Genetic Structure and Linkage Disequilibrium in a Diverse, Representative Collection of the C4 Model Plant, Sorghum bicolor

Wang, Y H and Upadhyaya, H D and Burrell, A M and Sahraeian, S M E and Klein, R R and Klein, P E (2013) Genetic Structure and Linkage Disequilibrium in a Diverse, Representative Collection of the C4 Model Plant, Sorghum bicolor. G3.Genes Genomes Genetics, 3 (5). pp. 783-793. ISSN 2160-1836

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Abstract

To facilitate the mapping of genes in sorghum [Sorghum bicolor (L.) Moench] underlying economically important traits, we analyzed the genetic structure and linkage disequilibrium in a sorghum mini core collection of 242 landraces with 13,390 single-nucleotide polymorphims. The single-nucleotide polymorphisms were produced using a highly multiplexed genotyping-by-sequencing methodology. Genetic structure was established using principal component, Neighbor-Joining phylogenetic, and Bayesian cluster analyses. These analyses indicated that the mini-core collection was structured along both geographic origin and sorghum race classification. Examples of the former were accessions from Southern Africa, East Asia, and Yemen. Examples of the latter were caudatums with widespread geographical distribution, durras from India, and guineas from West Africa. Race bicolor, the most primitive and the least clearly defined sorghum race, clustered among other races and formed only one clear bicolor-centric cluster. Genome-wide linkage disequilibrium analyses showed linkage disequilibrium decayed, on average, within 10−30 kb, whereas the short arm of SBI-06 contained a linkage disequilibrium block of 20.33 Mb, confirming a previous report of low recombination on this chromosome arm. Four smaller but equally significant linkage disequilibrium blocks of 3.5−35.5 kb were detected on chromosomes 1, 2, 9, and 10. We examined the genes encoded within each block to provide a first look at candidates such as homologs of GS3 and FT that may indicate a selective sweep during sorghum domestication.

Item Type: Article
Divisions: UNSPECIFIED
CRP: UNSPECIFIED
Uncontrolled Keywords: sorghum races, SNPs, Fsel-assisted genotyping, linkage disequilibrium
Subjects: Mandate crops > Sorghum
Others > Genetics and Genomics
Depositing User: Mr Siva Shankar
Date Deposited: 24 Jan 2014 10:09
Last Modified: 19 Oct 2016 04:44
URI: http://oar.icrisat.org/id/eprint/7364
Official URL: http://dx.doi.org/10.1534/g3.112.004861
Projects: UNSPECIFIED
Funders: UNSPECIFIED
Acknowledgement: The study was supported in part by the University of Louisiana at Lafayette (Y.-H.W.), International Crops Research Institute for the Semi-Arid Tropics (H.D.U.), the United States Department of Agriculture (USDA)-Agricultural Research Service (R.R.K.), Texas A&M AgriLife Research (P.E.K.), and the USDA–National Institute of Food and Agriculture, Award 2010-67009-21507 (P.E.K).
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