title: SNP discovery in complex allotetraploid genomes (Gossypium spp., Malvaceae) using genotyping by sequencing.
abstract: OBJECTIVE
  Single-nucleotide polymorphism (SNP) marker discovery in plants with complex allotetraploid genomes is often confounded by the presence of homeologous loci (along with paralogous and orthologous loci). Here we present a strategy to filter for SNPs representing orthologous loci.
  
  
  RESULTS
  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 combinations, including those that are polymorphic at both interspecific and intraspecific levels. Frequencies of predicted dual-homozygous (aa/bb) marker polymorphisms ranged from 6.7-11.6% of total shared fragments in intraspecific comparisons and from 15.0-16.4% in interspecific comparisons.
  
  
  CONCLUSIONS
  This resource provides dual-homozygous (aa/bb) marker polymorphisms. Both in silico and experimental validation efforts demonstrated that these markers are enriched for single orthologous loci that are homozygous for alternative alleles.
authors: Department of Biology, Texas A&M University, College Station, Texas 77843 USA.
authors: Carla Jo
authors: CJ
authors: Logan-Young
authors: USDA-ARS, Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, Texas 77845 USA.
authors: John Z
authors: JZ
authors: Yu
authors: Department of Biology, Texas A&M University, College Station, Texas 77843 USA.
authors: Surender K
authors: SK
authors: Verma
authors: USDA-ARS, Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, Texas 77845 USA.
authors: Richard G
authors: RG
authors: Percy
authors: Department of Biology, Texas A&M University, College Station, Texas 77843 USA.
authors: Alan E
authors: AE
authors: Pepper
keywords: Gossypium; genotyping by sequencing; interspecific; intraspecific; next-generation sequencing; polyploid; single-nucleotide polymorphisms