Identification of SNPs and candidate genes associate with growth performance in all-female mandarin fish (Siniperca chuatsi) by a genome-wide association study

Abstract

The all-female mandarin fish (Dinggui I, Siniperca Chuatsi) was recently approved by Ministry of Agriculture and Rural Affairs of the People's Republic of China as a new strain of mandarin fish (GS-04-001-2021). Select breeding of fast-growing lines is an important goal of the mandarin fish industry. However, single nucleotide polymorphisms (SNPs) associated with growth of Dinggui I mandarin fish remains unclear. Therefore, a genome-wide association study (GWAS) was performed on 5 growth traits (body weight, body length, whole length, body height and body thickness) of 192 mandarin fish. A total of 49,940 SNPs were identified by ddRAD-seq. Among them, a total of 6 significant SNPs were detected on multiple chromosomes. The proportion of phenotypic variance explained for these SNPs ranged from 9.66% to 19.47% for growth traits. Specifically, 4 SNPs were associated with all traits. Several candidate genes (AKT2, CCNT2, EPB41L2 and CAMKMT) were identified based on these SNPs. The loci were verified in 100 individuals, indicating the reliability of candidate SNPs. Our results contribute to understanding of growth traits and the development of molecular marker-assisted selection in all-female mandarin fish.