Directorate of Oilseeds Research, Rajendranagar, Hyderabad, Andhra Pradesh, India.
Genome. 2011 Aug;54(8):684-91. doi: 10.1139/g11-033. Epub 2011 Aug 17.
Expressed sequence tag (EST) databases offer opportunity for the rapid development of simple sequence repeat (SSR) markers in crops. Sequence assembly and clustering of 57 895 ESTs of castor bean resulted in the identification of 10 960 unigenes (6459 singletons and 4501 contigs) having 7429 SSRs. On an average, the unigenes contained 1 SSR for every 1.23 kb of unigene sequence. The identified SSRs mostly consisted of dinucleotide (62.4%) and trinucleotide (33.5%) repeats. The AG class was the most common among the dinucleotide motifs (68.9%), whereas the AAG class (25.9%) was predominant among the trinucleotide motifs. A total of 611 primer pairs were designed for the SSRs, having repeat length more than or equal to 20 nucleotides, of which a set of 130 markers were tested and 92 of these yielding robust amplicons were analyzed for their utility in genetic purity assessment of castor bean hybrids. Nine markers were able to detect polymorphism between the parental lines of nine commercial castor bean hybrids (DCH-32, DCH-177, DCH-519, GCH-2, GCH-4, GCH-5, GCH-6, GCH-7, and RHC-1), and their utility in genetic purity testing was demonstrated. These novel EST-SSR markers would be a valuable addition to the growing molecular marker resources that could be used in genetic improvement programmes of castor bean.
表达序列标签 (EST) 数据库为作物中简单重复序列 (SSR) 标记的快速开发提供了机会。对蓖麻的 57895 个 EST 进行序列组装和聚类，鉴定出 10960 个单基因 (6459 个单基因和 4501 个基因簇)，其中包含 7429 个 SSR。平均而言，每个单基因序列 1.23 kb 含有 1 个 SSR。鉴定出的 SSR 主要由二核苷酸 (62.4%) 和三核苷酸 (33.5%) 重复组成。二核苷酸基序中最常见的是 AG 类 (68.9%)，而三核苷酸基序中最常见的是 AAG 类 (25.9%)。共设计了 611 对 SSR 引物，重复长度大于或等于 20 个核苷酸，其中 130 对引物进行了测试，分析了 92 对产生稳健扩增子的引物在蓖麻杂种遗传纯度评估中的应用。9 个标记能够检测 9 个商业蓖麻杂种 (DCH-32、DCH-177、DCH-519、GCH-2、GCH-4、GCH-5、GCH-6、GCH-7 和 RHC-1) 亲本系之间的多态性，并证明了其在遗传纯度检测中的应用。这些新的 EST-SSR 标记将是日益增长的分子标记资源的宝贵补充，可用于蓖麻的遗传改良计划。
