Characterization and Development of EST-SSRs by Deep Transcriptome Sequencing in Chinese Cabbage (Brassica rapa L. ssp. pekinensis).
Characterization and Development of EST-SSRs by Deep Transcriptome Sequencing in Chinese Cabbage (Brassica rapa L. ssp. pekinensis).
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通过大白菜（Brassica rapa L. ssp pekinensis）深度转录组测序对 EST-SSR 进行表征和开发
DOI：
10.1155/2015/473028
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发表时间：
2015
影响因子：
2.9
通讯作者：
Gao J
中科院分区：
文献类型：
--
作者：
Ding Q;Li J;Wang F;Zhang Y;Li H;Zhang J;Gao J
简单重复序列（SSR）是群体分析中最重要的分子标记之一，已广泛应用于植物遗传作图和分子育种。位于基因编码区的EST-SSR标记在QTL定位、基因打靶和标记辅助育种等方面具有潜在的优势。在这项研究中，我们调查了51，694个非冗余单基因，使用Solexa/Illumina平台从深度转录组测序的干净读数组装，用于鉴定和开发大白菜的EST-SSR。共鉴定和鉴定了10,420个12 bp以上的EST-SSR，其中2744个为新的EST-SSR，2317个为已知的EST-SSR。共设计7877对引物，扩增1561个EST-SSR位点，筛选出24对EST-SSR引物进行引物评价。在19个EST-SSR位点（79.2%）中，成功扩增出高质量的扩增产物。24个大白菜品种中有17个（89.5%）表现多态性。对每个多态位点的多态性等位基因进行测序，结果表明，大部分多态性是由于SSR重复序列的变异引起的。本研究鉴定和表征的EST-SSRs对于开发大白菜遗传和分子育种的新工具具有重要意义。
Simple sequence repeats (SSRs) are among the most important markers for population analysis and have been widely used in plant genetic mapping and molecular breeding. Expressed sequence tag-SSR (EST-SSR) markers, located in the coding regions, are potentially more efficient for QTL mapping, gene targeting, and marker-assisted breeding. In this study, we investigated 51,694 nonredundant unigenes, assembled from clean reads from deep transcriptome sequencing with a Solexa/Illumina platform, for identification and development of EST-SSRs in Chinese cabbage. In total, 10,420 EST-SSRs with over 12 bp were identified and characterized, among which 2744 EST-SSRs are new and 2317 are known ones showing polymorphism with previously reported SSRs. A total of 7877 PCR primer pairs for 1561 EST-SSR loci were designed, and primer pairs for twenty-four EST-SSRs were selected for primer evaluation. In nineteen EST-SSR loci (79.2%), amplicons were successfully generated with high quality. Seventeen (89.5%) showed polymorphism in twenty-four cultivars of Chinese cabbage. The polymorphic alleles of each polymorphic locus were sequenced, and the results showed that most polymorphisms were due to variations of SSR repeat motifs. The EST-SSRs identified and characterized in this study have important implications for developing new tools for genetics and molecular breeding in Chinese cabbage.