influencing grain quality. Identifying genetic variants underlying this phenotypic variation allows plant breeders to develop genotypes with grain attributes optimized for their intended usage. Multiple sorghum mapping populations were rigorously phenotyped across two environments (SC Coastal Plain and Central TX) in 2 years for five major grain quality traits: amylose, starch, crude protein, crude fat, and gross energy. Coordinated association and linkage mapping revealed several robust QTLs that make prime targets to improve grain quality for food, feed, and fuel products. Although the amylose QTL interval spanned many megabases, the marker with greatest significance was located just 12 kb from waxy ( Wx), the primary gene regulating amylose production in cereal grains. This suggests higher resolution mapping in recombinant inbred line (RIL) populations can be obtained when genotyped at a high marker density. The major QTL for crude fat content, identified in both a RIL population and grain sorghum diversity panel, encompassed the DGAT1 locus, a critical gene involved in maize lipid biosynthesis. Another QTL on chromosome 1 was consistently mapped in both RIL populations for multiple grain quality traits including starch, crude protein, and gross energy. Collectively, these genetic regions offer excellent opportunities to manipulate grain composition and set up future studies for gene validation. [ABSTRACT FROM AUTHOR]

Background: Sorghum [Sorghum bicolor (L.) Moench] is an important cereal crop for dryland areas in the United States and for small-holder farmers in Africa. Natural variation of sorghum grain composition (protein, fat, and starch) between accessions can be used for crop improvement, but the genetic controls are still unresolved. The goals of this study were to quantify natural variation of sorghum grain composition and to identify singlenucleotide polymorphisms (SNPs) associated with variation in grain composition concentrations. Results: In this study, we quantified protein, fat, and starch in a global sorghum diversity panel using near-infrared spectroscopy (NIRS). Protein content ranged from 8.1 to 18.8%, fat content ranged from 1.0 to 4.3%, and starch content ranged from 61.7 to 71.1%. Durra and bicolor-durra sorghum from Ethiopia and India had the highest protein and fat and the lowest starch content, while kafir sorghum from USA, India, and South Africa had the lowest protein and the highest starch content. Genome-wide association studies (GWAS) identified quantitative trait loci (QTL) for sorghum protein, fat, and starch. Previously published RNAseq data was used to identify candidate genes within a GWAS QTL region. A putative alpha-amylase 3 gene, which has previously been shown to be associated with grain composition traits, was identified as a strong candidate for protein and fat variation. Conclusions: We identified promising sources of genetic material for manipulation of grain composition traits, and several loci and candidate genes that may control sorghum grain composition. This survey of grain composition in sorghum germplasm and identification of protein, fat, and starch QTL contributes to our understanding of the genetic basis of natural variation in sorghum grain nutritional traits. [ABSTRACT FROM AUTHOR]

With high productivity and stress tolerance, numerous grass genera of the Andropogoneae have emerged as candidates for bioenergy production. To optimize these candidates, research examining the genetic architecture of yield, carbon partitioning, and composition is required to advance breeding objectives. Significant progress has been made developing genetic and genomic resources for Andropogoneae, and advances in comparative and computational genomics have enabled research examining the genetic basis of photosynthesis, carbon partitioning, composition, and sink strength. To provide a pivotal resource aimed at developing a comparative understanding of key bioenergy traits in the Andropogoneae, we have established and characterized an association panel of 390 racially, geographically, and phenotypically diverse Sorghum bicolor accessions with 232,303 genetic markers. Sorghum bicolor was selected because of its genomic simplicity, phenotypic diversity, significant genomic tools, and its agricultural productivity and resilience. We have demonstrated the value of sorghum as a functional model for candidate gene discovery for bioenergy Andropogoneae by performing genome-wide association analysis for two contrasting phenotypes representing key components of structural and non-structural carbohydrates. We identified potential genes, including a cellulase enzyme and a vacuolar transporter, associated with increased non-structural carbohydrates that could lead to bioenergy sorghum improvement. Although our analysis identified genes with potentially clear functions, other candidates did not have assigned functions, suggesting novel molecular mechanisms for carbon partitioning traits. These results, combined with our characterization of phenotypic and genetic diversity and the public accessibility of each accession and genomic data, demonstrate the value of this resource and provide a foundation for future improvement of sorghum and related grasses for bioenergy production. [ABSTRACT FROM AUTHOR]

