Comparative population genetics of the panicoid grasses: sequence polymorphism, linkage disequilibrium and selection in a diverse sample of sorghum bicolor.
Levels of genetic variation and linkage disequilibrium (LD) are critical factors in association mapping methods as well as in identification of loci that have been targets of selection. Maize, an outcrosser, has a high level of sequence variation and a limited extent of LD. Sorghum, a closely related but largely self-pollinating panicoid grass, is expected to have higher levels of LD. As a first step in estimation of population genetic parameters in sorghum, we surveyed 27 diverse S. bicolor accessions for sequence variation at a total of 29,186 bp in 95 short regions derived from genetically mapped RFLPs located throughout the genome. Consistent with its higher level of inbreeding, the extent of LD is at least severalfold greater in sorghum than in maize. Total sequence variation in sorghum is about fourfold lower than that in maize, while synonymous variation is fivefold lower, suggesting a smaller effective population size in sorghum. Because we surveyed a species-wide sample, the mating system, which primarily affects population-level diversity, may not be primarily responsible for this difference. Comparisons of polymorphism and divergence suggest that both directional and diversifying selection have played important roles in shaping variation in the sorghum genome.
Hamblin
Martha T
MT
Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA.
Mitchell
Sharon E
SE
White
Gemma M
GM
Gallego
Javier
J
Kukatla
Rakesh
R
Wing
Rod A
RA
Paterson
Andrew H
AH
Kresovich
Stephen
S
D017343:Genes, Plant; D008040:Genetic Linkage; D014644:Genetic Variation; D005828:Genetics, Population; D018745:Genome, Plant; D015810:Linkage Disequilibrium; D008969:Molecular Sequence Data; D010641:Phenotype; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D012150:Polymorphism, Restriction Fragment Length; D012984:Software; D045868:Sorghum / Q000235:genetics*; D013045:Species Specificity; D003313:Zea mays / Q000235:genetics