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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 #323543

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

Location: Crop Germplasm Research

Title: Comparative analysis of genome-wide divergence, domestication footprints and genome-wide association study of root traits for Gossypium hirsutum and Gossypium barbadense

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: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/3/2015
Publication Date: N/A
Citation: N/A

Interpretive Summary:

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 genome-wide distributed SNPs, we examined levels and patterns of genetic diversity, haplotype distribution and runs of homozygosity (ROH) 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 revealed little sharing of alleles between the two cultivated allotetraploid genomes, which 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, in D-genome–derived chromosomes. The presence of conserved linkage disequilibrium (LD) blocks, haplotypes and ROHs between G. hirsutum and G. barbadense provide strong evidence for comparable patterns of evolution, either in their domestication processes or perhaps during the radiation of tetraploid species. 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 the evidence for convergent evolution. Our study illustrates the potential use of population genetic techniques to identify genomic regions for cotton breeding.