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Improving adaptation of staple crops in developing countries is important to ensure food security. In the West African country of Niger, the staple crop sorghum (Sorghum bicolor) is cultivated across diverse agroclimatic zones, but the genetic basis of local adaptation has not been described. The objectives of this study were to characterize the genomic diversity of sorghum from Niger and to identify genomic regions conferring local adaptation to agroclimatic zones and farmer preferences. We analyzed 516 Nigerien accessions for which local variety name, botanical race, and geographic origin were known. We discovered 144 299 single nucleotide polymorphisms (SNPs) using genotyping-by-sequencing (GBS). We performed discriminant analysis of principal components (DAPC), which identified six genetic groups, and performed a genome scan for loci with high discriminant loadings. The highest discriminant coefficients were on chromosome 9, near the putative ortholog of maize flowering time adaptation gene Vgt1. Next, we characterized differentiation among local varieties and used a genome scan of pairwise [F.sub.ST] values to identify SNPs associated with specific local varieties. Comparison of varieties named for light- versus dark-grain identified differentiation near Tannin1, the major gene responsible for grain tannins. These findings could facilitate genomics-assisted breeding of locally adapted and farmer-preferred sorghum varieties for Niger. Key words: sorghum, agroclimatic zones, genomics, local adaptation, genomics-enabled breeding, sub Saharan Africa. L'amelioration de cultures dans les pays en developpement est importante afin d'assurer securite alimentaire. En Afrique de l'Ouest, particulierement au Niger, le sorgho (Sorghum bicolor) est cultive dans differentes zones agroclimatiques. Cependant les bases genetiques de leur adaptation locale sont peu decrites. Cette etude a pour objectifs de caracteriser la structure genetique du sorgho au Niger et d'identifier les regions genomiques associees a l'adaptation locale aux zones agroclimatiques et aux preferences des agriculteurs. L'analyse par le genotypage par sequencage (GBS) de 516 accessions du Niger, dont le nom local, la race botanique et l'origine sont connus, nous a permis d'identifier 144 299 polymorphismes nucleotidiques (SNPs). La methode d'analyse discriminante des composantes principales a identifie six clusters genetiques. Le balayage genomique des coefficients de discrimination a montre des locus aux coefficients eleves au niveau du chromosome 9, colocalises avec le gene Vgt1 responsable de la variation de la date de floraison. Aussi, nous avons caracterise la differentiation des varietes locales. Le balayage genomique de [F.sub.ST] entre les varietes locales Mota (grains blancs) et Jenjari (grains sombres) a identifie des locus pres du Tannin1, le gene responsable des tanins. Ces resultats permettront de faciliter la selection assistee par la genomique de varietes de sorgho localement adaptees et preferees en Niger. Mots-cles: sorgho, zones agroclimatiques, genomique, adaptation locale, selection genomique, Afrique subsaharienne., Introduction Sorghum (Sorghum bicolor L. Moench) is a major staple crop that is adapted to multiple agroclimatic zones of the world (Smith and Frederiksen 2000). In smallholder production systems of [...]

