Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas).
Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas).
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栽培甘薯 (Ipomoea batatas) EST 衍生 SSR 标记的表征和开发
DOI：
10.1186/1471-2229-11-139
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发表时间：
2011-10-20
影响因子：
5.3
通讯作者：
Zhang X
中科院分区：
文献类型：
--
作者：
Wang Z;Li J;Luo Z;Huang L;Chen X;Fang B;Li Y;Chen J;Zhang X
背景：目前甘薯遗传标记资源有限，阻碍了甘薯遗传研究。因此，有必要开发更多的分子标记用于甘薯遗传研究。利用新一代测序技术，我们获得了大量甘薯转录序列，并可用于SSR标记的数据挖掘。结果：本研究共收集了181，615条EST序列，用于SSR标记的筛选和开发。从7,163个含有SSR的独特EST中总共鉴定出8,294个SSR。平均每7.1kb的EST序列中有1个SSR位点，其中以三核苷酸重复序列（42.9%）最多，其次为二核苷酸重复序列（41.2%）、四核苷酸重复序列（9.2%）、五核苷酸重复序列（3.7%）和六核苷酸重复序列（3.1%）。前5位基序依次为AG/CT（26.9%）、AAG/CTT（13.5%）、AT/TA（10.6%）、CCG/CGG（5.8%）和AAT/ATT（4.5%）。在剔除重复序列的基础上，共鉴定出7,958个非重复序列。根据这些SSR标记序列设计了1,060对高质量的SSR引物，对鄂薯3号和广2k-30两个作图群体的两个亲本和8份栽培甘薯材料进行了扩增验证和多态性分析。结果表明：816对引物可扩增出重复性好、扩增能力强的扩增产物，其中鄂薯3号和广2k-30之间多态性引物195对（23.9%），8个甘薯品种之间多态性引物342对（41.9%）。这些EST-SSR标记丰富了甘薯群体的分子标记资源，为甘薯及其近缘种的定性和定量性状定位、分子标记辅助选择、进化和遗传多样性研究奠定了基础。
Background:Currently there exists a limited availability of genetic marker resources in sweetpotato (Ipomoea batatas), which is hindering genetic research in this species. It is necessary to develop more molecular markers for potential use in sweetpotato genetic research. With the newly developed next generation sequencing technology, large amount of transcribed sequences of sweetpotato have been generated and are available for identifying SSR markers by data mining.Results:In this study, we investigated 181,615 ESTs for the identification and development of SSR markers. In total, 8,294 SSRs were identified from 7,163 SSR-containing unique ESTs. On an average, one SSR was found per 7.1 kb of EST sequence with tri-nucleotide motifs (42.9%) being the most abundant followed by di- (41.2%), tetra- (9.2%), penta- (3.7%) and hexa-nucleotide (3.1%) repeat types. The top five motifs included AG/CT (26.9%), AAG/CTT (13.5%), AT/TA (10.6%), CCG/CGG (5.8%) and AAT/ATT (4.5%). After removing possible duplicate of published EST-SSRs of sweetpotato, a total of non-repeat 7,958 SSR motifs were identified. Based on these SSR-containing sequences, 1,060 pairs of high-quality SSR primers were designed and used for validation of the amplification and assessment of the polymorphism between two parents of one mapping population (E Shu 3 Hao and Guang 2k-30) and eight accessions of cultivated sweetpotatoes. The results showed that 816 primer pairs could yield reproducible and strong amplification products, of which 195 (23.9%) and 342 (41.9%) primer pairs exhibited polymorphism between E Shu 3 Hao and Guang 2k-30 and among the 8 cultivated sweetpotatoes, respectively.Conclusion:This study gives an insight into the frequency, type and distribution of sweetpotato EST-SSRs and demonstrates successful development of EST-SSR markers in cultivated sweetpotato. These EST-SSR markers could enrich the current resource of molecular markers for the sweetpotato community and would be useful for qualitative and quantitative trait mapping, marker-assisted selection, evolution and genetic diversity studies in cultivated sweetpotato and related Ipomoea species.
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影响因子：
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作者：
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通讯作者：
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