Seedling establishment and seed nutritional quality require the sequestration of sufficient element nutrients. The identification of genes and alleles that modify element content in the grains of cereals, including sorghum (Sorghum bicolor), is fundamental to developing breeding and selection methods aimed at increasing bioavailable element content and improving crop growth. We have developed a high-throughput work flow for the simultaneous measurement of multiple elements in sorghum seeds. We measured seed element levels in the genotyped Sorghum Association Panel, representing all major cultivated sorghum races from diverse geographic and climatic regions, and mapped alleles contributing to seed element variation across three environments by genome-wide association. We observed significant phenotypic and genetic correlation between several elements across multiple years and diverse environments. The power of combining high-precision measurements with genome-wide association was demonstrated by implementing rank transformation and a multilocus mixed model to map alleles controlling 20 element traits, identifying 255 loci affecting the sorghum seed ionome. Sequence similarity to genes characterized in previous studies identified likely causative genes for the accumulation of zinc, manganese, nickel, calcium, and cadmium in sorghum seeds. In addition to strong candidates for these five elements, we provide a list of candidate loci for several other elements. Our approach enabled the identification of single-nucleotide polymorphisms in strong linkage disequilibrium with causative polymorphisms that can be evaluated in targeted selection strategies for plant breeding and improvement. [ABSTRACT FROM AUTHOR]

Background: African-American adults are disproportionately affected by stress-related chronic conditions like high blood pressure (BP), and both environmental stress and genetic risk may play a role in its development.Purpose: This study tested whether the dual risk of low neighborhood socioeconomic status (SES) and glucocorticoid genetic sensitivity interacted to predict waking cortisol and BP.Methods: Cross-sectional waking cortisol and BP were collected from 208 African-American adults who were participating in a follow-up visit as part of the Positive Action for Today's Health trial. Three single-nucleotide polymorphisms were genotyped, salivary cortisol samples were collected, and neighborhood SES was calculated using 2010 Census data.Results: The sample was mostly female (65 %), with weight classified as overweight or obese (M BMI = 32.74, SD = 8.88) and a mean age of 55.64 (SD = 15.21). The gene-by-neighborhood SES interaction predicted cortisol (B = 0.235, p = .001, r (2) = .036), but not BP. For adults with high genetic sensitivity, waking cortisol was lower with lower SES but higher with higher SES (B = 0.87). Lower neighborhood SES was also related to higher systolic BP (B = -0.794, p = .028).Conclusions: Findings demonstrated an interaction whereby African-American adults with high genetic sensitivity had high levels of waking cortisol with higher neighborhood SES, and low levels with lower neighborhood SES. This moderation effect is consistent with a differential susceptibility gene-environment pattern, rather than a dual-risk pattern. These findings contribute to a growing body of evidence that demonstrates the importance of investigating complex gene-environment relations in order to better understand stress-related health disparities. [ABSTRACT FROM AUTHOR]

