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.
Highlights
Upland cotton (Gossypium hirsutum L.) accounts for >95% of the world’s cotton production
single nucleotide polymorphism (SNP) markers have been widely used in genetic studies, mainly for the purposes of building genetic maps, investigating population genomics, and phylogeography
Poland et al were able to map over 34,000 SNPs and 240,000 tags on the Oregon Wolfe Barley reference map, and 20,000 SNPs and 367,000 tags on the Synthetic W97846Opata85 (SynOpDH) wheat reference map, they constructed a de novo genetic map using only SNP markers from GBS data [10]
Summary
Upland cotton (Gossypium hirsutum L.) accounts for >95% of the world’s cotton production. Many complexity reduction approaches such as genotyping-by-sequencing (GBS), IIB digest restriction-site associated DNA (2b-RAD) and reduced-representation libraries (RRLs) based on NGS platforms have been developed [6,7] These approaches have reduced the complexity of the genome and have been successfully applied in a number of organisms with large complex genomes, including wheat and oilseed rape. RAD sequencing provides a flexible, inexpensive platform for the genome scale genetic markers mining [8,9,10,11] To our knowledge, this method has not been applied to SNP based association studies in allotetraploid cotton
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