National Key Laboratory of Crop Genetic Improvement & National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, Hubei, China.
Genome. 2012 Jun;55(6):459-70. doi: 10.1139/g2012-032. Epub 2012 Jun 6.
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 BC(1) 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.
简单重复序列（SSR）标记广泛应用于植物遗传学和育种。然而，许多在棉花中并不表现多态性的 SSR 标记。传统的 SSR 基因分型方法仅提供有关产物大小的信息。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“爱民 22”和 3-79 之间的同质 SSR 进行单链构象多态性（SSCP）分析以揭示多态性。在 4194 对同质 SSR 引物中，有 158 对（3.77%）显示多态性，揭示了 174 个多态性位点。序列分析表明，作图亲本之间 PCR 产物的差异仅归因于碱基转换或颠换，这与 SSCP 原理一致。SSCP 还显示具有 AT/TA 和 GAA/CTT 基序的 SSR 在二核苷酸和三核苷酸中分别具有更高的多态性。遗传作图将 160 个位点整合到我们的种间 BC(1)连锁图谱中，其中 5 个与与棉花纤维品质相关的 QTL 相关。本研究中讨论的技术使我们能够检测同质 SSR 的多态性，并提高现有 SSR 引物的利用效率。