Chromatin Inc, Chicago, Illinois, USA Background Effective improvement in sorghum crop development necessitates a genomics-based approach to identify functional genes and QTLs. Sequenced in 2009, a comprehensive annotation of the sorghum genome and the development of functional genomics resources is key to enable the discovery and deployment of regulatory and metabolic genes and gene networks for crop improvement. Results This study utilizes the first commercially available whole-transcriptome sorghum microarray (Sorgh-WTa520972F) to identify tissue and genotype-specific expression patterns for all identified Sorghum bicolor exons and UTRs. The genechip contains 1,026,373 probes covering 149,182 exons (27,577 genes) across the Sorghum bicolor nuclear, chloroplast, and mitochondrial genomes. Specific probesets were also included for putative non-coding RNAs that may play a role in gene regulation (e.g., microRNAs), and confirmed functional small RNAs in related species (maize and sugarcane) were also included in our array design. We generated expression data for 78 samples with a combination of four different tissue types (shoot, root, leaf and stem), two dissected stem tissues (pith and rind) and six diverse genotypes, which included 6 public sorghum lines (R159, Atlas, Fremont, PI152611, AR2400 and PI455230) representing grain, sweet, forage, and high biomass ideotypes. Conclusions Here we present a summary of the microarray dataset, including analysis of tissue-specific gene expression profiles and associated expression profiles of relevant metabolic pathways. With an aim to enable identification and functional characterization of genes in sorghum, this expression atlas presents a new and valuable resource to the research community. [ABSTRACT FROM AUTHOR]

Accelerating crop improvement in sorghum, a staple food for people in semiarid regions across the developing world, is key to ensuring global food security in the context of climate change. To facilitate gene discovery and molecular breeding in sorghum, we have characterized ∼265,000 single nucleotide polymorphisms (SNPs) in 971 worldwide accessions that have adapted to diverse agroclimatic conditions. Using this genome-wide SNP map, we have characterized population structure with respect to geographic origin and morphological type and identified patterns of ancient crop diffusion to diverse agroclimatic regions across Africa and Asia. To better understand the genomic patterns of diversification in sorghum, we quantified variation in nucleotide diversity, linkage disequilibrium, and recombination rates across the genome. Analyzing nucleotide diversity in landraces, we find evidence of selective sweeps around starch metabolism genes, whereas in landrace-derived introgression lines, we find introgressions around known height and maturity loci. To identify additional loci underlying variation in major agroclimatic traits, we performed genome-wide association studies (GWAS) on plant height components and inflorescence architecture. GWAS maps several classical loci for plant height, candidate genes for inflorescence architecture. Finally, we trace the independent spread of multiple haplotypes carrying alleles for short stature or long inflorescence branches. This genome-wide map of SNP variation in sorghum provides a basis for crop improvement through marker-assisted breeding and genomic selection. [ABSTRACT FROM AUTHOR]

Background: Acid soils comprise up to 50% of the world's arable lands and in these areas aluminum (Al) toxicity impairs root growth, strongly limiting crop yield. Food security is thereby compromised in many developing countries located in tropical and subtropical regions worldwide. In sorghum, SbMATE, an Al-activated citrate transporter, underlies the AltSB locus on chromosome 3 and confers Al tolerance via Al-activated root citrate release. Methodology: Population structure was studied in 254 sorghum accessions representative of the diversity present in cultivated sorghums. Al tolerance was assessed as the degree of root growth inhibition in nutrient solution containing Al. A genetic analysis based on markers flanking AltSB and SbMATE expression was undertaken to assess a possible role for AltSB in Al tolerant accessions. In addition, the mode of gene action was estimated concerning the Al tolerance trait. Comparisons between models that include population structure were applied to assess the importance of each subpopulation to Al tolerance. Conclusion/Significance: Six subpopulations were revealed featuring specific racial and geographic origins. Al tolerance was found to be rather rare and present primarily in guinea and to lesser extent in caudatum subpopulations. AltSB was found to play a role in Al tolerance in most of the Al tolerant accessions. A striking variation was observed in the mode of gene action for the Al tolerance trait, which ranged from almost complete recessivity to near complete dominance, with a higher frequency of partially recessive sources of Al tolerance. A possible interpretation of our results concerning the origin and evolution of Al tolerance in cultivated sorghum is discussed. This study demonstrates the importance of deeply exploring the crop diversity reservoir both for a comprehensive view of the dynamics underlying the distribution and function of Al tolerance genes and to design efficient molecular breeding strategies aimed at enhancing Al tolerance. [ABSTRACT FROM AUTHOR]

