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