Sorghum is one of the world's most important food, feed, and fiber crops as well as a potential feedstock for lignocellulosic bioenergy. Early-season planting extends sorghum's growing season and increases yield in temperate regions. However, sorghum's sensitivity to low soil temperatures adversely impacts seed germination. In this study, we evaluated the 242 accessions of the ICRISAT sorghum mini core collection for seed germination and seedling vigor at 12°C as a measure of cold tolerance. Genome-wide association analysis was performed with approximately 162177 single nucleotide polymorphism markers. Only one marker locus (Locus 7-2) was significantly associated with low-temperature germination and none with vigor. The linkage of Locus 7-2 to lowtemperature germination was supported by four lines of evidence: strong association in three independent experiments, co-localization with previously mapped cold tolerance quantitative trait loci (QTL) in sorghum, a candidate gene that increases cold tolerance and germination rate when its wheat homolog is overexpressed in tobacco, and its syntenic region in rice co-localized with two cold tolerance QTL in rice. This locus may be useful in developing tools for molecular breeding of sorghums with improved low-temperature germinability. Key words: sorghum, association mapping, SNP, early-season cold tolerance. Le sorgho est l'une des plus importantes cultures au monde, autant pour sa production de fibres que d'aliments pour les humains et les animaux, ainsi que pour son potentiel en tant que matiere premiere pour la production de bioenergie lignocellulosique. Un semis hatif permet de rallonger la saison de croissance et d'augmenter les rendements dans les regions temperees. Cependant, la sensibilite du sorgho aux basses temperatures du sol a des impacts negatifs sur la germination des graines. Dans cette etude, les auteurs ont evalue 242 accessions de la collection nucleaire minimale (<< mini core collection>>) de l'ICRISAT pour leur germination et la vigueur des plantules a 12 °C afin d'en mesurer la tolerance au froid. Une analyse d'association pangenomique a ete realisee au moyen d'environ 162177 marqueurs mononucleotidiques (SNP). Seul un marqueur (Locus 7-2) a montre une association significative avec la germination a basse temperature et aucun a la vigueur des plantules. L'association entre le Locus 7-2 et la germination a basse temperature etait supportee par quatre evidences : une forte association au sein de trois experiences independantes, une colocalisation avec des locus de caracteres quantitatifs (QTL) identifies anterieurement chez le sorgho, la presence d'un gene candidat qui accroit la tolerance au froid et le taux de germination lorsque l'orthologue de ce gene present chez le ble est surexprime chez le tabac, et le fait que la region correspondante chez le riz contient deux QTL pour la tolerance au froid. Ce locus pourrait s'averer utile en vue du developpement de sorghos dotes d'une meilleure germination a basse temperature a l'aide d'outils de selection moleculaires. [Traduit par la Redaction] Mots-cles : sorgho, cartographie par association pangenomique, SNP, basses temperatures en debut de saison., Introduction The response of plants to suboptimal temperatures is in part related to the center of origin of a given plant species. Plants with centers of origin in temperate regions [...]

* Premise of the study: Gene flow from crops to wild relatives has received considerable attention since the advent genetically modified crops. Numerous researchers have found wild-crop hybrids to be nearly as fit as their wild parents, which suggests that crop genes may persist in wild populations. Components of the ecological fitness of cultivated sorghum, its wild relative, shattercane, and their hybrids have not been studied. * Methods: To assess the potential for gene introgression into shattercane, we crossed cultivated sorghum to a single inbred shattercane line to produce [F.sub.1] hybrids and measured growth and several components of ecological fitness in relation to both parents in Nebraska, USA. * Key results: Germination of [F.sub.1] seeds was similar to that of its shattercane parent except at high temperatures, where it was as sensitive as the sorghum parent. The [F.sub.1] grew taller and produced more biomass than either parent, but the [F.sub.1] leaf area index was intermediate. Fecundity of the [F.sub.1] plant was similar to that of shattercane and much greater than that of cultivated sorghum. * Conclusions: Considering all data, the ecological fitness of shattercane x cultivated sorghum [F.sub.1] hybrids may be equivalent to the wild shattercane parent, which suggests that crop genes that are either neutral or beneficial to shattercane would persist in populations within agroecosystems. Key words: fecundity; fitness; germination; introgression; phenology; wild-crop gene flow. doi: 10.3732/ajb.0900170

Although heterosis is well established in grain and forage sorghum [Sorghum bicolor (L.) Moench], reports of heterosis in sweet sorghum are limited to results from grain sorghum x sweet sorghum hybrids. Recent development of cytoplasmic male-sterile sweet sorghum lines allows creation of sweet sorghum hybrids for research and industry. Male sterility may also affect allocation of photosynthate to plant parts, creating the potential to increase sugar content in stems by eliminating seed as a sink. The objectives of this study were to compare performance of [A.sub.3] cytoplasmic male-sterile lines and [A.sub.3] cytoplasmic male-sterile hybrids to fertile [B.sub.3] counterparts and to each other. [A.sub.3] cytoplasmic male-sterile 'Dale', 'Wray', 'Sugar Drip', and N100 were crossed in all combinations to their male-fertile counterparts, resulting in 20 genotypes including the male-fertile lines. The 20 genotypes were grown in a randomized complete block in 2004 and 2005 at Lexington, KY. Male-sterile hybrids and lines had higher brix than male-fertile lines. Hybrids produced greater stalk yield due to taller plants with greater stem diameter. Juice fraction and juice composition remained relatively unchanged. Only six hybrids showed positive heterosis for brix. The greater juice yield and higher sugar content of selected hybrids such as [A.sub.3] N100 x Dale could produce more total syrup or ethanol than current pure-line sweet sorghum varieties. doi: 10.2135/cropsci2009.09.0475

