Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China.
BMC Plant Biol. 2011 Oct 20;11:139. doi: 10.1186/1471-2229-11-139.
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.
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.
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.
目前，甘薯（Ipomoea batatas）中遗传标记资源的可用性有限，这阻碍了该物种的遗传研究。有必要开发更多的分子标记，以便在甘薯遗传研究中潜在应用。随着新一代测序技术的发展，大量甘薯转录序列已经生成，可通过数据挖掘来鉴定 SSR 标记。
本研究通过对 181615 个 EST 进行分析，以鉴定和开发 SSR 标记。从 7163 个含有 SSR 的独特 EST 中共鉴定到 8294 个 SSR，平均每个 SSR 出现在 7.1kb 的 EST 序列中，三核苷酸基序（42.9%）最为丰富，其次是二核苷酸（41.2%）、四核苷酸（9.2%）、五核苷酸（3.7%）和六核苷酸（3.1%）重复类型。前 5 个基序包括 AG/CT（26.9%）、AAG/CTT（13.5%）、AT/TA（10.6%）、CCG/CGG（5.8%）和 AAT/ATT（4.5%）。去除甘薯已发表的 EST-SSR 可能的重复后，共鉴定到 7958 个非重复 SSR 基序。基于这些含有 SSR 的序列，设计了 1060 对高质量的 SSR 引物，并用于验证扩增，评估一个作图群体（E Shu 3 Hao 和 Guang 2k-30）的两个亲本以及 8 个栽培甘薯之间的多态性。结果表明，816 对引物可以产生可重复和强扩增产物，其中 195（23.9%）和 342（41.9%）对引物在 E Shu 3 Hao 和 Guang 2k-30 以及 8 个栽培甘薯之间表现出多态性。
本研究深入了解了甘薯 EST-SSR 的频率、类型和分布，并成功开发了栽培甘薯的 EST-SSR 标记。这些 EST-SSR 标记可以丰富甘薯群体目前的分子标记资源，并可用于栽培甘薯和相关的旋花科植物的定性和定量性状作图、标记辅助选择、进化和遗传多样性研究。
