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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETIC ANALYSES AND TRAIT MAPPING TO EXPLOIT UNTAPPED GENETIC DIVERSITY IN SORGHUM Title: Genetic structure and linkage disequilibrium in a diverse, representative collection of the C4 model plant, Sorghum bicolor

Authors
item Wang, Yi-Hong -
item Upadhyaya, Hari -
item Burrell, A. Millie -
item Sahraeian, S. Mohammad -
item Klein, Robert
item Klein, Patricia -

Submitted to: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 8, 2013
Publication Date: May 1, 2013
Citation: Wang, Y., Upadhyaya, H.D., Burrell, A., Sahraeian, S., Klein, R.R., Klein, P.E. 2013. Genetic structure and linkage disequilibrium in a diverse, representative collection of the C4 model plant, Sorghum bicolor. Genes, Genomes, Genetics. 3:783-793.

Interpretive Summary: Major advancements in science hinge on the identification of genes controlling plant and animal traits that are critically important to agriculture. Genes are tiny packets of genetic blueprint material that are found inside the cells of all plants and animals and control all of the physical characteristics of these organisms. Our work focuses on improving major grain and biofuel crops and, with gene sequences, the genetic blueprint will be visible and this information can make improving the plants more efficient. This study details the efforts to develop and characterize with genetic markers a collection of sorghum lines and use this information to develop a resource to clone important genes. Characterizing this panel of sorghum lines represents a genetic tool and resource for the sorghum community, and will allow scientists to understand those key features of the genetic blueprint that make sorghum's physical appearance differ from that of other cereals. Information will be primarily used by fellow scientists but the work should ultimately result in better adapted, higher producing crop varieties available to American farmers.

Technical 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 14,739 SNPs. The SNPs 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 amongst 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, while 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. Association analysis identified SbPGP1, a previously cloned height gene in sorghum, which demonstrates the utility of the collection in mapping sorghum quantitative traits.

Last Modified: 10/25/2014
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