Sixty-three sorghum [Sorghum bicolor (L.) Moench] hybrids that are, or have been, widely used in the United States were profiled using 167 simple sequence repeat (SSR) markers. Genetic distance and cluster analysis determined that 43 (68%) of the hybrids formed seven groupings, with each group containing hybrids commercialized by a single breeding organization. Groupings were also reflective of known pedigrees. Hybrids released by different organizations were not very closely associated with one exception of two hybrids. Groupings had limited association with the decade that the hybrid was released. Numbers of alleles per locus have been constant during the past three decades with gain in new alleles being balanced by loss of other alleles. Hybrids released during the 2000s showed the least number of new alleles compared to the previous two decades. Much of the SSR allelic diversity that was introduced via the Sorghum Conversion Program that converted tropical germplasm to be day-length neutral has been deployed on U.S. farms. Continued monitoring of genetic gain and genetic diversity are important components of sustainable plant breeding strategies. doi: 10.2135/cropsci2009.10.0619

Sorghum [Sorghum bicolor (L.) Moench] and sugarcane (Saccharum spp.) are now being bred to enhance the quantity and quality of biomass while maintaining or improving biotic and abiotic stress tolerances. Introgression of complementary traits between sorghum and sugarcane may be an important tool for breeders as they work toward these objectives. We show that by using a sorghum line with the lap mutant, intergeneric Sorghum bicolor x Saccharum spp. hybrids can be readily produced. Using Tx3361 as sorghum seed parent, 14,141 seed were produced from 252 sorghum x Saccharum spp. crosses. Seed set frequency in the intergeneric crosses was affected by sugarcane pollinators. The best pollinators had an above average pollen rating and favorable genetic and/ or genomic compatibility, implying that breeding and selection of sugarcane pollen parents could further enhance successful hybridization. Avoiding vMpary through premature seed harvest and eliminating a physical barrier by removing the seed coat increased seedling recovery rates from 1.5 to 33%. Using these methods, our programs have grown 1371 sorghum-saccharum intergeneric hybrid plants. Sufficient quantities of seedlings were produced to impose selection criteria with the goal of developing a new intergeneric cultivar with potential to be used for sugar or as a biomass feedstock. doi: 10.2135/cropsci2009.09.0486

Large-seededness can increase grain yield in sorghum [Sorghum bicolor (L.) Moench] if larger kernel size more than compensates for the associated reduction in kernel number. The aim of this research was to investigate kernel filling characteristics associated with the high kernel weight of KS115 germplasm and consider implications for grain yield improvement. Germplasm with a twofold range in potential kernel size was grown in two field experiments. In both experiments, a large-seeded hybrid based on KS115 yielded significantly more grain than a normal-seeded hybrid with the same female parent. Genotypic differences in final kernel weight were associated with both an increased rate and extended duration of kernel filling. A high kernel filling rate was associated with a high rate of increase in kernel water content and kernel volume, which resulted in large maximum water content and volume per kernel. The long kernel filling duration of KS115-based germplasm was associated with an extended duration of the period of rapid water uptake into the kernel following the onset of rapid dry mass accumulation in the grains. For this particular germplasm, this was likely due to the presence of large ovaries before fertilization. Because of a trade-off between potential kernel weight and number, prolonged duration, rather than an increased rate of kernel filling, appeared to be the main mechanism through which large-seededness of KS115 could increase grain yield. doi: 10.2135/cropsci2009.06.0294

Despite the major ecological and economic impacts of gene flow between domesticated plants and their wild relatives, many aspects of the process, particularly the relative roles of natural and human selection in facilitating or constraining gene flow, are still poorly understood. We developed a multidisciplinary approach, involving both biologists and social scientists, to investigate the dynamics of genetic diversity of a sorghum weed-crop complex in a village of Duupa farmers in northern Cameroon. Farmers distinguish a gradient from weedy morphotypes (naa baa see, haariya, and genkiya) to domesticated morphotypes; haariya and genkiya have intermediate morphological traits. We investigated the pattern of diversity in this complex using both morphological and genetic data. Our biological results are interpreted in the light of data on farmers' taxonomy and practices such as spatial pattern of planting and plant selection. Both morphological and genetic data are congruent with farmers' taxonomy and confirm the introgressed status of intermediate weedy morphotypes. Farmers actively select against weedy morphotypes, but several practices unconsciously lavor gene flow. Furthermore, haariya and genkiya may facilitate introgression between naa baa see and domesticated morphotypes by virtue of their intermediate flowering period and their mode of management by farmers. Key words: agrobiodiversity: anthropology; farmers' practices; hybridization; microsatellites: natural introgression; Poaceae; population genetics; selection; Sorghum bicolor. doi: 10.3732/ajb.0800284

