Molecular Mapping of Restriction-Site Associated DNA Markers In Allotetraploid Upland Cotton

PLoS One. 2015 Apr 20;10(4):e0124781. doi: 10.1371/journal.pone.0124781. eCollection 2015.

Abstract

Upland cotton (Gossypium hirsutum L., 2n = 52, AADD) is an allotetraploid, therefore the discovery of single nucleotide polymorphism (SNP) markers is difficult. The recent emergence of genome complexity reduction technologies based on the next-generation sequencing (NGS) platform has greatly expedited SNP discovery in crops with highly repetitive and complex genomes. Here we applied restriction-site associated DNA (RAD) sequencing technology for de novo SNP discovery in allotetraploid cotton. We identified 21,109 SNPs between the two parents and used these for genotyping of 161 recombinant inbred lines (RILs). Finally, a high dense linkage map comprising 4,153 loci over 3500-cM was developed based on the previous result. Using this map quantitative trait locus (QTLs) conferring fiber strength and Verticillium Wilt (VW) resistance were mapped to a more accurate region in comparison to the 1576-cM interval determined using the simple sequence repeat (SSR) genetic map. This suggests that the newly constructed map has more power and resolution than the previous SSR map. It will pave the way for the rapid identification of the marker-assisted selection in cotton breeding and cloning of QTL of interest traits.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosome Mapping / methods*
  • DNA, Plant / chemistry*
  • Genetic Linkage
  • Genetic Markers*
  • Genome
  • Genome, Plant
  • Genotype
  • Gossypium / genetics*
  • High-Throughput Nucleotide Sequencing
  • Microsatellite Repeats
  • Polymorphism, Single Nucleotide
  • Polyploidy
  • Quantitative Trait Loci
  • Sequence Analysis, DNA
  • Temperature

Substances

  • DNA, Plant
  • Genetic Markers

Grants and funding

This work was supported by the Major State Basic Research Development Program of China (973 Program) (2011CB109300), the National High Technology Research and Development Program of China (863 Program) (2011AA10A102), and Jiangsu province (BE2012329). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.