Identification of a large dataset of SNPs in Larimichthys polyactis using high-throughput 2b-RAD sequencing

Abstract

The small yellow croaker (Larimichthys polyactis) is one of the most commercially exploited marine fishes along the coast of the Yellow-Bohai Sea and the East China Sea. In this study, we used next-generation high-throughput 2b-RAD-seq technology to identify novel SNPs in L. polyactis. We scored a total of 1 374 008 putative SNPs genome-wide. Further filtration yielded a final dataset of 6457 high-quality SNPs. These SNP markers presented sufficient power in detecting genetic distinction between two wild samples from the Yellow-Bohai Sea and one captive sample from the East China Sea, and inbreeding reflected by strong heterozygote deficiency within the samples; some of the genetic polymorphisms are diagnostic among the samples and related to biological functions. The panel of SNPs could be used as powerful tools in further population genetic and stock assessment research in L. polyactis as it has relatively scarce genomic resources. The findings from this study will advance our understanding of population and functional genomics for facilitating fishery resource management and developing desirable characteristics for the benefit of culture and farming of L. polyactis.

Keywords: biological function; genetic distinction; genome; inbreeding; small yellow croaker.