Single-nucleotide polymorphism was used in the construction of an expressed sequence tag map of Aegilops tauschii, the diploid source of the wheat D genome. Comparisons of the map with the rice and sorghum genome sequences revealed 50 inversions and translocations; 2, 8, and 40 were assigned respectively to the rice, sorghum, and Ae. tauschii lineages, showing greatly accelerated genome evolution in the large Triticeae genomes. The reduction of the basic chromosome number from 12 to 7 in the Triticeae has taken place by a process during which an entire chromosome is inserted by its telomeres into a break in the centromeric region of another chromosome. The original centromere-telomere polarity of the chromosome arms is maintained in the new chromosome. An intrachromosomal telomere-telomere fusion resulting in a pericentric translocation of a chromosome segment or an entire arm accompanied or preceded the chromosome insertion in some instances. Insertional dysploidy has been recorded in three grass subfamilies and appears to be the dominant mechanism of basic chromosome number reduction in grasses. A total of 64% and 66% of Ae, tauschii genes were syntenic with sorghum and rice genes, respectively. Synteny was reduced in the vicinity of the termini of modern Ae. tauschii chromosomes but not in the vicinity of the ancient termini embedded in the Ae. tauschii chromosomes, suggesting that the dependence of synteny erosion on gene location along the centromere--telomere axis either evolved recently in the Triticeae phylogenetic lineage or its evolution was recently accelerated. dysploidy | linkage map | rice | sorghum | wheat

The sorghum [Sorghum bicolor (L.) Moench] germplasm collection at the ICRISAT gene bank exceeds 37,000 accessions. A core collection of 2247 accessions was developed in 2001 to enable researchers to have access to a smaller set of germplasm. However, this core collection was found to be too large. To overcome this, a sorghum mini core (10% accessions of the core or 1% of the entire collection) was developed from the existing core collection. The core collection was evaluated for 11 qualitative and 10 quantitative traits in an augmented design using three control cultivars in the 2004-2005 post-rainy season. The hierarchical cluster analysis of data using phenotypic distances resulted in 21 clusters. From each cluster, about 10% or a minimum of one accession was selected to form a mini core that comprised 242 accessions. The data in the mini core and core collections were compared using statistical parameters such as homogeneity of distribution for geographical origin, biological races, qualitative traits, means, variances, phenotypic diversity indices, and phenotypic correlations. These tests revealed that the mini core collection represented the core collection, which can be evaluated extensively for agronomic traits including resistance to biotic and abiotic stresses to identify accessions with desirable characteristics for use in crop improvement research and genomic studies.

Decreased water availability and increased food demand worldwide require development of more water-efficient crops. This study was conducted to examine preflower transpiration ratio (C[O.sub.2] assimilation rate [A]/transpiration rate [E], A:E) in four inbred sorghum [Sorghum bicolor (L.) Moench] lines and 12 of their [F.sub.1] hybrids in terms of phenotypic and genetic variation, inheritance (i.e., additive and nonadditive genetic effects), and its relationship to water use efficiency (WUE) (i.e., the ratio of whole-plant biomass to cumulative transpiration). Lines were selected with contrasting A and A:E in a field trial and then crossed in a full diallel pattern. All hybrids and lines were further analyzed for A, E, A:E, biomass, and WUE in a greenhouse. Variation among hybrids and lines was significant for all traits evaluated. In both environments, the most contrasting lines for A:E were Tx430 and Tx7078. Average A:E was 3.10 mmol C[O.sub.2] [mol.sup.-1] [H.sub.2]O for Tx430 and 2.91 for Tx7078. Both Tx430 and Tx7078 had highest A. Genetic effects resulting from general (GCA) and specific combining ability (SCA) for A, E, and A:E were significant for all traits. Tx430 had positive and Tx7078 negative GCA effects on A:E. Tx430 hybrids had the highest A:E values, and Tx7078 hybrids the lowest. The A:E ratio was correlated with total biomass and WUE for all crosses. Data suggest that concomitant selection for high A:E and A at preflowering could result in improved WUE and biomass of mature sorghum.

