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

The
large yellow croaker (Larimichthys crocea)
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 L. crocea, which playing a significant
role in swimming, ingesting and avoiding predators. Moreover, due to the market
preference of slender L. crocea, 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 start5, apt2, igfbps and ac1, 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.