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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #297015
Title: Population genomic and genome-wide association studies of agroclamatic traits in sorghum

Author
item MORRIS, GEOFFREY - University Of South Carolina
item RAMU, PUNNA - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item DESHPANDE, SANTOSH - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item HASH, THOMAS - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item SHAH, TRUSHAR - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item UPADHYAYA, HARI - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item RIERA-LIZARAZU, OSCAR - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item BROWN, PATRICK - University Of Illinois
item ACHARYA, CHARLOTTE - Cornell University
item MITCHELL, SHARON - Cornell University
item HARRIMAN, JAMES - Cornell University
item GLAUBITZ, JEFFREY - Cornell University
item Buckler, Edward - Ed
item KRESOVICH, STEPHEN - University Of South Carolina

Submitted to: Proceedings of the National Academy of Sciences (PNAS)
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.