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.

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.

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 B-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 [beta]-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.

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 megabases 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: Sorghum has been improved by public and private breeding programs utilizing germplasm mostly from within the species Sorghum bicolor. Until recently, cross-incompatibilities have prevented hybridization of S. bicolor with [...]

Abstract: A comparison of approximately 4.5 kb of nucleotide sequence from the waxy locus (the granule-bound starch synthase I [GBSS I] locus) from a waxy line, BTxARGl, and a non-waxy [...]

Information about the potential for crop-wild hybridization is needed to understand how crop genes, including transgenes, affect the population genetics and ecology of sexually compatible relatives. Transgenic sorghum is under development for use by traditional farmers in Africa, the center of origin for sorghum [Sorghum bicolor (L.) Moench], but systematic surveys of the current extent of contact with wild and weedy relatives are lacking. We studied wild and weedy sorghums that are interfertile with the crop and constitute a crop-wild-weed complex. The survey was conducted in 2005 in areas of traditional sorghum cultivation in three regions of Ethiopia and two regions of Niger. Within each region, we examined eight representative sorghum fields at each of 10 locations during peak flowering of the crop. In all regions, wild and weedy sorghum occurred intermixed with and adjacent to cultivated sorghum. Wild and weedy sorghums were detected at 56, 44, and 13% of the Ethiopian sites (Amhara, Tigray, and Hararghe regions, respectively), and 74 and 63% of sites in Niger (Maradi-Tahoua and TillaberyDosso regions, respectively). Flowering periods of wild and weedy sorghum populations overlapped with those of cultivated sorghum at most sites where the two co-occurred, especially in Ethiopia, and many putative crop-wild hybrids were observed. Therefore, current gene transfer from cultivated sorghum to wild and weedy sorghum populations in Ethiopia and Niger is likely to be widespread.

Sorghum has shown the adaptability necessary to sustain its improvement during time and geographical extension despite a genetic foundation constricted by domestication bottlenecks. Initially domesticated in the northeastern part of sub-Saharan Africa several millenia ago, sorghum quickly spread throughout Africa, and to Asia. We performed phylogeographic analysis of sequence diversity for six candidate genes for grain quality (Shrunken2, Brittle2, Soluble starch synthaseI, Waxy, Amylose extender1, and Opaque2) in a representative sample of sorghum cultivars. Haplotypes along 1-kb segments appeared little affected by recombination. Sequence similarity enabled clustering of closely related alleles and discrimination of two or three distantly related groups depending on the gene. This scheme indicated that sorghum domestication involved structured founder populations, while confirming a specific status for the guinea margaritiferum subrace. Allele rooted genealogy revealed derivation relationships by mutation or, less frequently, by recombination. Comparison of germplasm compartments revealed contrasts between genes. Sh2, Bt2, and SssI displayed a loss of diversity outside the area of origin of sorghum, whereas O2 and, to some extent, Wx and Ae1 displayed novel variation, derived from postdomestication mutations. These are likely to have been conserved under the effect of human selection, thus releasing valuable neodiversity whose extent will influence germplasm management strategies.

Graphical genotypes have been generated for o set of sorghum [Sorghum bicolor (L.) Moench] germplasm, which includes selected public inbreds, germplasm from the world collection, and ancestral lines central to the early breeding efforts of sorghum. We have focused our present examination on sorghum chromosome SBI-06, which encodes [ma.sub.1] and [dw.sub.2], two genes critical to sorghum improvement dating to the original introduction of tropical sorghums into the United States. Utilizing the pedigree relationship between sorghum cultivars, the patterns of genetic variation were detailed within segmental chromosomal blocks of SBI-06. Segmental genomic blocks were traced back through multiple generations of a pedigree, often back to founder tropical accessions. The graphical genotypes reveal genomic signatures of historical breeding decisions, especially evidence of directional selection during the conversion of tropical accessions to temperate adaptation. This information is central to our efforts to understand those crop improvement processes that have shaped the genomic diversity of elite sorghum cultivars.