Nested association mapping (NAM) offers power to resolve complex, quantitative traits to their causal loci. The maize NAM population, consisting of 5,000 recombinant inbred lines (RILs) from 25 families representing the global diversity of maize, was evaluated for resistance to southern leaf blight (SLB) disease. Joint-linkage analysis identified 32 quantitative trait loci (QTLs) with predominantly small, additive effects on SLB resistance. Genome-wide association tests of maize HapMap SNPs were conducted by imputing founder SNP genotypes onto the NAM RILs. SNPs both within and outside of QTL intervals were associated with variation for SLB resistance. Many of these SNPs were within or near sequences homologous to genes previously shown to be involved in plant disease resistance. Limited linkage disequilibrium was observed around some SNPs associated with SLB resistance, indicating that the maize NAM population enables high-resolution mapping of some genome regions. [ABSTRACT FROM AUTHOR]

We characterized allelic variation at barren inflorescence2 ( bif2), a maize co-ortholog of the Arabidopsis PINOID protein kinase ( PID), and tested for trait associations with bif2 in both an association mapping population of 277 diverse maize inbreds and in the inter-mated B73 × Mo17 (IBM) linkage population. Results from the quantitative analyses were compared with previous reports of bif2 phenotypes in mutagenesis studies. All three approaches (association, linkage, and mutagenesis) detect a significant effect of bif2 on tassel architecture. Association mapping implicates bif2 in an unexpectedly wide range of traits including plant height, node number, leaf length, and flowering time. Linkage mapping finds a significant interaction effect for node number between bif2 and other loci, in keeping with previous reports that bif2; spi1 and Bif2; Bif1 double mutants produce fewer phytomers. The Mo17 allele is associated with a reduced tassel branch zone and shows lower expression than the B73 allele in hybrid B73–Mo17 F1 inflorescences, consistent with the complete absence of tassel branches in the bif2 knockout mutant. Overall, these data suggest that allelic variation at bif2 affects maize architecture by modulating auxin transport during vegetative and inflorescence development. [ABSTRACT FROM AUTHOR]

We describe the first isolation of SSR (simple sequence repeat) markers for Anoplophora glabripennis, a pest of forests in China and urban trees in the USA. Ten markers were developed using FIASCO (fast isolation by AFLP of sequences containing repeats) with an (AC)17 probe, and five markers were identified in expressed sequence tags found on the NCBI database. Twenty-seven beetles from a population in Gansu Province, China, were assayed. The number of alleles ranged from 3 to 9; observed and expected heterozygosities ranged from 0.07 to 0.79 and from 0.30 to 0.78, respectively. [ABSTRACT FROM AUTHOR]

Digestion and fermentation of lignocellulosic biomass (i.e., structural carbohydrates) are predicted to deliver higher yields of energy per hectare than sugar and starch (nonstructural carbohydrates), yet little research on genetic variation in crop feedstock biomass traits has been conducted. We investigated the genetic basis of leaf and stem biomass yield and composition in a population derived from a high-biomass sweet sorghum, 'Rio', and a grain sorghum inbred line, 'BTx623', and compared these results with those from analyses of grain and stem sugar traits that we reported previously. Thirty-one traits were evaluated and a total of 110 quantitative trait loci (QTL) were identified across three locations. Many QTL for structural and nonstructural carbohydrate yields colocalized with loci for height, flowering time, and stand density-tillering. Quantitative trait loci for composition had little colocalization across tissues and environments. Separate genetic control for leaf and stem structural carbohydrate composition was identified, as well as separate genetic control of protein accumulation in leaf, stem, and grain. To maximize energy yields from grain and dedicated biomass sorghums, results suggest yield traits should be targeted for improvement before composition traits. [ABSTRACT FROM AUTHOR]

