Genetic diversity analysis of different populations of Lutjanus kasmira based on SNP markers

Abstract Lutjanus kasmira belongs to family Lutjanidae. Over the past 20 years, the L. kasmira population in the South China Sea has been shrinking due to climate change, pressure from human activities and inadequate food supplies. Moreover, the allometric factors of this species show interannual variation and seasonal fluctuations. The ratio of females to males is increasing annually, the proportion of sexually mature individuals and body length at sexual maturity have decreased continuously, and the mean feeding intensity and fattening degree have decreased gradually. In this study, single nucleotide polymorphism (SNP) data obtained from restriction site-associated DNA sequencing (RAD-seq) were used to assess the genetic diversity of L. kasmira in Zhubi Dao (ZB) and Meiji Dao (MJ). The genome-wide nucleotide diversity (π) of the ZB population and MJ population was 0.02478 and 0.02154, respectively. The inbreeding coefficient (Fis) of the ZB population and MJ population was − 0.18729 and 0.03256, respectively. The genetic differentiation (Fst) between the ZB and MJ subpopulations was 0.00255102. The expected heterozygosity (He) of individuals from ZB and MJ was 0.33585 and 0.22098, respectively. The observed heterozygosity (Ho) of individuals from the ZB population and MJ population was 0.46834 and 0.23103, respectively. Although the ZB and MJ populations did not show significant genetic differences, genetic differentiation between them was confirmed using population structure, phylogenetic, and principal component analyses. These results indicated that the genetic diversity of the ZB and MJ populations was relatively low at the genome level, and their genetic differences were small.