克氏原螯虾养殖群体的SLAF测序及遗传多样性分析

【目的】探究克氏原螯虾养殖群体内和群体间的遗传多样性，为引种和群体间杂交以改善养殖群体种质提供参考依据。【方法】以湖北、江西、安徽、浙江和江苏5省克氏原螯虾主产地14个养殖群体的120个个体为研究对象，采用简化基因组测序技术——特定区点扩增片段测序技术（SLAF-seq）进行基因组测序，获得基因组SNP基因型数据，构建群体系统发育进化树，并进行群体结构、主成分和遗传多样性分析。【结果】共鉴定出741147个单核苷酸多态性（SNP）位点，群体系统进化分析表明，14个群体的种源主要来自浙江金华和江苏宿迁，然后再向各地引种迁徙。群体结构分析结果与系统进化分析结果相吻合。主成分分析结果揭示了安徽长丰和滁州群体、湖北荆州龙口及和平2个群体，以及浙江东阳群体等5个群体与其他群体间存在相对较远的亲缘关系，是杂交引种的潜在种源。群体遗传多样性分析显示，14个群体的Ho介于0.2171~0.2801，平均值为0.2476，He介于0.3424~0.3598，平均值为0.3534，PIC介于0.2750~0.2878，群体间相差不大，接近0.25，各群体均接近遗传多样性中等水平的下限。【结论】14个克氏原螯虾养殖群体内的遗传多样性较低，群体间的亲缘关系较接近，品种单一、长期内交迹象明显。通过群体的基因组重测序，能以较低的成本实现对养殖群体遗传多样性的定期监测。

Analysis of genetic diversity among the farmed Procambarus clarkii populations using the SLAF-seq technology

【Objective】This study was designed to investigate the intra-group and inter-group genetic diversity of farmed Procambarus clarkii populations，and to provide fundamental data bases for improving the germplasm of breeding groups through required introduction and crossbreeding.【Method】A total of 120 individuals of 14 farmed populations collected in Hubei，Jiangxi，Anhui，Zhejiang and Jiangsu were sequenced with a Specific-Locus Amplified Fragment Sequencing（SLAF-seq）technology，one of the restriction site-associated DNA sequencing technologies. The single nucleotide polymorphisms（SNPs）were identified to conduct the analyzation of phylogeny，population structure，principal component and genetic diversity.【Result】According to the identified 741147 SNPs in this study，the phylogenic analysis suggested that the 14 populations originated from two main origins，Jinhua and Suqian. Then they were introduced and migrated to different places. The results of the population structure analysis agreed with the phylogenetic analysis. The principal component analysis revealed that the five populations，including Changfeng（Anhui），Chuzhou（Anhui），Longkou， Jingzhou（Hubei），Heping，Jingzhou（Hubei）and Dongyang（Zhejiang）had relatively distant genetic relationships to the others，which might be the potential provenances for the future hybridization. The estimated genetic diversity of the 14 populations exhibited that Ho ranged from 0.2171 to 0.2801 with a mean of 0.2476，He from 0.3424 to 0.3598 with a mean of 0.3534 and PIC from 0.2750 to 0.2878，the difference among populations was small，especially for the PIC all close to 0.25. Each population approached the lower limit of intermediate levels of genetic diversity.【Conclusion】Comparison of sequence variations reveals a considerably low genetic diversity within and among the 14 farmed P. clarkii populations. The kinship between groups is close，with obvious signs of single breed and long-term crossing. As a lowcost and effective approach，the SLAF-seq sequencing should be suited to regularly monitor the genetic diversity of the farmed populations