Abstract
Muscle fat content is an important phenotypic trait in fish, as it affects the nutritional, technical and sensory qualities of flesh. To identify loci and candidate genes associated with muscle fat content and abdominal fat traits, we performed a genome-wide association study (GWAS) using the common carp 250 K SNP assay in a common carp F2 resource population. A total of 18 loci surpassing the genome-wide suggestive significance level were detected for 4 traits: fat content in dorsal muscle (MFdo), fat content in abdominal muscle (MFab), abdominal fat weight (AbFW), and AbFW as a percentage of eviscerated weight (AbFP). Among them, one SNP (carp089419) affecting both AbFW and AbFP reached the genome-wide significance level. Ten of those loci were harbored in or near known genes. Furthermore, relative expressions of 5 genes related to MFdo were compared using dorsal muscle samples with high and low phenotypic values. The results showed that 4 genes were differentially expressed between the high and low phenotypic groups. These genes are, therefore, prospective candidate genes for muscle fat content: ankyrin repeat domain 10a (ankrd10a), tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2 (tanc2), and four jointed box 1 (fjx1) and choline kinase alpha (chka). These results offer valuable insights into the complex genetic basis of fat metabolism and deposition.
Highlights
Common carp (Cyprinus carpio) is one of the most widely cultured fish species in the world
Eviscerated weight (EW) was weighed, and the percentage of abdominal fat weight (AbFW) to eviscerated weight (EW) was calculated as AbFP
A set of 85,818 SNPs was included for genome-wide association study (GWAS) (S3 Table)
Summary
Common carp (Cyprinus carpio) is one of the most widely cultured fish species in the world. In 2012, the world production of common carp exceeded 4.16 million tons and, in China, the yield reached more than 3.17 million tons (ftp://ftp.fao.org/FI/STAT/summary/default.htm, archived on July 18, 2016). The species is important in the global aquaculture industry, and it is a traditional food in China. It serves as a model species for many research areas, e.g. toxicology, ecology, physiology, nutrition and evolution. Significant progress has been made in developing common carp genomic tools in recent years. A greater amount of genomic resources is available for common carp research, such as a medium-density [1] and PLOS ONE | DOI:10.1371/journal.pone.0169127. A greater amount of genomic resources is available for common carp research, such as a medium-density [1] and PLOS ONE | DOI:10.1371/journal.pone.0169127 December 28, 2016
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