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EST(表达序列标签)数据库发掘是单核苷酸多态性标记(SNP)开发的重要途径。本研究利用栉孔扇贝转录组测序数据进行SNP筛选,在含有4条EST以上的18 780条contig(拼接序列)中,共获得21 813个候选SNP位点。利用高分辨率熔解曲线结合非标记探针技术,对其中90个位点在4个野生群体中进行了位点多态性检测。得到33个(36.7%)具有二等位基因位点,并对其中26个位点进行了功能注释。进一步的标记验证显示,33个多态位点在青岛野生群体的48个个体中均成功分型,其观测杂合度Ho和期望杂合度He的分布范围分别为0.062 5～0.744 7和0.099 8～0.504 6,其中5个位点偏离Hardy-Weinberg平衡,各位点间没有检测到连锁不平衡。研究为栉孔扇贝群体遗传学和遗传育种分析提供了候选标记。
Abstract：A total of 21,813 putative SNPs were detected from 18,780 contigs containing ≥4 EST sequences in Chlamys farreri.Using high resolution melting(HRM) technology with unlabelled probe,90 of the putative SNPs were selected for validation,of which 33(36.7%) were proved to be polymorphic among 48 individuals from 4 populations.After further evaluation with 48 individuals from Qingdao population,all the polymorphic loci had two alleles with the minor allele frequency ranged between 0.0521 and 0.4796.The expected and observed heterozygosities of the SNPs ranged from 0.0625 to 0.7447 and from 0.0998 to 0.5046,respectively.No significant linkage disequilibria were detected and five loci exhibited significant departures from Hardy-Weinberg equilibrium.The results show that through EST database exploration and HRM with unlabelled probe,EST-SNPs could be developed in an efficient and robust way for non-model organisms.
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基本信息:
DOI：10.16441/j.cnki.hdxb.2013.01.008
中图分类号:S917.4
引用信息:
[1]李纪勤,包振民,李玲,等.栉孔扇贝EST-SNP标记开发及多态性分析[J],2013,43(01):56-63.DOI:10.16441/j.cnki.hdxb.2013.01.008.
基金信息:
国家重点基础发展计划项目(2010CB126406;010CB126402);; 国家高技术研究发展计划项目(2012AA10A402,2012AA10A405);; 中国海洋大学水生生物种质资源标准化及资源共享项目资助