U.S. flag

An official website of the United States government

Dot gov

Official websites use .gov
A .gov website belongs to an official government organization in the United States.


Secure .gov websites use HTTPS
A lock ( ) or https:// means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.


Main content area

Linkage Map Construction and Quantitative Trait Locus Analysis of Agronomic and Fiber Quality Traits in Cotton

Michael A. Gore, David D. Fang, Jesse A. Poland, Jinfa Zhang, Richard G. Percy, Roy G. Cantrell, Gregory Thyssen, Alexander E. Lipka
The plant genome 2014 v.7 no.1 pp. -
Gossypium barbadense, Gossypium hirsutum, agronomic traits, chromosome mapping, cotton, fiber quality, genetic improvement, genetic markers, genetic variation, geneticists, genome, genomics, genotyping, hybrids, inbred lines, inheritance (genetics), introgression, loci, microsatellite repeats, plant breeders, population, quantitative trait loci, sequence analysis, single nucleotide polymorphism, tetraploidy
The superior fiber properties of Gossypium barbadense L. serve as a source of novel variation for improving fiber quality in Upland cotton (G. hirsutum L.), but introgression from G. barbadense has been largely unsuccessful due to hybrid breakdown and a lack of genetic and genomic resources. In an effort to overcome these limitations, we constructed a linkage map and conducted a quantitative trait locus (QTL) analysis of 10 agronomic and fiber quality traits in a recombinant inbred mapping population derived from a cross between TM-1, an Upland cotton line, and NM24016, an elite G. hirsutum line with stabilized introgression from G. barbadense. The linkage map consisted of 429 simple-sequence repeat (SSR) and 412 genotyping-by-sequencing (GBS)-based single-nucleotide polymorphism (SNP) marker loci that covered half of the tetraploid cotton genome. Notably, the 841 marker loci were unevenly distributed among the 26 chromosomes of tetraploid cotton. The 10 traits evaluated on the TM-1 × NM24016 population in a multienvironment trial were highly heritable, and most of the fiber traits showed considerable transgressive variation. Through the QTL analysis, we identified a total of 28 QTLs associated with the 10 traits. Our study provides a novel resource that can be used by breeders and geneticists for the genetic improvement of agronomic and fiber quality traits in Upland cotton.