eprintid: 6357 rev_number: 15 eprint_status: archive userid: 128 dir: disk0/00/00/63/57 datestamp: 2012-12-26 08:02:43 lastmod: 2016-10-19 08:15:14 status_changed: 2012-12-26 08:02:43 type: article metadata_visibility: show contact_email: Library-ICRISAT@CGIAR.ORG creators_name: Morris, G P creators_name: Ramu, P creators_name: Desphande, S creators_name: Hash, C T creators_name: Shah, T creators_name: Upadhyaya, H D creators_name: Riera-Lizarazu, O creators_name: Brown, P J creators_name: Acharjee, C B creators_name: Mitchell, S E creators_name: Harriman, J creators_name: Glaubitz, J C creators_name: Buckler, E S creators_name: Kresovich, S icrisatcreators_name: Ramu, P icrisatcreators_name: Deshpande, S P icrisatcreators_name: Hash, C T icrisatcreators_name: Shah, T icrisatcreators_name: Upadhyaya, H D icrisatcreators_name: Riera-Lizarazu, O affiliation: ICRISAT(Patancheru) affiliation: ICRISAT(Niamey) country: India country: Niger title: Population genomic and genome-wide association studies of agroclimatic traits in sorghum ispublished: pub subjects: s1.4 divisions: D4 crps: crp1.4 full_text_status: public keywords: Sorghum bicolor,Quantitative trait locus, Adaptation note: 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 abstract: 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. date: 2013 date_type: published publication: Proceedings of the National Academy of Sciences volume: 110 number: 2 publisher: National Academy of Sciences pagerange: 453-458 id_number: 10.1073/pnas.1215985110 refereed: TRUE issn: 1091-6490 official_url: http://dx.doi.org/10.1073/pnas.1215985110 related_url_url: http://scholar.google.co.in/scholar?as_q=%22Population+genomic+and+genome-wide+association+studies+of+agroclimatic+traits+in+sorghum%22&as_epq=&as_oq=&as_eq=&as_occt=title&as_sauthors=&as_publication=&as_ylo=&as_yhi=&btnG=&hl=en&as_sdt=0%2C5 related_url_type: pub funders: National Science Foundation (NSF), USA projects: Basic Research to Enable Agricultural Development Project IOS-0965342 citation: 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 document_url: http://oar.icrisat.org/6357/1/Sorghum_BREAD_manuscript_2nd_draft.pdf document_url: http://oar.icrisat.org/6357/7/PNAS_110_02_453-458_2013.pdf