Department of Biology, Texas A&M University, College Station, Texas 77843 USA.
USDA-ARS, Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, Texas 77845 USA.
Appl Plant Sci. 2015 Mar 9;3(3). doi: 10.3732/apps.1400077. eCollection 2015 Mar.
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.
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.
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.
在具有复杂异源四倍体基因组的植物中，单核苷酸多态性（SNP）标记的发现常常受到同系基因座（以及旁系和直系基因座）的存在所干扰。在这里，我们提出了一种筛选代表直系基因座的 SNP 的策略。
使用 Illumina 新一代测序，从各种棉属植物的限制性内切酶消化 DNA 文库中收集了 5400 万条reads。使用 Stacks 软件包发现了具有一个到三个 SNP 的基因座，产生了 25529 个新的棉花 SNP 组合，包括在种间和种内水平都多态性的 SNP 组合。预测的双纯合（aa/bb）标记多态性的频率在种内比较中占总共享片段的 6.7-11.6%，在种间比较中占 15.0-16.4%。
该资源提供了双纯合（aa/bb）标记多态性。无论是在计算机模拟还是实验验证方面的努力都表明，这些标记富含具有替代等位基因的单一同源基因座的纯合子。