Genetic improvement of sorghum [Sorghum bicolor (L.) Moench] has traditionally focused on a single nonstructural carbohydrate, either grain starch or stem sugar. Sorghum starch and sugar may both be used as feedstocks for biofuel production. To investigate genetic tradeoffs between grain and stem sugar, a population derived from sweet sorghum cultivar Rio and grain sorghum 'BTx623' was evaluated for 27 traits related to grain and stem sugar yield and composition. Across three environments, a total of 129 quantitative trait loci (QTL) were identified. Tradeoffs identified between grain and stem sugar yield QTL colocalized with height and flowering time QTL. Most importantly, QTL were identified that increased yield and altered the composition of stem sugar and grain without pleiotropic effects. For example, a QTL on chromosome 3 that explained 25% of the genetic variance for stem sugar concentration did not colocalize with any grain QTL. These results suggest that total nonstructural carbohydrate yield could be increased by selecting for major QTL from both grain and sweet sorghum types. We conclude that altering grain and stem sugar genetic potential for yield traits should lead to greater feedstock improvement than altering composition traits. [ABSTRACT FROM AUTHOR]

Vitamin A deficiency affects approximately 250 million people in semiarid regions of Africa and Asia, where sorghum (Sorghum bicolor Moench) is a major staple crop. Yellow endosperm sorghums contain carotenoids, some of which can be transformed by humans into vitamin A. Our objective was to study the genetic basis of variation in carotenoid levels in sorghum endosperm by mapping quantitative trait loci (QTL) associated with carotenoid content and endosperm color, as a putative predictor of carotenoid concentration. A recombinant inbred line population developed from a yellow ('KS115') by a white endosperm ('Macia') parental cross was evaluated in two locations in 2005. A genetic map was generated using 112 molecular markers including nine carotenoid candidate genes. Lutein, zeaxanthin, and β-carotene were the major carotenoids identified. Several QTL were detected for each compound as well as for color and total carotenoids. Color was significantly correlated with the levels of all compounds, and color QTL co-localized with carotenoid QTL. For 13-carotene (provitamin A), five QTL were localized on chromosomes 1, 2, and 10. One of them, on chromosome 2, was stable across both environments, had positive additive effects (1.179 and 1.379), explained large proportions of the phenotypic variance (11.6% and 15.15%), and was associated with a new phytoene synthase gene (Psy3). This first report of QTL for carotenoid content in sorghum grain provides a starting point for breeding high-provitamin A sorghums. [ABSTRACT FROM AUTHOR]

Of the four major dwarfing genes described in sorghum, only Dw3 has been cloned. We used association mapping to characterize the phenotypic effects of the dw3 mutation and to fine map a second, epistatic dwarfing QTL on sorghum chromosome 9 (Sb-HT9.1). Our panel of 378 sorghum inbreds includes 230 sorghum conversion (SC) lines, which are exotic lines that have been introgressed with dwarfing quantitative trait loci (QTL) from a common parent. The causal mutation in dw3 associates with reduced lower internode length and an elongation of the apex, consistent with its role as an auxin efflux carrier Lines carrying the dw3 mutation display high haplotype homozygosity over several megahases in the Dw3 region, but most markers linked to Dw3 do not associate significantly with plant height due to allele sharing between Dw3 and dw3 individuals. Using markers with a high mutation rate and the dw3 mutation as an interaction term, significant trait associations were detected across a 7-Mb region around Sb-HT9.1, largely due to higher detection power in the SC lines. Conversely, the likely QTL interval for Sb-HT9.1 was reduced to ~100 kb, demonstrating that the unique structure of this association panel provides both power and resolution for a genomewide scan. [ABSTRACT FROM AUTHOR]

Association mapping is a powerful strategy for identifying genes underlying quantitative traits in plants. We have assembled and characterized genetic and phenotypic diversity of a sorghum [Sorghum bicolor (L.) Moench] panel suitable for association mapping, comprised of 377 accessions representing all major cultivated races (tropical lines from diverse geographic and climatic regions), and important U.S. breeding lines and their progenitors. Accessions were phenotyped for eight traits, and levels of population structure and familial relatedness were assessed with 47 simple sequence repeat (SSR) loci. The panel exhibited substantial morphological variation and little genotypic differentiation was observed between the converted tropical and breeding lines. The phenotypic and genotypic data were used to evaluate the performance of several association models in controlling for spurious associations. Our analysis indicated that association models that accounted for both population structure and kinship performed better than those that did not. In addition, we found that the optimal number of subpopulations used to correct for population structure was trait dependent. Although augmentation of the genotypic data with additional SSR loci may be necessary, the association models, genotypic data, and germplasm panel described here provide a starting point for sorghum researchers to begin association studies of traits and markers or candidate genes of interest. [ABSTRACT FROM AUTHOR]

