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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 #221822

Title: Genome-wide linkage disequilibruim revealed by microsatellite markers and association study of fiber quality traits in cotton

item Kohel, Russell
item Saha, Sukumar
item PEPPER, A
item Yu, John
item BURIEV, Z
item Jenkins, Johnie
item Scheffler, Brian

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 12/10/2006
Publication Date: 1/12/2007
Citation: Abdurakhmonov, I.Y., Kohel, R.J., Saha, S., Pepper, A.E., Yu, J., Buriev, Z.T., Abdullaev, A., Shermatov, S., Jenkins, J.N., Scheffler, B.E., Abdukarimov, A. 2007. Genome-wide linkage disequilibruim revealed by microsatellite markers and association study of fiber quality traits in cotton [abstract]. In: Proceedings of Plant and Animal Genome XV Conference, January 13-17, 2007, San Diego, California. Paper No. W199.

Interpretive Summary:

Technical Abstract: The application of association mapping based on existing genome-wide linkage disequilibrium (LD) between DNA polymorphisms and genes underlying traits is becoming powerful tool that overcome many limitations (high cost, poor resolution, requirement for bi-parentally crossed lines assessing only two alleles) of linkage mapping in experimental populations. Therefore, estimation of genome-wide LD patterns for cotton is essential to study the genetic basis of complex polygenic traits such as fiber quality in cotton. A thousand Gossypium hirsutum, including wild (ssp. palmeri, richmondi, morilli, mexicanum, latifolium, malum, yucatanense) and variety (from 37 countries of origin) accessions from Uzbek Cotton Germplasm Collection were selected for association mapping study. These selected variety and exotic cotton accessions were grown in Uzbekistan and Mexico environments and phenotypically analyzed for at least 14 morphological traits as well as for fiber quality and yield characteristics. Further, 288 exotic G. hirsutum accessions were genotyped with a core set of 100 SSR markers and 337 variety accessions (from Uzbekistan, Latin American and Australian ecotypes) were genotyped with 210 chromosome-specific SSR markers, covering 21 chromosomes (an average 10 SSR primer pairs per chromosome) of cotton. We estimated genome-wide linkage disequilibrium level between pairs of genotyped marker loci, analyzed the population structure and kinship among these diverse cotton germplasms, and conducted an association mapping of fiber quality traits (lint percentage, micronire length &strength, and uniformity) using the general linear model (GLM), structured association test, and the mixed linear model (MLM) implemented in TASSEL. The details genome-wide LD estimates and association mapping of fiber quality traits of cotton will be discussed.