Reproduction and Breeding (Jun 2021)
Genome-wide association analysis reveals genetic variations and candidate genes associated with growth-related traits and condition factor in Takifugu bimaculatus
Abstract
Takifugu bimaculatus is a new breed of pufferfish that has emerged in the recent twenty years. As a euryhaline species, the habitat of T. bimaculatus ranges from the Yangtze River estuary to the South China Sea. It is always mix-bred with Penaeus monodon and Ruditapes philippinarum. The strong adaptability to temperature and salinity makes it become a candidate species for Takifugu aquaculture in south china. But the slower growth rate and smaller body size limit the further development and promotion of the T. bimaculatus breeding industry. In addition, the sexual maturity of the three years hinders the efficiency of traditional breeding methods. With the increasing demand of market, selecting and breeding new strains with excellent growth-related traits by the markers-assistance selection (MAS) and genome selection (GS) will accelerate the T. bimaculatus breeding industrial upgrading. In this study, 5 traits were employed to represent the growth, including body length (BL), body weight (BW), body length gain (BLG), body weight gain (BWG), and condition factor (K) at 8, 20 and 32-month after hatch. 167 individuals of a full-sib family were genotyped by Whole-genome Resequencing (WGS) and 122,573 SNPs were identified on 22 chromosomes. 9 genome-wide significant SNPs were identified to be associated with different growth-related traits through the Genome-wide association study by Mixed Linear Model (MLM). Surrounding these SNPs, we identified 17 growth-related candidate genes, including mstn1, igfbp5, igfbp2b, igf1r, fgfr3, fgf10 and tgfbr3. These genes are involved in the muscle growth, Insulin-like growth factor (IGF) pathway, Transforming growth factor-β (TGF-β) pathway and Fibroblast growth factor (FGF) pathway. Besides, 10 genome-wide significant SNPs and 5 candidate genes were identified to be associated with K, including pth2r, myh7b, gdf10, hspb8a and midnb, which are involved in osteoblast differentiation, adipogenesis and heat stress response. These results above will contribute to the understanding of the genetic basis of growth and provide several reliable molecular markers for the MAS and GS in T. bimaculatus breeding project.