Artificial selection during the domestication of maize is thought to have been predominantly positive and to have had little effect on the surrounding neutral diversity because linkage disequilibrium breaks down rapidly when physical distance increases. However, the degree to which indirect selection has shaped neutral diversity in the maize genome during domestication remains unclear. In this study, we investigate the relationship between local recombination rate and neutral polymorphism in maize and in teosinte using both sequence and microsatellite data. To quantify diversity, we estimate 3 parameters expected to differentially reflect the effects of indirect selection and mutation. We find no general correlation between diversity and recombination, indicating that indirect selection has had no genome-wide impact on maize diversity. However, we detect a weak correlation between heterozygosity and recombination for trinucleotide microsatellites deviating from the stepwise mutation model and located within genes (p = 0.32, P < 0.03). This result can be explained by a background selection hypothesis. The fact that the same correlation is not confirmed for nucleotide diversity suggests that the strength of purifying selection at or near this class of microsatellites is higher than for nucleotide mutations. [ABSTRACT FROM AUTHOR]

Sorghum bicolor, an important component of human diets in many parts of the developing world, has attributes that should make it very suitable for linkage disequilibrium (LD) mapping of complex traits: low sequence diversity, moderately extensive LD, and natural homozygosity. Sorghum endosperm quality, which determines the grain's suitability for preparation of local food products, varies greatly among cultivors, and is genetically complex; some of the genes involved are likely to be in the starch metabolism pathway. To assess the prospects for linkage disequilibrium mapping of variation in endosperm quality, we have surveyed DNA sequence variation in 15 genes in the starch metabolism pathway in a panel of cultivars that vary in groin quality traits. Single nucleotide polymorphism (SNP) variation was found at all loci, including a strong candidate for the causal mutation underlying a waxy phenotype. Levels of LD varied but were generally moderate to high (overage ZnS = 0.56), while non-singleton SNP frequency was low to moderate (πt at silent sites ranged from 0.00026 to 0.0068), resulting in a fairly low haplotype diversity that can be captured by a moderate number of ‘tug SNPs’ at most loci. These results suggest that association mapping of candidate genes in sorghum can be done with relatively few markers, resulting in lower costs and a smaller multiple testing problem than in more diverse species such as maize (Zea mays L.). [ABSTRACT FROM AUTHOR]

Recently, a simple sequence repeat (SSR)-based genome-wide diversity scan of Sorghum bicolor (L.) Moench identified several candidate loci with patterns of variation consistent with directional selection in cultivated lines. Data were insufficient, however, to determine if selection had actually occurred at or near candidate SSR loci or if the unusual diversity patterns observed were due to the effects of demographic factors such as population bottlenecks or mating system. In the present study, we collected DNA sequences from 10 segments within a 99 kb region flanking one of the previously identified candidates, SSR locus Xcup15, located near the distal end of chromosome 1. We performed statistical tests bath to address alternative hypotheses to selection and to aid in localizing the selection target. Analyses of genomic DNA sequences from a panel of 17 cultivated and 13 wild accessions indicated that cultivated lines bud reduced diversity in this region (about one-third of the diversity present in wild sorghums) and a moderate degree of differentiation was observed between cultivated and wild groups (Fst = 0.15). Several features of the data support the hypothesis that recent directional selection shaped diversity patterns around Xcup15, including overall low levels of variation and extensive haplotype structure (a predominant haplotype occurred over the 99 kb region) in cultivated sorghum, and a derived fixed difference at the 5' untranslated region (DIR) of u protein phosphates 2C (PP2C) gene between cultivated and wild sorghums. Moreover, two of the four tests employed to detect deviations from the neutral, equilibrium model, the Hudson Kreitman Aguadé (HKA), and the composite likelihood ratio (CLR) tests indicated that patterns of diversity in the Xcup15 region were consistent with a selective sweep. Although we were unable to rule out demography as a possible explanation for the diversity patterns observed along this region, this study supported previous findings based on SSR diversity and identified candidates fur the target of selection; the confirmation of which will require functional and association studies. [ABSTRACT FROM AUTHOR]