Politica and environmental concerns have resulted in a growing interest in renewable energy, especially transportation fuels. In the United States the majority of fuel etnanol s currently produced from corn (Zea mays L.) starcn but grain supplies will be insufficient to meet anticipated demands. Enzymatic hydrolysis of lignocellulosic biomass such as corn and sorghum [Sorghum bicolor [L.) Moench] stover can provide an abundant alternative source of fermentable sugars. While production of cellulosic ethanol from stover is feasible from an energy-balance perspective, its production is currently not economically competitive Along with improvements n bioprocessing, enhancing the yield and composition of the biomass has the potential to make ethanol production considerably more cost effective. This requires (i) a petter understanding of now cell wall composition and structure affect the efficiency of enzymatic hydrolysis. (ii) the development of traits that enhance biomass conversion efficiency and increase biomass yield, and (iii) the development of rapid screening protocols to evaluate biomass conversion efficiency. Several genetic resources are available to improve maize and soronum as sources of lignocellulosic biomass. This includes the use of existing mutants, forward and reverse genetics to obtain novel mutants, and transgenic approaches in which the expression of genes of interest is modified. Plant breeding can be implemented to improve biomass yield, biomass quality, and biomass conversion efficiency, either through selection among progeny obtained by crossing parents with desirable traits, or as a way to enhance the agronomic performance of promising mutants and transgenics. Examples from current research will be used to illustrate progress in these different areas.

An irradiation-induced bloomless mutant of sorghum [Sorghum bicolor (L.) Moench.], KFS2021, which visually exhibits an absence of white fluffy epicuticular wax in leaf and sheath, was characterized using a combination of genetic and physiological approaches. Study of the phenotypic segregation for the bloomless trait in [F.sub.2] and [F.sub.2:3 ]populations from a cross between KFS2021 and BTx623 (a cultivar with bloom showing profuse deposition of white epicuticular wax) suggests that bloomless is controlled by a single nuclear recessive gene. The bloomless parent (KFS2021) and [F.sub.2] individuals had lower frequency of guttation, leakier epidermal layer (based on percentage of chlorophyll leaching), and higher rate of seedling water loss than the BTx623 and [F.sub.2] bloom individuals. Bloomless [F.sub.2] individuals showed 3- to 6-fold higher nighttime transpiration rates relative to [F.sub.2] bloom individuals based on nighttime conductance. Correlation analysis showed significant negative associations between leaf epicuticular wax load with epidermal permeability and nighttime conductance, which indicate the important role of epicuticular wax in these traits. These results suggest that epicuticular wax may enhance water use efficiency of sorghum by regulating nighttime water loss.

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.

A cytogenetic FISH map of maize pachytene-stage chromosome 9 was produced with 32 maize marker-selected sorghum BACs as probes. The genetically mapped markers used are distributed along the linkage maps at an average spacing of 5 cM. Each locus was mapped by means of multicolor direct FISH with a fluorescently labeled probe mix containing a whole-chromosome paint, a single sorghum BAC clone, and the centromeric sequence, CentC. A maize-chromosome-addition line of oat was used for bright unambiguous identification of the maize 9 fiber within pachytene chromosome spreads. The locations of the sorghum BAC--FISH signals were determined, and each new cytogenetic locus was assigned a centiMcClintock position on the short (9S) or long (9L) arm. Nearly all of the markers appeared in the same order on linkage and cytogenetic maps but at different relative positions on the two. The CentC FISH signal was localized between cdo17 (at 9L.03) and tda66 (at 9S.03). Several regions of genome hyperexpansion on maize chromosome 9 were found by comparative analysis of relative marker spacing in maize and sorghum. This transgenomic cytogenetic FISH map creates anchors between various maps of maize and sorghum and creates additional tools and information for understanding the structure and evolution of the maize genome.

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 cultivars, 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 e panel of cultivars that vary in grain 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 (average ZnS = 0.56), while non-singleton SNP frequency was low to moderate ([pi] 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 'tag 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.).

Forty-six converted exotic sorghum lines representing all five races and nine intermediate races of sorghum were fingerprinted using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers. A total of 453 scored AFLP and SSR loci were used to calculate genetic similarities between the lines. The dendrogram constructed using UPGMA grouped 31 lines into three major clusters with Jaccard coefficients greater than 0.75. The remaining 15 lines were grouped into four small sub-clusters each with two lines and seven single accession nodes. Phenetic analysis using AFLP and SSR markers resulted in clusters corresponding to the kafir, guinea, caudatum and durra morphological groupings. Cluster and principal coordinate analyses indicate that the guinea, kafir and intermediate lines in this study are more closely related than phenotype would suggest. Likewise, caudatum and intermediates involving caudatum showed close genetic relationship with durra and durra intermediates. For the most part, morphological classification of race based on panicle traits was also reflected by similarity in DNA based polymorphisms. The molecular diversity of bicolor and associated intermediate races is not reflective of their common morphological classification, since this race and its intermediates are quite heterogenous.

