Abstract:

In this study, a total of 45 699 ESTs derived from deep sequencing of seed transcriptome in tartary buckwheat were used for screening of SSR loci. Using MISA software, a total of 2 700 SSRs were detected in 2 624 ESTs, and the mean distance between SSRs was 1/1.73 kb. The proportion of EST contained SSR was raised with the length of EST increasing. Higher proportion of EST contained SSR was observed among EST with length above 800 bp compared to EST with length below 800 bp. Mononucleotide, dinucleotide and trinucleotide SSRs were major types of tartary buckwheat EST-SSR, accounting for 52.11%, 13.33% and 30.63% of the total SSR, respectively, among which, (A)n, (AG)n and (AAG)n were repeated advantage motifs accounting for 51.85%, 7.11% and 8.93% of the total SSR, respectively. 150 pairs EST-SSR primer were designed and compounded, among which 91 pairs primer (60.67%) yielded ideal PCR products in 40 assessions of tartary buckwheat germplasm resources, and 30 of them (32.97%)showed polymorphic bands with 3.53 alleles per primer pair; polymorphism information content (PIC) ranged between 0.10~0.71, with an average of 0.40. These results indicated that exploring SSR markers from transcriptome EST of tartary buckwheat by large scale was a convenient and feasible way.

Key words: buckwheat, transcriptome sequencing, EST, SSR

摘要：

利用Misa软件对苦荞种子转录组高通量测序获得的45 699条EST序列进行了SSR位点扫描，共得到2 700个SSR位点，分布于2 624条EST序列中，SSR位点平均距离为1/1.73 kb。随着EST序列长度的增加，含SSR位点序列的比例也随之升高，800 bp以上EST序列含SSR的比例明显高于800 bp以下序列。单核苷酸、二核苷酸和三核苷酸重复是苦荞EST-SSR主导类型，分别占总SSR的52.11%、13.33%和30.63%,其中(A)n、(AG)n和(AAG)n是单核苷酸、二核苷酸和三核苷酸的优势重复基序，分别占总SSR的51.85%、7.11%和8.93%。设计合成了150对 EST-SSR 引物，其中91对引物（60.67%）在40份苦荞种质中获得有效扩增，30对引物（32.97%）具有多态性。平均每对引物能检测到3.53个等位变异;多态信息含量（PIC）在 0.10~0.71之间，平均达0.40。以上结果说明，从苦荞转录组EST序列中大规模开发SSR标记是一条简便而可行的途径。

关键词: 苦荞；转录组测序；EST；SSR