Population genomic and genome-wide association studies of agroclimatic traits in sorghum

Morris, G P and Ramu, P and Desphande, S and Hash, C T and Shah, T and Upadhyaya, H D and Riera-Lizarazu, O and Brown, P J and Acharjee, C B and Mitchell, S E and Harriman, J and Glaubitz, J C and Buckler, E S and Kresovich, S (2013) Population genomic and genome-wide association studies of agroclimatic traits in sorghum. Proceedings of the National Academy of Sciences, 110 (2). pp. 453-458. ISSN 1091-6490

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Accelerating crop improvement in sorghum, a staple food for people in semiarid regions across the developing world, is key to ensuring global food security in the context of climate change. To facilitate gene discovery and molecular breeding in sorghum, we have characterized ∼265,000 single nucleotide polymorphisms (SNPs) in 971 worldwide accessions that have adapted to diverse agroclimatic conditions. Using this genome-wide SNPmap,we have characterized population structure with respect to geographic origin and morphological type and identified patterns of ancient crop diffusion to diverse agroclimatic regions across Africa and Asia. To better understand the genomic patterns of diversification in sorghum, we quantified variation in nucleotide diversity, linkage disequilibrium, and recombination rates across the genome. Analyzing nucleotide diversity in landraces, we find evidence of selective sweeps around starch metabolism genes, whereas in landrace-derived introgression lines, we find introgressions around known height and maturity loci. To identify additional loci underlying variation in major agroclimatic traits, we performed genome-wide association studies (GWAS) on plant height components and inflorescence architecture. GWAS maps several classical loci for plant height, candidate genes for inflorescence architecture. Finally, we trace the independent spread of multiple haplotypes carrying alleles for short stature or long inflorescence branches. This genome-wide map of SNP variation in sorghum provides a basis for crop improvement through marker-assisted breeding and genomic selection.

Item Type: Article
Divisions: RP-Dryland Cereals
CRP: CGIAR Research Program on Dryland Cereals
Uncontrolled Keywords: Sorghum bicolor,Quantitative trait locus, Adaptation
Subjects: Mandate crops > Sorghum
Depositing User: Mr Siva Shankar
Date Deposited: 26 Dec 2012 08:02
Last Modified: 19 Oct 2016 08:15
URI: http://oar.icrisat.org/id/eprint/6357
Official URL: http://dx.doi.org/10.1073/pnas.1215985110
Projects: Basic Research to Enable Agricultural Development Project IOS-0965342
Funders: National Science Foundation (NSF), USA
Acknowledgement: We thank two anonymous reviewers for helpful comments. This work was also supported by Department of Agriculture- National Institute of Food and Agriculture Plant Feedstock Genomics for Bioenergy Program Grant 2011-03502 (to S.K.). Supporting Information: http://www.pnas.org/content/suppl/2012/12/19/1215985110.DCSupplemental
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