Two hypotheses for the origin of crop pathogen species, one that human-mediated agricultural practices are the cause of divergence of crop plant pathogen species or secondly that coevolutional processes in natural populations of the crops' ancestors drove divergence of pathogen species are investigated by using smut fungi. It is seen that smut species diverged in the ecological context of natural host plant and fungal populations before the time of domestication and modern agriculture.

Abstract: Sorghum bicolor (L.) Moench is an important grain and forage crop grown worldwide. We developed a simple sequence repeat (SSR) linkage map for sorghum using 352 publicly available SSR [...]

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 Xcup 15, located near the distal end of chromosome 1. We performed statistical tests both 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 had 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 ([F.sub.st]- 0.15). Several features of the data support the hypothesis that recent directional selection shaped diversity patterns around Xcup 15, 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 (UTR) of a protein phosphatase 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 Aguade (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 far the target of selection; the confirmation of which will require functional and association studies.

Wild Australian Sorghum species are a tertiary gene pool to grain sorghum [Sorghum bicolor (L.) Moench], and they are of interest to breeders because of their resistance to important insects and pathogens. However, strong reproductive barriers have prevented hybridization between S. bicolor and these wild species. The purpose of this study was to determine if the recessive tap allele (dominant allele Iap = inhibition of alien pollen) would reduce or eliminate the pollen-pistil incompatibilities that prevent hybridization between S. bicolor and divergent Sorghum species. Cytoplasmic male-sterile S. bicolor plants, homozygous for the tap allele, were pollinated with three divergent Sorghum species, S. angustum Blake, S. nitidum (Vahl) Pers., and S. macrospermum Garber. The pollen of these three wild species readily germinated and the pollen tubes grew to the base of the S. bicolor ovary within 2 h after pollination. Hybrid embryos were detected in the S. bicolor florets 13 to 20 d post-pollination. Sorghum bicolor x S. angustum and S. bicolor x S. nitidum hybrids were obtained using embryo rescue followed by in vitro culture techniques and hybrids between S. bicolor and S. macrospermum were obtained by simply germinating the hybrid seed. These hybrids were confirmed by their morphological and cytological traits. These findings clearly demonstrate that the recessive tap allele circumvents pollen-pistil incompatibilities in the genus Sorghum and permits hybrids to be made between S. bicolor and species of the tertiary gene pool.

Ergot (caused predominantly by Claviceps africana Freder., Mantle & De Milliano) is a disease of sorghum (Sorghum bicolor L. Moench), with pollen trails reported to be associated with resistance. This study investigated the genetic architecture and the role of pollen quantity (PQ) and pollen viability (PV) in ergot resistance in an F5 recombinant inbred line (RIL) sorghum population developed from the cross between an elite germplasm line, 31945-2-2 from Australia, and a recently reported putatively resistance source line, IS8525. Percentage ergot infection (PCERGOT) in IS8525 was very low, while in contrast, 31945-2-2 was heavily infected at all inoculation dates of the two field trials conducted under artificial epiphytotic conditions during 2001 and 2002. The distribution of the predicted means for PCERGOT, PQ, and PV was normal, suggesting that the traits are polygenic in nature. Genetic correlations between the two pollen traits and PCERGOT were moderately negative, indicating that there might be some common genetic factors controlling these traits. However, low [R.sup.2] values of PQ (11%) and PV (9%) suggest that only a small part of the total variability in ergot resistance in this population was due In the variability in PQ and PV. Correlations between ergot scores for different sampling dates (SDATEs) and years were moderate to high, indicating relatively low levels of genotype x environment interaction. Genetic variance and broad sense heritability were also high, indicating that ergot resistance is likely to respond well to conventional selection.