Multilocus surveys of sequence variation can be used to identify targets of directional selection, which are expected to have reduced levels of variation. Following a population bottleneck, the signal of directional selection may be hard to detect because many loci may have low variation by chance and the frequency spectrum of variation may be perturbed in ways that resemble the effects of selection. Cultivated Sorghum bicolor contains a subset of the genetic diversity found in its wild ancestor(s) due to the combined effects of a domestication bottleneck and human selection on traits associated with agriculture. As a framework for distinguishing between the effects of demography and selection, we sequenced 204 loci in a diverse panel of 17 cultivated S. bicolor accessions. Genomewide patterns of diversity depart strongly from equilibrium expectations with regard to the variance of the number of segregating sites, the site frequency spectrum, and haplotype configuration. Furthermore, gene genealogies of most loci with an excess of low frequency variants and/or an excess of segregating sites do not show the characteristic signatures of directional and diversifying selection, respectively. A simple bottleneck model provides an improved but inadequate fit to the data, suggesting the action of other population-level factors, such as population structure and migration. Despite a known history of recent selection, we find little evidence for directional selection, likely due to low statistical power and lack of an appropriate null model. [ABSTRACT FROM AUTHOR]

As population structure can result in spurious associations, it has constrained the use of association studies in human and plant genetics. Association mapping, however, holds great promise if true signals of functional association can be separated from the vast number of false signals generated by population structure. We have developed a unified mixed-model approach to account for multiple levels of relatedness simultaneously as detected by random genetic markers. We applied this new approach to two samples: a family-based sample of 14 human families, for quantitative gene expression dissection, and a sample of 277 diverse maize inbred lines with complex familial relationships and population structure, for quantitative trait dissection. Our method demonstrates improved control of both type I and type II error rates over other methods. As this new method crosses the boundary between family-based and structured association samples, it provides a powerful complement to currently available methods for association mapping. [ABSTRACT FROM AUTHOR]

Conservation of agricultural genetic resources, whether in situ (in farmers' fields) or ex situ (in a germplasm repository), provides variation for breeding and selection efforts. In this study, we assayed levels of genetic diversity from in situ and ex situ populations of Jala, a very tall, large-eared race of maize (Zea mays L. subsp. mays), using 22 simple sequence repeat (SSR) loci. For comparison, we also analyzed diversity in reference populations of other maize races and wild relatives of maize, the teosintes (both Zea spp. and Z. mays subsp.). As expected, both the in situ and ex situ Jala populations were not as diverse as the teosintes (gene diversity, He, ≈0.60 and 0.7, respectively), but they were surprisingly more diverse than the populations representing other maize races (He = 0.55). The older ex situ Jala populations were less diverse and more differentiated than more recently collected accessions. Despite this fact, we observed similar levels of overall genetic diversity in the ex situ and in situ populations (He = 0.62 and 0.61, respectively), and little differentiation between these groups (Fst = 0.01). Therefore, the ex situ Jala collections, as a whole, contained the diversity found today in the field, even though diversity was under-represented in individual repository populations. [ABSTRACT FROM AUTHOR]

