Zhu Qian-Hao, Spriggs Andrew, Taylor Jennifer M, Llewellyn Danny, Wilson Iain
CSIRO Plant Industry, Canberra, ACT 2601, Australia
CSIRO Plant Industry, Canberra, ACT 2601, Australia.
G3 (Bethesda). 2014 Aug 7;4(10):1893-905. doi: 10.1534/g3.114.012542.
Varietal single nucleotide polymorphisms (SNPs) are the differences within one of the two subgenomes between different tetraploid cotton varieties and have not been practically used in cotton genetics and breeding because they are difficult to identify due to low genetic diversity and very high sequence identity between homeologous genes in cotton. We have used transcriptome and restriction site-associated DNA sequencing to identify varietal SNPs among 18 G. hirsutum varieties based on the rationale that varietal SNPs can be more confidently called when flanked by subgenome-specific SNPs. Using transcriptome data, we successfully identified 37,413 varietal SNPs and, of these, 22,121 did not have an additional varietal SNP within their 20-bp flanking regions so can be used in most SNP genotyping assays. From restriction site-associated DNA sequencing data, we identified an additional 3090 varietal SNPs between two of the varieties. Of the 1583 successful SNP assays achieved using different genotyping platforms, 1363 were verified. Many of the SNPs behaved as dominant markers because of coamplification from homeologous loci, but the number of SNPs acting as codominant markers increased when one or more subgenome-specific SNP(s) were incorporated in their assay primers, giving them greater utility for breeding applications. A G. hirsutum genetic map with 1244 SNP markers was constructed covering 5557.42 centiMorgan and used to map qualitative and quantitative traits. This collection of G. hirsutum varietal SNPs complements existing intra-specific SNPs and provides the cotton community with a valuable marker resource applicable to genetic analyses and breeding programs.
品种单核苷酸多态性（SNP）是不同四倍体棉花品种两个亚基因组之一内的差异，由于棉花中同源基因间遗传多样性低且序列一致性非常高，难以识别，因此尚未在棉花遗传育种中实际应用。我们利用转录组和限制性位点相关DNA测序，基于这样的原理来鉴定18个陆地棉品种间的品种SNP：当品种SNP两侧有亚基因组特异性SNP时，能更可靠地进行鉴定。利用转录组数据，我们成功鉴定出37413个品种SNP，其中22121个在其20bp侧翼区域内没有额外的品种SNP，因此可用于大多数SNP基因分型检测。从限制性位点相关DNA测序数据中，我们在两个品种间又鉴定出3090个品种SNP。在使用不同基因分型平台进行的1583次成功的SNP检测中，有1363次得到验证。由于同源位点的共扩增，许多SNP表现为显性标记，但当在检测引物中加入一个或多个亚基因组特异性SNP时，作为共显性标记的SNP数量增加，使其在育种应用中更具实用性。构建了一张包含1244个SNP标记的陆地棉遗传图谱，覆盖5557.42厘摩，并用于定位质量性状和数量性状。这组陆地棉品种SNP补充了现有的种内SNP，为棉花界提供了一种适用于遗传分析和育种计划的宝贵标记资源。
