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ARS Home » Southeast Area » New Orleans, Louisiana » Southern Regional Research Center » Cotton Fiber Bioscience Research » Research » Publications at this Location » Publication #281751
Title: A microsatellite-based genome-wide analysis of genetic diversity and linkage disequilibrium in Upland cotton (Gossypium hirsutum L.) cultivars from major cotton-growing countries

Author
item Fang, David
item Hinze, Lori
item Percy, Richard
item Li, Ping
item Deng, Dewayne
item Thyssen, Gregory

Submitted to: Euphytica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/8/2013
Publication Date: 2/19/2013
Citation: Fang, D.D., Hinze, L.L., Percy, R.G., Li, P., Deng, D.D., Thyssen, G.N. 2013. A microsatellite-based genome-wide analysis of genetic diversity and linkage disequilibrium in Upland cotton (Gossypium hirsutum L.) cultivars from major cotton-growing countries. Euphytica. 191:391-401.

Interpretive Summary: Genetic diversity is the foundation for and provides the building blocks of cotton improvement. To better understand the genetic diversity of the cultivated Upland cotton and its structure at the molecular level, 193 Upland cotton cultivars collected from 26 countries were analyzed using 448 microsatellite (a kind of DNA marker) markers. These markers were selected based on their positions in the high density Upland cotton TM-1 x Pima cotton 3-79 map, and they covered the whole genome. In addition, the physical locations of these markers were also partially identified based on the reference sequence of the diploid G. raimondii (a relative of Upland cotton). The marker orders in the genetic map were largely in agreement with their orders in the physical map. These markers revealed 1590 alleles belonging to 732 loci (sites in chromosome). Analysis of unique marker allele numbers indicated that the modern US Upland cotton had been losing its genetic diversity during the past century. Linkage disequilibrium (LD) between marker pairs was clearly un-even among chromosomes, and among regions within a chromosome. The average size of a LD block was 6.75 cM at r2 =0.10. A phylogenic tree of these cultivars was generated using marker allele frequencies based on the genetic distance. The cultivars were grouped into 15 groups according to the phylogenic tree. Grouping results were largely congruent with the breeding history and pedigrees of the cultivars with a few exceptions.

Technical Abstract: To better understand the genetic diversity of the cultivated Upland cotton (Gossypium hirsutum L.) and its structure at the molecular level, 193 Upland cotton cultivars collected from 26 countries were genotyped using 448 microsatellite markers. These markers were selected based on their mapping positions in the high density G. hirsutum TM-1 x G. barbadense 3-79 map, and they covered the whole genome. In addition, the physical locations of these markers were also partially identified based on the reference sequence of the diploid G. raimondii (D5) genome. The marker orders in the genetic map were largely in agreement with their orders in the physical map. These markers revealed 1590 alleles belonging to 732 loci. Analysis of unique marker allele numbers indicated that the modern US Upland cotton had been losing its genetic diversity during the past century. Linkage disequilibrium (LD) between marker pairs was clearly un-even among chromosomes, and among regions within a chromosome. The average size of a LD block was 6.75 cM at r2 =0.10. A neighbor-joining phylogenic tree of these cultivars was generated using marker allele frequencies based on Nei’s genetic distance. The cultivars were grouped into 15 groups according to the phylogenic tree. Grouping results were largely congruent with the breeding history and pedigrees of the cultivars with a few exceptions.