Increasing cotton genome coverage with polymorphic SSRs as revealed by SSCP
Increasing cotton genome coverage with polymorphic SSRs as revealed by SSCP
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DOI：
10.1139/g2012-032
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发表时间：
2012-06-01
期刊：
影响因子：
3.1
通讯作者：
Zhang, Xianlong
中科院分区：
文献类型：
--
作者：
Li, Ximei;Yuan, Daojun;Zhang, Xianlong
简单序列重复（SSR）标记广泛应用于植物遗传和育种中。然而，有许多 SSR 标记没有揭示棉花的多态性。传统的 SSR 基因分型方法仅提供有关产品大小的信息。这使得许多标记多态性未被检测到，从而降低了 SSR 的实用性。在本研究中，对两个作图亲本“Emian22”和3-79之间的单态SSR进行单链构象多态性(SSCP)分析以揭示多态性。在4194对单态SSR引物中，158对（3.77%）表现出多态性，并揭示了174个多态性位点。序列分析表明，定位亲本之间PCR产物的差异完全是由于碱基转换或颠换造成的，这符合SSCP原理。 SSCP还揭示，具有AT/TA和GAA/CTT基序的SSR分别在二核苷酸和三核苷酸方面具有更多的多态性。遗传图谱将 160 个基因座整合到我们的种间 BC1 连锁图谱中，其中 5 个与棉花纤维品质相关的 QTL 相关。本研究讨论的技术使我们能够检测单态SSR的多态性，并提高现有SSR引物的利用效率。
Simple sequence repeat (SSR) markers are widely used in plant genetics and breeding. However, there are many SSR markers that do not reveal polymorphism in cotton. Traditional SSR genotyping methods only provide information on product sizes. This leaves many marker polymorphism undetected, thus, lowering the utility of SSRs. In the present study, monomorphic SSRs between two mapping parents, 'Emian22' and 3-79, were subjected to single-strand conformation polymorphism (SSCP) analysis to reveal polymorphism. Of the 4194 monomorphic SSR primer pairs, 158 pairs (3.77%) showed polymorphism and revealed 174 polymorphic loci. Sequence analysis showed that the differences in PCR products between the mapping parents were solely due to base transition or transversion, which was in agreement with SSCP principles. SSCP also revealed SSRs with motifs of AT/TA and GAA/CTT were more polymorphic in dinucleotides and trinucleotides, respectively. Genetic mapping integrated 160 loci into our interspecific BC1 linkage map, 5 of which associated with QTLs related to cotton fiber quality. The technique discussed in the present study enables us to detect polymorphism of monomorphic SSRs, and increase the utilization efficiency of the existing SSR primers.