Genetics, Vol. 167, 471-483, May 2004, Copyright © 2004

Comparative Population Genetics of the Panicoid Grasses: Sequence Polymorphism, Linkage Disequilibrium and Selection in a Diverse Sample of Sorghum bicolor

Martha T. Hamblina, Sharon E. Mitchella, Gemma M. Whitea, Javier Gallegoa, Rakesh Kukatlaa, Rod A. Wingb, Andrew H. Patersonc, and Stephen Kresovicha
a Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853,
b Department of Agronomy, Clemson University, Clemson, South Carolina 29634-0359
c Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602

Corresponding author: Stephen Kresovich, 157 Biotechnology Bldg., Cornell University, Ithaca, NY 14853., sk20{at}cornell.edu (E-mail)

Communicating editor: M. AGUADÉ

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.




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