Community Resources and Strategies for Association Mapping in Sorghum

Abstract

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.

Nutritionally Enhanced Staple Food Crops

“…Yellow-endosperm color QTL in sorghum colocalized with carotenoid QTL, with major b-carotene QTL Bc-2.2 found close to Psy3 gene, which is significantly associated with b-carotene concentration and endosperm color (Salas Fernandez et al 2008). Furthermore, Salas Fernandez et al (2009) reported that 164 yellow endosperm landraces from Niger and Nigeria clustered separately from the genotypes in a 68 individual diversity panel (Casa et al 2008) with accessions differing in geographic origin and carotenoids content, which may provide The first step toward understanding how carotenoids are synthesized is to identify the enzymes involved and isolate the corresponding genes. Several maize complementary deoxyribonucleic acids (cDNAs) encoding carotenogenic enzymes have been cloned and genes identified: psy1, psy2, and psy3 (phytoene synthase), pds (phytoene desaturase), zds (z-carotene desaturase), lcyb (lycopene b-cyclase), and LCYE (Li et al 2010a).…”

Multilocus sequence data reveal extensive departures from equilibrium in domesticated tomato (Solanum lycopersicum L.)

“…LD estimates are valuable for understanding whether association mapping will be efficient within (Simko et al, 2006), soybean (Hyten et al, 2007), rice (Mather et al, 2007), maize (Yu et al, 2008), sorghum (Casa et al, 2008), sugarcane (Saccharum spp. ; Raboin et al, 2008), sunflower (H. annuus;Fusari et al, 2008), tomato (Mazzucato et al, 2008;van Berloo et al, 2008) and wheat (Triticum spp.…”

Population structure and genetic differentiation associated with breeding history and selection in tomato (Solanum lycopersicum L.)

“…An advantage of the analysis implemented with the software STRUCTURE (Pritchard et al, 2000), relative to other methods of quantifying subdivision, is its ability to estimate the proportion of the genome of an individual that belongs to each inferred population (admixture). STRUCTURE's quantitative clustering method uses a Bayesian approach and has been utilized in numerous genetic diversity and association mapping studies in plant species including rice (Garris et al, 2005), Arabidopsis (Schmid et al, 2006), wheat (Breseghello and Sorrells, 2006), sorghum (Casa et al, 2008) and tomato (Mazzucato et al, 2008;van Berloo et al, 2008).…”