栉孔扇贝转录组来源单核苷酸多态性位点的多态性分析

Evaluation of SNPs from Transcriptome Dataset in Zhikong Scallop Chlamys farreri

应用高分辨率熔解曲线技术对栉孔扇贝转录组来源的单核苷酸多态性位点进行验证分型和多态性分析。根据栉孔扇贝转录组单核苷酸多态性位点序列信息,对其中150个位点设计引物和探针,在4个栉孔扇贝野生群体中进行验证分型。其中,103对引物扩增出目的产物,76个位点成功分型,58个多态位点中51个是二等位多态性单核苷酸多态性(34.0%)。进一步在荣成野生群体中对51个二态单核苷酸多态性位点进行多态性验证和群体遗传学分析,其中49个位点呈现多态性,且均为二态,最小等位基因频率为0.0610～0.5000,观测杂合度和期望杂合度分别为0.0833～0.8889和0.0833～0.5833。经Boferroni校正,有2个位点(C1630S115_AG和C19848S286_CA)在该群体中偏离Hardy-Weinberg平衡。各位点之间未检测到连锁不平衡。这些多态单核苷酸多态性位点可用于栉孔扇贝连锁图谱构建、分子标记辅助育种以及数量性状的基因定位等遗传学研究。

Single nucleotide polymorphisms （SNPs） screened from transcriptome dataset in Zhikong scallop （Chlarnys farreri） were evaluated and genotyped using high resolution melting （HRM） assays. A total of 150 SNPs were selected for primers and probes designing. Of which, 103 loci were successfully amplified using pooled DNA templates from individuals of four wild Zhikong Scallop populations （Changdao, Rongcheng, Rizhao, and Qingdao）. HRM assays showed that 76 loci were successfully genotyped in 48 individuals from the four populations, and among the 58 polymorphic loci, 51 were found to be biallelic （34.0%）. Further polymorphism assessment was performed in 60 individuals from Rongcheng population, and 49 of the 51 SNPs were polymorphic. The minor allele frequency （MAF） was ranged from 0. 0610 to 0. 5000, the observed heterozygosity （Ho） was varied from 0.0833 to 0.8889 and expected heterozygosity （H,） from 0. 0833 to 0. 5833. After sequential Bonferroni correction, two loci （C1630Sl15_ AG and C19848S286_CA） were significantly deviated from Hardy-Weinberg equilibrium （HWE）, and significant linkage disequilibrium （LD） was not detected between the loci. These SNP markers will be useful for genetic linkage map construction, marker assist selection and QTL mapping in Zhikong scallop.