辣椒EST-SSRs分布特征及其应用

Distribution Characterization and Application of SSR-containing ESTs(EST-SSRs) in Pepper

从NCBI数据库获得116 952条辣椒ESTs序列,通过软件除去赝象序列后得86 496条非冗余序列,利用SSRLoctor软件分析后共发现1 736个微卫星分布于1 658条ESTs序列中,EST-SSRs序列出现频率为1.92%。在辣椒EST-SSRs中,二核苷酸重复类型出现频率最高,占总SSR的56.4%,其次是三核苷酸重复类型,占总SSR的23.3%。共检测到149种基序重复类型,重复基序出现频率最高的为GA/TC,AG/CT次之。1 658条EST序列中可设计出引物810对,功能注释结果表明,具有生物进程、细胞组成和分子功能的EST序列分别为297条、271条和316条。随机选择100对EST-SSR引物对17份辣椒材料进行遗传多样性分析,结果表明,80对EST-SSR引物能够得到有效扩增,其中46对引物表现出多态性扩增,每对引物检测到等位基因数1~3个,平均1.9个。经由NT-SYS2.10软件聚类,在相似系数为0.718时,供试的17份辣椒种质资源分为6个亚类,表明开发的EST-SSR可用于辣椒种质资源遗传多样性分析。

Using SSRLocator,1 658 SSR-containing ESTs（EST-SSRs） were detected by analyzing 116,952 pepper sequences retrieved from GenBank.The most abundant repeat type was dinucleotide（56.4%） followed by tri-（23.2%）,penta-nucleotide（9.7%）,hexa-（5.5%）,and tetra-（5.1%）.The top six repeat types included GA/TC（23.33%）,AG/CT（16.99%）,AT/TA（7.49%）,TA/AT（5.01%）,AGA/TCT（2.48%） and AAT/ATT（2.25%）.According to 1 658 EST-SSRs,a total of 810 primer pairs were designed.Corresponding sequences were annotated,showing that 297,271 and 316 EST sequences having function in cellular component,biological process and molecular function,respectively.Genetic diversity of 17 pepper cultivars was estimated using 100 randomly selected primers pairs.The results revealed that 80 primer pairs could be used for effective amplification and 46 of which exhibited polymorphism,with an average of 1.9 alleles.These 17 pepper cultivars were divided into six groups by NTSYS2.10 based on the similarity coefficient of 0.718.The genetic correlation of 17 cultivars was related to their origin,and the results indicated that the developed SSRs from ESTs of Capsicum will facilitate the analysis of diversity in pepper.