Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat
Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat
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DOI：
10.1007/s00438-003-0921-4
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发表时间：
2003-12-01
影响因子：
3.1
通讯作者：
Balyan, HS
中科院分区：
文献类型：
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作者：
Gupta, PK;Rustgi, S;Balyan, HS
在属于面包小麦 (Triticum aestivum L.) 的 15,000 个 EST（表达序列标签）中鉴定出近 900 个 SSR（简单序列重复）。 SSR 由其最小长度定义，范围为 14 至 21 bp。最大长度范围为 24 至 87 bp，具体取决于重复单元本身的长度 (1-7 bp)。 SSR 的平均密度为每 9.2 kb 筛选的 EST 序列 1 个 SSR。三核苷酸重复是检测到的最丰富的 SSR。作为代表性样本，设计了 78 个引物对，这些引物对也用于使用 0.01 的截止 E（期望）值筛选大麦和小麦（栽培小麦 D 基因组的供体）的 dbEST 条目。基于计算机分析，高达55.12%的引物对表现出从小麦到大麦的可转移性，表明SSR侧翼的序列不仅在单个属内保守，而且在禾本科相关属之间也保守。合成了 78 个 SSR 的引物对，并成功用于以下研究：(1) 它们向 18 个相关野生物种和 5 个谷物物种（大麦、燕麦、黑麦、水稻和玉米）的可转移性； (2)我们现有的四个作图群体的父母之间的多态性。 20 个 EST-SSR 引物的子集还用于评估 52 个优良外来小麦基因型集合中的遗传多样性。这样做的目的是比较它们相对于我们之前出于相同目的使用同一组 52 个面包小麦基因型的其他分子标记（gSSR、AFLP 和 SAMPL）的效用。尽管仅检测到低水平的多态性，但相对于基因组 SSR 观察到的多态性，该研究表明 EST-SSR 可以成功地用于多种目的，并且实际上可能证明优于从基因组文库中提取的 SSR 标记，用于多样性估计和可转移性。
Nearly 900 SSRs (simple sequence repeats) were identified among 15,000 ESTs (expressed sequence tags) belonging to bread wheat ( Triticum aestivum L.). The SSRs were defined by their minimum length, which ranged from 14 to 21 bp. The maximum length ranged from 24 to 87 bp depending upon the length of the repeat unit itself (1-7 bp). The average density of SSRs was one SSR per 9.2 kb of EST sequence screened. The trinucleotide repeats were the most abundant SSRs detected. As a representative sample, 78 primer pairs were designed, which were also used to screen the dbEST entries for Hordeum vulgare and Triticum tauschii (donor of the D-genome of cultivated wheat) using a cut-off E (expectation) value of 0.01. On the basis of in silico analysis, up to 55.12% of the primer pairs exhibited transferability from Triticum to Hordeum, indicating that the sequences flanking the SSRs are not only conserved within a single genus but also between related genera in Poaceae. Primer pairs for the 78 SSRs were synthesized and used successfully for the study of (1) their transferability to 18 related wild species and five cereal species (barley, oat, rye, rice and maize); and (2) polymorphism between the parents of four mapping populations available with us. A subset of 20 EST-SSR primers was also used to assess genetic diversity in a collection of 52 elite exotic wheat genotypes. This was done with a view to compare their utility relative to other molecular markers (gSSRs, AFLPs, and SAMPL) previously used by us for the same purpose with the same set of 52 bread wheat genotypes. Although only a low level of polymorphism was detected, relative to that observed with genomic SSRs, the study suggested that EST-SSRs can be successfully used for a variety of purposes, and may actually prove superior to SSR markers extracted from genomic libraries for diversity estimation and transferability.