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United States Department of Agriculture

Agricultural Research Service

Research Project: Development and Application of Genetic, Genomic, and Bioinformatic Resources in Maize

Location: Plant, Soil and Nutrition Research

Title: Population genomic and genome-wide association studies of agroclamatic traits in sorghum

item Morris, Geoffrey
item Ramu, Punna
item Deshpande, Santosh
item Hash, Thomas
item Shah, Trushar
item Upadhyaya, Hari
item Riera-lizarazu, Oscar
item Brown, Patrick
item Acharya, Charlotte
item Mitchell, Sharon
item Harriman, James
item Glaubitz, Jeffrey
item Buckler, Edward - Ed
item Kresovich, Stephen

Submitted to: Proceedings of the National Academy of Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/21/2012
Publication Date: 1/8/2013
Publication URL: http://DOI: 10.1073/pnas.1215985110/-/DCSupplemental
Citation: Morris, G.P., Ramu, P., Deshpande, S.P., Hash, T.C., Shah, T., Upadhyaya, H.D., Riera-Lizarazu, O., Brown, P., Acharya, C.B., Mitchell, S.E., Harriman, J., Glaubitz, J.C., Buckler IV, E.S., Kresovich, S. 2013. Population genomic and genome-wide association studies of agroclamatic traits in sorghum. Proceedings of the National Academy of Sciences. 110(2):453-458.

Interpretive Summary: Sorghum is a highly productive grain for regions of the US and world that have low water. While some advanced genomics has been conducted in Sorghum, the community tools for high resolution breeding in the developing world are just now becoming available. This research used next generation DNA sequencing approaches to develop hundreds of thousands of molecular markers that can be used for breeding of Sorghum for developing world environments. These markers were then used to evaluate two traits important to sorghum breeding: (1) Plant height, which is critical so plant do not fall over, yet can fully use the nutrients, and (2) Panicle morphology, which is key for harvesting the seeds and to yield potential. Key genes were identified for both traits. These genomic resources provide the basis for accelerating breeding of Sorghum in some of the most challenging environments.

Technical 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 SNP map, 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.

Last Modified: 10/16/2017
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