Li Xiao Bai, Zhang Ming Long, Cui Hai Rui
Institute of Nuclear and Agricultural Sciences, Zhejiang University, Hangzhou 310029, China.
Fen Zi Xi Bao Sheng Wu Xue Bao. 2007 Apr;40(2):137-44.
Totally 2803 SSRs distributed in 2443 ESTs were mined out and accounted for 13.58% of 17987 non-redundant ESTs from oilseeed rape, with the average distance of distribution about 4.26 kb. Dinucleotide and trinucleotide repeats are the dominant type, with similar frequency and accounting for 89.05% together in all SSRs. AG/CT and AAG/CTT are the most frequent motifs, accounting for 84.31% and 37.71% in dinucleotide and trinucleotide repeats respectively. Further, 23 primer pairs for EST-SSRs were designed and the suitable annealing temperature for each primer pair was determined by gradient PCR. The amplification and polymorphism displayed by these primers in 10 varieties of oilseed rape were detected by using silver staining of nondenaturing polyacrylamide gel. 21 primer pairs showed the amplification, accounting for 91.30% of total primers, and 12 primer sets showed polymorphisms, accounting for 57.14% of primers available. These results indicate that it is an effective and feasible approach to develop SSR markers based on ESTs in oilseed rape.
从油菜的17987条非冗余EST序列中挖掘出分布于2443条EST序列中的2803个SSR，占比13.58%，平均分布距离约为4.26 kb。二核苷酸和三核苷酸重复是主要类型，频率相似，在所有SSR中合计占89.05%。AG/CT和AAG/CTT是最常见的基序，分别在二核苷酸和三核苷酸重复中占84.31%和37.71%。此外，设计了23对EST-SSR引物，并通过梯度PCR确定了每对引物的适宜退火温度。使用非变性聚丙烯酰胺凝胶银染法检测这些引物在10个油菜品种中的扩增和多态性。21对引物显示出扩增，占引物总数的91.30%，12对引物显示出多态性，占可用引物的57.14%。这些结果表明，基于油菜EST开发SSR标记是一种有效且可行的方法。
