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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.

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.

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.).

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.

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, [H.sub.e], ≅ 0.60 and 0.7, respectively), but they were surprisingly more diverse than the populations representing other maize races ([H.sub.e] = 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 ([H.sub.e] = 0.62 and 0.61, respectively), and little differentiation between these groups ([F.sub.st], = 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., IN A WORLD of increasing population, changing cultures, globalization, and emigration of indigenous communities, the loss of genetic diversity from farmers' fields in centers of origin is a subject of [...]

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., IOWA CORN BORER Synthetic #1 and Iowa Stiff Stalk Synthetic maize populations are important for research because they characterize the basis of the modern hybrid corn industry (Senior et al., [...]

Tens-of-thousands of open-pollinated cultivars of corn (Zea mays L.) are being maintained in germplasm banks. Knowledge of the amount and distribution of genetic variation within and among accessions can aid end users in choosing among them. We estimated molecular genetic variation and looked for influences of pedigree, adaptation, and migration in the genetic makeup of conserved Corn-Belt Dent-related germplasm. Plants sampled from 57 accessions representing Corn-Belt Dents, Northern Flints, Southern Dents, pins 12 public inbreds, were genotyped at 20 simple sequence repeat (SSR) loci. For 47 of the accessions, between 5 and 23 plants per accession were genotyped (mean = 9.3). Mean number of alleles per locus was 6.5 overall, 3.17 within accessions, and 3.20 within pooled inbreds. Mean gene diversity was 0.53 within accessions and 0.61 within pooled inbreds. Open-pollinated accessions showed a tendency toward inbreeding ([F.sub.IS] = 0.09), and 85% of genetic variation was shared among them. A Fitch-Margoliash tree strongly supported the distinctiveness of flint from dent germplasm but did not otherwise reveal evidence of genetic structure. Mantel tests revealed significant correlations between genetic distance and geographical (r = 0.54, P = 0.04) or maturity zone (r = 0.33, P = 0.03) distance only if flint germplasm was included in the analyses. A significant correlation (r = 0.76, P < 0.01) was found between days to pollen shed and maturity zone of accession origin. Pedigree, rather than migration or selection, has most influenced the genetic structure of the extant representatives of the open-pollinated cultivars at these SSR loci., TEN RACIAL COMPLEXES of corn have been described in the USA, the economically most important one being the Corn-Belt Dents (Goodman and Brown, 1988). Many Corn-Belt Dents originated in the [...]

Historically important public inbred lines continue to play au important role in maize (Zea mays L.) improvement in many different breeding programs. Their continued use means they have undergone numerous seed increases in diverse programs since their original release. Our objective was to estimate the level of genetic diversity among and within inbred lines from different sources using SSR markers. We sampled six inbred lines (B73, CM105, Mo17, Oh43, W153R, and Wf9) obtained from 14 sources (breeding programs). The data were analyzed by analysis of molecular variance (AMOVA), genetic diversity statistics, and genetic distance (Dice's coefficient). Of the total variation observed in gene frequency, 87.8% was found among inbred lines, 7.6% among sources within inbred lines, and 4.6% within sources. Genotypes of identically named inbred lines from eight different sources differed slightly on the basis of 44 SSR loci. The mean genetic similarity between sources of the same inbred was greater than 85%. It can be concluded that although more diversity exists among these six inbred lines than within them, a small but significant amount of variation exists among seed sources within inbreds. This variation may have arisen through differences in seed maintenance, since we found no evidence to suggest high mutation rates or extensive outcrossing. The small but statistically significant level of variation raises concerns in germplasm conservation, mapping studies, marker development, and long-term recombinant inbred line development, especially when high resolution is desired., HYBRID MAIZE PRODUCTION in the USA is based on development and crossing of inbred lines. Since the 1920s, over 600 public inbred lines have been developed, some of which are [...]

For future progress, effective conservation of plant genetic resources will require the integration of technologies and Protocols that provide for the acquisition of large quantities of genetic information for improved gene and genotype identification. As a contribution to this integration, simple sequence repeat (SSR) marker analysis in Brassica spp. was evaluated as a prototype system for establishing the potential of multiplex polymerase chain reactions (PCRS) coupled with Fluorescence-based DNA detection and semi-automated sizing technology for mass genotyping of plant genetic resources. Consistent results were achieved for multiplex PCRs (simultaneous amplification of several genetic markers in a single reaction) with 11 fluorescently labeled primer pairs. Comparison of computer-derived estimates of fragment sizes between gels demonstrated that automated sizing was accurate enough to achieve reliable and repeatable plant genotypes. To establish a genetic basis for putative SSR loci previously identified in Brassica spp., segregation data were analyzed. Three polymorphic SSRs in Brassica napus L. (canola and rapeseed) exhibited simple Mendelian inheritance and were not linked. One of these polymorphic loci was duplicated, i.e., a single copy marked each of the 'aa' and 'c' genomes originating from progenitor species B. rapa and B. oleracea, respectively. Technologies that provide for high genetic resolution and throughput at reasonable costs will find ready application in plant genetic resources conservation. In addition, these same tools and marker systems can be applied to questions of pedigree analysis and intellectual property rights., The development and application of molecular genetic markers provide the opportunity to establish and evaluate measures of quality for genetic resources collections (Kresovich et al., 1993). However, prior to routine [...]

Germplasm collections worldwide are increasing in both size and quality, but quantitative data on user needs and their perceptions of collection management are limited. Such information would enable more effective planning and management by collection curators. In 1991, we surveyed and analyzed the opinions of 47 scientists working with crucifer crops, including oilseed Brassica napus L. and B. rapa L., vegetable coles [B. oleracea subsp. italica (broccoli), B. oleracea subsp. capitata L. (cabbage), B. rapa subsp. pekinensis Lour. (Chinese cabbage), etc.], and wild and weedy relatives. Survey respondents were located in 19 countries and represented a broad range of institutional affiliations, professional interests, educational backgrounds, and research programs. Significant differences occurred among respondents' opinions on various activities (acquisition, preservation and distribution, documentation, and research). Respondents utilized genetic resources from all gene pool categories, obtained them from an array of sources, and expected to increase their use about 30% by 1994. Nearly 80% of respondents maintained a germplasm collection for their own use. They estimated ex situ genebanks held

Because (i) origins and genealogies of vetiver grass have been poorly documented, and (ii) morphological uniformity and infrequent flowering precluded accurate identification of selected clones, an investigation was undertaken to link molecular methods with rigorous biometric analysis to discriminate accessions and clones. Successful DNA profiling is highly dependent on the reproducibility of the assay. Our ability to generate consistent results may have been a result of (i) genomic DNA quality, (ii) rigorous oligonucleotide primer selection, and (iii) DNA amplification protocol stringency. Because of the low level of replicate variability, we were able to bring a high level of resolution to the analysis of identity. Though genetic redundancy may be more difficult to establish than genetic uniqueness, the data support with a high degree of certainty that the accessions 'Huffman' and 'Boucard' were essentially the same genotype. A contrasting case to the Huffman-Boucard example was found among the putative clones of 'PI 196257'. Our analysis indicated that each clone of PI 196257 was genetically unique.