Development of EST-based SNP and InDel markers and their utilization in tetraploid cotton genetic mapping.
Development of EST-based SNP and InDel markers and their utilization in tetraploid cotton genetic mapping.
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基于EST的SNP和InDel标记的开发及其在四倍体棉花遗传图谱中的应用
DOI：
10.1186/1471-2164-15-1046
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发表时间：
2014-12-01
期刊：
影响因子：
4.4
通讯作者：
Lin Z
中科院分区：
文献类型：
--
作者：
Li X;Gao W;Guo H;Zhang X;Fang DD;Lin Z
背景分子标记的可用性已被证明是促进植物育种进展的有效工具，对于棉花等研究较少的作物来说，这一点尤其重要。鉴于单核苷酸多态(SNPs)和插入-缺失多态(INDELs)具有明显的优势，本研究利用表达序列标签(ESTs)对棉花的SNPs和INDELs进行了分析，旨在开发更多的分子标记。Barbadense，MiningG。并对3‘非翻译区(3’UTR)序列进行了分析。根据单链构象多态性(SSCP)分析，利用作图群体的双亲进行标记多态性分析。其中多态标记137个，占10.16%，共检测到142个座位。利用BC_1群体进行连锁分析，在26条染色体上定位了133个座位。对SNPs碱基变异的统计分析表明，碱基转换占碱基变异总数的55.78%，基因本体论表明棉花基因的SNPs差异很大，每个基因含有1.00~24.00个SNPs。对随机选择的三个SNP标记进行Sanger测序，结果显示预测序列与实际测序结果存在差异。结论在电子分析中，开发EST-SNP/Indel标记是一把双刃剑。一方面，所设计的标记可以很好地应用于四倍体棉花遗传作图。它在揭示棉花基因的转换偏好和SNP频率方面有一定的作用。另一方面，所设计的标记和多态标记的开发效率较低。
BackgroundAvailability of molecular markers has proven to be an efficient tool in facilitating progress in plant breeding, which is particularly important in the case of less researched crops such as cotton. Considering the obvious advantages of single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (InDels), expressed sequence tags (ESTs) were analyzedin silicoto identify SNPs and InDels in this study, aiming to develop more molecular markers in cotton.ResultsA total of 1,349 EST-based SNP and InDel markers were developed by comparing ESTs betweenGossypium hirsutumandG. barbadense, miningG. hirsutumunigenes, and analyzing 3′ untranslated region (3′UTR) sequences. The marker polymorphisms were investigated using the two parents of the mapping population based on the single-strand conformation polymorphism (SSCP) analysis. Of all the markers, 137 (10.16%) were polymorphic, and revealed 142 loci. Linkage analysis using a BC1population mapped 133 loci on the 26 chromosomes. Statistical analysis of base variations in SNPs showed that base transitions accounted for 55.78% of the total base variations and gene ontology indicated that cotton genes varied greatly in harboring SNPs ranging from 1.00 to 24.00 SNPs per gene. Sanger sequencing of three randomly selected SNP markers revealed discrepancy between thein silicopredicted sequences and the actual sequencing results.ConclusionsIn silicoanalysis is a double-edged blade to develop EST-SNP/InDel markers. On the one hand, the designed markers can be well used in tetraploid cotton genetic mapping. And it plays a certain role in revealing transition preference and SNP frequency of cotton genes. On the other hand, the developmental efficiency of markers and polymorphism of designed primers are comparatively low.
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影响因子：
3.7
作者：
Li X;Yuan D;Zhang J;Lin Z;Zhang X
通讯作者：
Zhang X
影响因子：
5.4
作者：
Byers, Robert L.;Harker, David B.;Yourstone, Scott M.;Maughan, Peter J.;Udall, Joshua A.
通讯作者：
Udall, Joshua A.
影响因子：
5.4
作者：
An, Chuanfu;Saha, Sukumar;Stelly, David M.
通讯作者：
Stelly, David M.
影响因子：
3.1
作者：
Li, Ximei;Yuan, Daojun;Zhang, Xianlong
通讯作者：
Zhang, Xianlong
影响因子：
2
作者：
Lin, Z;He, D;Stewart, JM
通讯作者：
Stewart, JM