Crop improvement and the dissection of complex genetic traits require germplasm diversity. Although this necessary phenotypic variability exists in diverse maize, most research is conducted using a small subset of inbred lines. An association population of 302 lines is now available – a valuable research tool that captures a large proportion of the alleles in cultivated maize. Provided that appropriate statistical models correcting for population structure are included, this tool can be used in association analyses to provide high-resolution evaluation of multiple alleles. This study describes the population structure of the 302 lines, and investigates the relationship between population structure and various measures of phenotypic and breeding value. On average, our estimates of population structure account for 9.3% of phenotypic variation, roughly equivalent to a major quantitative trait locus (QTL), with a high of 35%. Inclusion of population structure in association models is critical to meaningful analyses. This new association population has the potential to identify QTL with small effects, which will aid in dissecting complex traits and in planning future projects to exploit the rich diversity present in maize. [ABSTRACT FROM AUTHOR]

Patterns of linkage disequilibrium (LD) are of interest because they provide evidence of both equilibrium (e.g., mating system or long-term population structure) and nonequilibrium (e.g., demographic or selective) processes, as well as because of their importance in strategies for identifying the genetic basis of complex phenotypes. We report patterns of short and medium range (up to 100 kb) LD in six unlinked genomic regions in the partially selfing domesticated grass, Sorghum bicolor. The extent of allelic associations in S. bicolor, as assessed by pairwise measures of LD, is higher than in maize but lower than in Arabidopsis, in qualitative agreement with expectations based on mating system. Quantitative analyses of the population recombination parameter, ρ, however, based on empirical estimates of rates of recombination, mutation, and self-pollination, show that LD is more extensive than expected under a neutral equilibrium model. The disparity between ρ and the population mutation parameter, θ, is similar to that observed in other species whose population history appears to be complex. From a practical standpoint, these results suggest that S. bicolor is well suited for association studies using reasonable numbers of markers, since LD typically extends at least several kilobases but has largely decayed by 15 kb. [ABSTRACT FROM AUTHOR]

Much research has been devoted to understanding the biology of plant-pathogen interactions. The extensive genetic analysis of disease resistance in rice, coupled with the sequenced genome and genomic resources, provides the opportunity to seek convergent evidence implicating specific chromosomal segments and genes in the control of resistance. Published data on quantitative and qualitative disease resistance in rice were synthesized to evaluate the distributions of and associations among resistance loci. Quantitative trait loci (QTL) for resistance to multiple diseases and qualitative resistance loci (R genes) were clustered in the rice genome. R genes and their analogs of the nucleotide binding site-leucine-rich repeat class and genes identified on the basis of differential representation in disease-related EST libraries were significantly associated with QTL. Chromosomal segments associated with broad-spectrum quantitative disease resistance (BS-QDR) were identified. These segments contained numerous positional candidate genes identified on the basis of a range of criteria, and groups of genes belonging to two defense-associated biochemical pathways were found to underlie one BS-QDR region. Genetic dissection of disease QTL confidence intervals is needed to reduce the number of positional candidate genes for further functional analysis. This study provides a framework for future investigations of disease resistance in rice and related crop species. [ABSTRACT FROM AUTHOR]

How domestication bottlenecks and artificial selection shaped the amount and distribution of genetic variation in the genomes of modern crops is poorly understood. We analyzed diversity at 462 simple sequence repeats (SSRs) or microsatellites spread throughout the maize genome and compared the diversity, observed at these SSRs in maize to that observed in its wild progenitor, teosinte. The results reveal a modest genome-wide deficit of diversity in maize relative to teosinte. The relative deficit of diversity is less for SSRs with dinucleotide repeat motifs than for SSRs with repeat motifs of more than two nucleotides, suggesting that the former with their higher mutation rate have partially recovered from the domestication bottleneck. We analyzed the relationship between SSR diversity and proximity to QTL for domestication traits and observed no relationship between these factors. However, we did observe a weak, although significant, spatial correlation for diversity statistics among SSRs within 2 cM of one another, suggesting that SSR diversity is weakly patterned across the genome. Twenty-four of 462 SSRs (5%) show some evidence of positive selection in maize under multiple tests. Overall, the pattern of genetic diversity at maize SSRs can he explained largely by a bottleneck effect with a smaller effect from selection. [ABSTRACT FROM AUTHOR]