Sequence variation at candidate loci in the starch metabolism pathway in sorghum: prospects for linkage disequilibrium mapping

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.).