辣椒疫霉EST-SSRs标记的发掘

通过对GenBank上发布的55 848条辣椒疫霉EST的鉴定,在328条EST中发现331个SSR.在筛选的EST序列中SSR平均密度为每23.7 kb含有1个SSR.在鉴定的SSR中,三核苷酸重复基元的SSR类型最多,占鉴定总数的59.5%;其次为二核苷酸乖复基元的SSR类型,为39.3%;四核苷酸重复基元的SSR类型最少,为1.2%.设计40对SSR引物对5个辣椒疫霉菌株基因组DNA进行PCR扩增,有27对引物扩增出SSR特征条带,其中有18对引物在5个辣椒疫霉菌株间扩增出多态性条带25条.基于SSR标记进行聚类分析,可将5个检测大豆疫霉菌菌株划分为3类.该研究是辣椒疫霉的SSR标记开发的首次报道,为辣椒疫霉的遗传变异和分子作图等分析提供了一种有效的分子标记系统.

Mining simple sequence repeats markers in expressed sequence tags of Phytophthora capsici

Simple sequence repeats (SSRs) were identified through bioinformatic mining of 55 848 publicly available expressed sequence tags (ESTs) of Phytophthora capsici in dbEST GenBank. The 331 SSRs were identified in 328 unique ESTs with each containing one or two SSRs and an average density of one SSR per 23. 7 kb of EST sequence screened. The trinucleotide motifs were the most abundant type of SSRs (59.5%) followed by dinucleotide (39.3%) and tetranucleotide repeats (1.2%). Forty EST-SSR primer pairs were designed and 27 primer pairs amplified characteristic SSR fragments of expected sizes when tested with genomic DNA of five P. capsici strains. Eighteen primer pairs amplified polymorphic microsatellite markers and 25 polymorphic markers were characterized for the five test strains. The dendrogram of the five strains was generated using the UPGMA clustering methods and the strains were clustered into three groups according to the 25 polymorphic EST-SSR markers. This is the first report of developing SSR markers of P. capsici that may contrib-ute to more comprehensive analyses of genetic diversity of this important pathogen.