Analysis of genetic diversity by the SLAF-seq among the farmed Onychostoma macrolepis populations

Abstract

Abstract Objective The objective of this study was to examine the genetic diversity within and between farmed populations of Onychostoma macrolepis, and to establish a foundation for enhancing the genetic resources of breeding groups through the introduction of new individuals and crossbreeding. A total of 49 individuals were subjected to sequencing using Specific-Locus Amplified Fragment Sequencing (SLAF-seq), 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. Results A total of 853,067 SNPs were identified. The results of the phylogenetic analysis revealed that each sample was genetically clustered into three distinct groups: ZhenPing (ZP), LanGao parents (LG), and their progeny population (LG-F1). Each population was observed to be clustered together. Analysis of population genetic diversity revealed that the observed heterozygosity (Ho) ranged from 0.200 to 0.230, the expected heterozygosity (He) ranged from 0.280 to 0.282, and the polymorphic information content (PIC) ranged from 0.228 to 0.230. These results indicate that the genetic diversity of the population is low and the signs of long-term interbreeding are obvious, but there are differences between the populations, and the genetic diversity of the population can be improved by hybridization in different regions.