从公共数据库中利用数据挖掘的方法开发15条黄金鲈EST-SSR标记（英文）

DEVELOPMENT OF FIFTEEN EST-SSR MARKERS IN YELLOW PERCH PERCA FLAVESCENS BY DATA MINING FROM PUBLIC EST SEQUENCES

黄金鲈是美国中西部地区重要的淡水经济型鱼类。TypeⅠ型标记对于比较作图和遗传学研究有相当重要的作用,但是黄金鲈的TypeⅠ标记数量相当少。研究通过数据挖掘的方法从公共数据库中挖掘黄金鲈的TypeⅠ型即EST-SSR标记。实验结果分析了21968条EST序列,约14.4%的序列包含不同类型的核心重复单元。CA重复是最丰富的二碱基重复单元。从中挑选62条包含SSR的EST序列设计引物,筛选得到15对多态的微卫星位点。群体遗传学参数显示15对EST-SSR位点的等位基因数范围为4—19(平均数为9),观测杂合度和期望杂合度的范围分别为0.103—0.929和0.116—0.934,有4个位点偏离HWE平衡。研究得到的EST-SSR标记适用于黄金鲈的群体遗传学和基因组作图研究。

The yellow perch,Perca flavescens,is an economically significant freshwater fish species in the Midwest of the United States.TypeⅠmarkers are useful for comparative mapping and other genetic analyses,but limited quantities in yellow perch.In the present study,EST containing microsatellite sequences were identified and characterized for yellow perch by data mining from updated public EST databases.Out of 21968 EST sequences of yellow perch,about 14.4%of ESTs contain repeat motifs of various types and length.CA repeat was the most abundant dinucleotides.Out of the 62 EST-SSRs for which PCR primers were designed,15 loci showed polymorphic in a yellow perch population with the alleles per locus ranging from 4 to 19(average 9).The observed(HO)and expected(HE)heterozygosity of these EST-SSRs were 0.103-0.929 and 0.116-0.934,respectively.Four EST-SSR loci significantly deviated from the Hardy-Weinberg equilibrium(HWE)expectation,and the remaining 11 loci were in HWE.These new EST-SSR markers should provide sufficient polymorphism for population genetic studies and genomic mapping of yellow perch.