title: Genome-wide divergence, haplotype distribution and population demographic histories for Gossypium hirsutum and Gossypium barbadense as revealed by genome-anchored SNPs.
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 linkage disequilibrium patterns in the G. hirsutum and G. barbadense genomes to clarify 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. We found a high number of new alleles, representing increased nucleotide diversity, on chromosomes 1 and 2 in cultivated G. hirsutum as compared with low nucleotide diversity on these chromosomes in landrace G. hirsutum. In contrast, G. barbadense chromosomes showed negative Tajima's D on several chromosomes for both cultivated and landrace types, which indicate that speciation of G. barbadense itself, might have occurred with relatively narrow genetic diversity. The presence of conserved linkage disequilibrium (LD) blocks and haplotypes between G. hirsutum and G. barbadense provides strong evidence for comparable patterns of evolution in their domestication processes. Our study illustrates the potential use of population genetic techniques to identify genomic regions for domestication.
authors.affiliation: Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA.
authors.forename: Umesh K
authors.initials: UK
authors.lastname: Reddy
authors.affiliation: Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA.
authors.forename: Padma
authors.initials: P
authors.lastname: Nimmakayala
authors.affiliation: Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA.
authors.forename: Venkata Lakshmi
authors.initials: VL
authors.lastname: Abburi
authors.affiliation: Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA.
authors.forename: C V C M
authors.initials: CV
authors.lastname: Reddy
authors.affiliation: Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA.
authors.forename: Thangasamy
authors.initials: T
authors.lastname: Saminathan
authors.affiliation: USDA-ARS, Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX 77845, USA.
authors.forename: Richard G
authors.initials: RG
authors.lastname: Percy
authors.affiliation: USDA-ARS, Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX 77845, USA.
authors.forename: John Z
authors.initials: JZ
authors.lastname: Yu
authors.affiliation: USDA-ARS, Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX 77845, USA.
authors.forename: James
authors.initials: J
authors.lastname: Frelichowski
authors.affiliation: WIDB, Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602, USA.
authors.forename: Joshua A
authors.initials: JA
authors.lastname: Udall
authors.affiliation: WIDB, Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602, USA.
authors.forename: Justin T
authors.initials: JT
authors.lastname: Page
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Room 228, Athens, GA 30605, USA.
authors.forename: Dong
authors.initials: D
authors.lastname: Zhang
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Room 228, Athens, GA 30605, USA.
authors.forename: Tariq
authors.initials: T
authors.lastname: Shehzad
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Room 228, Athens, GA 30605, USA.
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Paterson
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D000071278:Domestication; D014644:Genetic Variation; D005828:Genetics, Population; D018745:Genome, Plant / Q000235:genetics*; D003368:Gossypium / Q000235:genetics*; D006239:Haplotypes; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D057891:Tetraploidy