Comparative population genetics of the panicoid grasses: Sequence polymorphism, linkage disequilibrium and selection in a diverse sample of Sorghum bicolor

Martha T. Hamblin, Sharon E. Mitchell, Gemma M. White, Javier Gallego, Rakesh Kukatla, Rod A Wing, Andrew H. Paterson, Stephen Kresovich

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Abstract

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.

Original languageEnglish (US)
Pages (from-to)471-483
Number of pages13
JournalGenetics
Volume167
Issue number1
DOIs
StatePublished - May 2004

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Sorghum
Linkage Disequilibrium
Population Genetics
Poaceae
Zea mays
Genome
Genetic Linkage
Inbreeding
Population Density
Restriction Fragment Length Polymorphisms
Population

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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Comparative population genetics of the panicoid grasses : Sequence polymorphism, linkage disequilibrium and selection in a diverse sample of Sorghum bicolor. / Hamblin, Martha T.; Mitchell, Sharon E.; White, Gemma M.; Gallego, Javier; Kukatla, Rakesh; Wing, Rod A; Paterson, Andrew H.; Kresovich, Stephen.

In: Genetics, Vol. 167, No. 1, 05.2004, p. 471-483.

Research output: Contribution to journalArticle

Hamblin, Martha T. ; Mitchell, Sharon E. ; White, Gemma M. ; Gallego, Javier ; Kukatla, Rakesh ; Wing, Rod A ; Paterson, Andrew H. ; Kresovich, Stephen. / Comparative population genetics of the panicoid grasses : Sequence polymorphism, linkage disequilibrium and selection in a diverse sample of Sorghum bicolor. In: Genetics. 2004 ; Vol. 167, No. 1. pp. 471-483.
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