Genome wide Association Study of Body Shape Related Traits in Large Yellow Croaker (Larimichthys crocea)

The large yellow croaker (<i>Larimichthys crocea</i>) is one of the most economically important marine culture fish mainly cultivated in the coastal areas of Southeast China. Body shape is an important economic trait for <i>L. crocea</i>, which playing a significant role in swimming, ingesting and avoiding predators. Moreover, due to the market preference of slender <i>L. crocea</i>, body shape has seriously impacted the economic benefits of the breeding industry. Thus, it’s vital to understand the genetic basis of body shape differentiation. Here, a total of 281 individuals from multiple families were genotyped using double-digest restriction-site associated DNA (ddRAD) strategies and retained 51,928 SNPs after quality control. We then performed genome-wide association study to identify SNP and genes potentially associated with body shape related traits including head length/body length ratio (HBR), body thickness/body length ratio (TLR), caudal peduncle depth/caudal peduncle length ratio (CPLHR), body mass index (BMI), body length/body height ratio (LHR), and body height/body thickness ratio (HTR). Twenty-seven SNPs on 11 LGs were identified to be significantly associated with body shape traits in GWAS. Candidate genes underlying body shape traits were identified surrounding the significant SNPs, including <i>start5</i>, <i>apt2</i>, <i>igfbps</i> and <i>ac1</i>, which identified with potential functions on lipid metabolism, energy metabolism, bone and other important regulatory pathways. Our results may provide insights into the genetic basis of body shape evolution and facilitate the molecular marker-assisted selection design of slender population large yellow croaker.