Genome-wide association study reveals growth-related SNPs and candidate genes in mandarin fish (Siniperca chuatsi)

Abstract

Mandarin fish (Siniperca chuatsi) is a popular inland farmed fish species with high an economic value. Molecular selective breeding programs are urgently required to improve the growth traits of mandarin fish for farming industry. In this study, using 160 mandarin fish individuals, specific locus-amplified fragment sequencing and SNP genotyping, we performed a genome-wide association study (GWAS) to identify genomic regions and candidate genes that are potentially associated with various growth traits of mandarin fish, such as body weight (BW), body thickness (BT), body height (BH) total length (TL), slaughter weight (SW), and body length (BL). Through genotyping, 5205 high-quality SNPs were found located on 24 chromosomes. A total of 11 significant and 37 suggestive SNPs related to growth traits were obtained, among which five SNPs significantly related to BW were located in the linkage group (LG) 8, 17, 21, and 23, two SNPs significantly related to TL were located in LG 7 and 17, two SNPs significantly related to BH were located on LG 17 and 23, two SNPs significantly related to BT were located on LG 14 and 19, respectively. Furthermore, LG17_937,734 and LG23_23,856,613 were growth-related traits overlap. Within 300 kb upstream and downstream of these significant SNPs, 65 candidate genes were identified within the associated QTLs, many of which were related to bone differentiation, growth and development, cell division and neurogenesis. In particular, asns, tg, mkk6, htra1, rnf213, ttn, tgfbr2, and nck2, were shown to be closely associated with growth, fat, muscle and bone formation. To our knowledge, this is the first GWAS focusing on growth traits of mandarin fish. Our findings establish a foundation for molecular marker-assisted selecting, genomic selecting, and functional analyzing the growth traits of mandarin fish.