Cytoplasmic-nuclear male sterility (CMS) in sorghum [Sorghum bicolor (L.) Moench] is integral to hybrid seed production. One such CMS, A3, is controlled by a two gene gametophytic fertility restoration system involving two restoration alleles, Rf3 and Rf4, which are required for individual male gamete viability. A survey of the allelic frequencies of RJ3 and Rf4 in the sorghum germplasm collection was undertaken using 140 lines from the Sorghum Conversion Program. These lines were hybridized to two testers, A3FL3 (Rf3Rf3rf4rf4) and A3FL4 (rf3rf3Rf4Rf4). The resulting hybrids were evaluated for [I.sub.2]-KI pollen stainability and seed set to determine their fertility restoration reaction. Transcript analyses were performed on lines that contained restoration alleles to determine whether they fit the expected genetic model of fertility restoration. Three lines (SC306, SC512, and SC215) were found to restore fertility with both testers and thus contain both restoration alleles. The surveyed allelic frequency of Rf3 and Rf4 was 5.1 and 4.8%, respectively. Using transcript analyses, two exceptional lines were identified (SC306 and SC215) that carried Rf3 but did not confer enhanced transcript processing activity (TPA) of mitochondrial orf107. Enhanced TPA was thought to be tightly linked to or represent gene action of Rf3, but identification of these lines demonstrates that enhanced TPA is not required for fertility restoration and does not represent gene action of Rf3.

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 bicolorcontains 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: Sorghum, Sorghum bicolor (L.) Moench, is the fifth most important cereal crop grown worldwide and the fourth in the United States. Greenbug, Schizaphis graminum (Rondani), is a major insect [...]

Abstract: We report here an analysis of the structure of genetic diversity in cultivated sorghums. A core collection of 210 landraces representative of race, latitude of origin, response to day [...]

Cytogenetic maps of sorghum chromosomes 3-7, 9, and 10 were constructed on the basis of the fluorescence in situ hybridization (FISH) of ~18-30 BAC probes mapped across each of these chromosomes. Distal regions of euchromatin and pericentromeric regions of heterochromatin were delimited for all 10 sorghum chromosomes and their DNA content quantified. Euchromatic DNA spans ~50% of the sorghum genome, ranging from ~60% of chromosome 1 (SBI-01) to ~33% of chromosome 7 (SBI-07). This portion of the sorghum genome is predicted to encode ~70% of the sorghum genes (~1 gene model/12.3 kbp), assuming that rice and sorghum encode a similar number of genes. Heterochromafin spans ~411 Mbp of the sorghum genome, a region characterized by a ~34-fold lower rate of recombination and ~3-fold lower gene density compared to euchromatic DNA. The sorghum and rice genomes exhibit a high degree of macrocolinearity; however, the sorghum genome is ~2-fold larger than the rice genome. The distal euchromatic regions of sorghum chromosomes 3-7 and 10 are ~1.8-fold larger overall and exhibit an ~1.5-fold lower average rate of recombination than the colinear regions of the homeologous rice chromosomes. By contrast, the pericentromeric heterochromatic regions of these chromosomes are on average ~3.6-fold larger in sorghum and recombination is suppressed ~15-fold compared to the colinear regions of rice chromosomes.

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, p, 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 9 and the population mutation parameter, 0, 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.

Nearly finished sequences for model organisms provide a foundation from which to explore genomic diversity among other taxonomic groups. We explore genome-wide microsynteny patterns between the rice sequence and two sorghum physical maps that integrate genetic markers, bacterial artificial chromosome (BAC) fingerprints, and BAC hybridization data. The sorghum maps largely tile a genomic component containing 41% of BACs but 80% of single-copy genes that shows conserved microsynteny with rice and partially tile a nonsyntenic component containing 46% of BACs but only 13% of single-copy genes. The remaining BACs are centromeric (4%) or unassigned (8%). The two genomic components correspond to cytologically discernible 'euchromatin' and 'heterochromatin.' Gene and repetitive DNA distributions support this classification. Greater microcolinearity in recombinogenic (euchromatic) than nonrecombinogenic (heterochromatic) regions is consistent with the hypothesis that genomic rearrangements are usually deleterious, thus more likely to persist in nonrecombinogenic regions by virtue of Muller's ratchet. Interchromosomal centromeric rearrangements may have fostered diploidization of a polyploid cereal progenitor. Model plant sequences better guide studies of related genomes in recombinogenic than nonrecombinogenic regions. Bridging of 35 physical gaps in the rice sequence by sorghum BAC contigs illustrates reciprocal benefits of comparative approaches that extend at least across the cereals and perhaps beyond. comparative genomics | Oryza | synteny