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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 #308277

Research Project: Developing Genomic and Genetic Tools for Exploiting Cotton Genetic Variation

Location: Crop Germplasm Research

Title: SNP discovery in complex allotetraploid genomes (Gossypium spp., Malvaceae) using genotyping by sequencing

Author
item LOGAN-YOUNG, CARLA - Texas A&M University
item Yu, John
item VERMA, SURENDER - Central Institute For Cotton Research
item Percy, Richard
item PEPPER, ALAN - Texas A&M University

Submitted to: Applications in Plant Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/3/2015
Publication Date: 3/9/2015
Citation: Logan-Young, C.J., Yu, J., Verma, S.K., Percy, R.G., Pepper, A.E. 2015. SNP discovery in complex allotetraploid genomes (Gossypium spp., Malvaceae) using genotyping by sequencing. Applications in Plant Sciences. 3(3):1400077.

Interpretive Summary: Expanding the genetic base for cotton improvement is essential, but it requires the development of very large numbers of portable markers that are based on single nucleotide polymorphism (SNP) between individual cotton plants. This study took advantage of dramatic decreases in the cost of the Illumina next-generation DNA sequencing, and it collected 54 million reads from restriction enzyme-digested DNA libraries of a diverse panel of several cotton species. Using a computer software program called STACKs, 25,529 new cotton SNP markers were identified including those that are polymorphic in one to three loci at both interspecific and intraspecific levels among cotton species. Intraspecific comparisons revealed 6.7-11.6% for the most informative class of polymorphisms, and interspecific comparisons 15.0%-16.4%. This collection of cotton SNP markers, developed by a simplified genotyping-by-sequencing (GBS) technique, is a valuable genomic resource that will facilitate further investigations for genetic mapping and marker-assisted selection for traits of interest in cotton improvement.

Technical Abstract: Dramatic decreases in the cost of DNA sequencing have enabled the development of very large numbers of markers based on single nucleotide polymorphism (SNP) for phylogenetic studies, population genetics, linkage mapping, marker-assisted breeding and other applications. Using Illumina next-generation sequencing, 54 million reads were collected from restriction enzyme-digested DNA libraries of a diversity of Gossypium taxa. Loci with one to three SNPs were discovered using the Stacks software package, yielding 25,529 new cotton SNP markers, including those that are polymorphic at both interspecific and intraspecific levels. Frequencies of the most informative class of polymorphisms ranged from 6.7-11.6% in intraspecific comparisons and from 15.0%-16.4% in interspecific comparisons. This resource provides dual-homozygous (aa/bb) marker polymorphisms likely representing alternative alleles at single loci. The methylation-sensitive restriction enzyme HinP1I yielded substantial numbers of polymorphic genotyping-by-sequencing (GBS)-derived SNP markers in gene-rich components of the genome.