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ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Crop Germplasm Research » Research » Publications at this Location » Publication #324765

Research Project: Developing Genomic and Genetic Tools for Exploiting Cotton Genetic Variation

Location: Crop Germplasm Research

Title: Genome-wide divergence, haplotype distribution and population demographic histories for Gossypium hirsutum and Gossypium barbadense as revealed by genome-anchored SNPs

Author
item REDDY, UMESH - West Virginia State University
item NIMMAKAYALA, PADMA - West Virginia State University
item ABBURI, VENKATA - West Virginia State University
item REDDY, C. V. C. M. - West Virginia State University
item SAMINATHAN, THANGASAMY - West Virginia State University
item Percy, Richard
item Yu, John
item Frelichowski, James - Jim
item UDALL, JOSHUA - Brigham Young University
item PAGE, JUSTIN - Brigham Young University
item ZHANG, DONG - University Of Georgia
item SHEHZAD, TARIQ - University Of Georgia
item PATERSON, ANDREW - University Of Georgia

Submitted to: Nature Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/19/2016
Publication Date: 1/27/2017
Citation: Reddy, U., Nimmakayala, P., Abburi, V., Reddy, C., Saminathan, T., Percy, R.G., Yu, J., Frelichowski, J.E., Udall, J., Page, J., Zhang, D., Shehzad, T., Paterson, A. 2017. Genome-wide divergence, haplotype distribution and population demographic histories for Gossypium hirsutum and Gossypium barbadense as revealed by genome-anchored SNPs. Nature Scientific Reports. 7:41285.

Interpretive Summary: Among the most remarkable stories in crop domestication is the origin of cultivated cotton. Understanding cotton evolution, domestication and genetic diversity, especially in the two major cultivated species, is essential for cotton improvement. In this study, we developed and used over 10,000 molecular markers called single nucleotide polymorphism (SNP) markers to characterize genetic diversity among 440 Upland cottons and 219 Sea Island cottons of widespread origin. The demographic history, genomic architecture, and domestication process of this natural cotton population were clarified in great detail. This study explored at a new level of resolution how breeding histories and selective pressures shaped the gene pools of the two cotton species. It provided strong evidence for comparable patterns of evolution in the domestication process of the two species in which common SNP markers were identified for a set of seedling root traits. The results shed light into the potential for breeders to apply these techniques to identify and incorporate other useful genes for crop improvement.

Technical Abstract: Use of 10,129 singleton SNPs of known genomic location in tetraploid cotton provided unique opportunities to characterize genome-wide diversity among 440 Gossypium hirsutum and 219 G. barbadense cultivars and landrace accessions of widespread origin. Using the SNPs distributed genome-wide, we examined genetic diversity, haplotype distribution and runs of homozygosity (ROH) patterns in the G. hirsutum and G. barbadense genomes to clarify the genomic architecture, domestication process and population demographic history. Diversity and identity-by-state analyses have revealed little sharing of alleles between the two cultivated allotetraploid genomes, with a few exceptions that indicated sporadic gene flow. An important finding was the location of a high number of selective sweeps, as represented by low diversity regions common to both species, mostly in D-genome–derived chromosomes. The presence of conserved linkage disequilibrium (LD) blocks, haplotypes and ROHs between G. hirsutum and G. barbadense provides strong evidence for comparable patterns of evolution in their domestication processes. Our comparative genome-wide association study (GWAS) of a set of seedling root traits revealed common SNPs in G. hirsutum and G. barbadense, which strengthens evidence for their convergent evolution. Our study illustrates the potential use of population genetic techniques to identify genomic regions for cotton breeding.