Whole-genome resequencing of large yellow croaker (Larimichthys crocea) reveals the population structure and signatures of environmental adaptation

Yingying Ye,Baoying Guo,Atsushi Ogura,Hiromasa Tabata,Weiye Li,Ping Wang,Chunyan Chen,Lihua Jiang,Ikuyo Takemura,Hagai Nsobi Lauden,Tetsuo Kon,Xiaojun Yan,Ryota Ichikawa,Liyi Pei,Yoshihiro Omori,Hao Pan

doi:10.1038/s41598-021-90645-1

Abstract

Large yellow croaker is an economically important fish in China and East Asia. Despite its economic importance, genome-wide adaptions of domesticated large yellow croaker are largely unknown. Here, we performed whole-genome resequencing of 198 individuals of large yellow croaker obtained in the sea or from farmers in Zhoushan or Ningde. Population genomics analyses revealed the genetic population structure of our samples, reflecting the living environment. Each effective population size is estimated to be declining over generations. Moreover, we identified genetically differentiated genomic regions between the sea-captured population in the Zhoushan Sea area and that of the Ningde Sea area or between the sea-captured population and the farmed population in either area. Gene ontology analyses revealed the gene groups under selective sweep for the adaptation to the domesticated environment. All these results suggest that individuals of the large yellow croaker populations show genomic signatures of adaptation to different living environments.

Highlights

Large yellow croaker is an economically important fish in China and East Asia
As the large yellow croaker wild population collapsed in the 1970s, artificial breeding was established in China in the 1980s as an important fish resource in China, with millions of enhanced releases conducted annually[18]
Studies have indicated that the genetic structure of large yellow croaker reared in captivity is different from that of captured populations and further expresses concerns over the genetic diversity of local populations perturbed by large-scale hatchery r eleases[20]; these studies were limited to microsatellite markers and single nucleotide polymorphism (SNP) loci, which did not provide an in-depth discussion on the impact of domesticated programs on the large yellow croaker genome

Summary

Introduction

Large yellow croaker is an economically important fish in China and East Asia. Despite its economic importance, genome-wide adaptions of domesticated large yellow croaker are largely unknown. The culture performance of farmed large yellow croaker populations has declined, mainly because of irrational artificial breeding, inbreeding, and blind introduction. Previous genetic studies of the population structure of large yellow croaker are available for both domesticated and sea-captured populations; these studies have been limited by putative neutral markers; e.g., microsatellites[5] and single nucleotide polymorphism (SNP) loci[6] including narrow regions of the genome[7]. This is not enough genetic data to describe the structure of the population. Whole-genome resequencing of the 198 croakers were performed to obtain a better information of the critical uncertainties associated with population structure, genetic diversity and the analysis of mixed stocks across the domesticated and sea-captured populations of large yellow croaker

Methods

Results

Conclusion