Identification of SNPs associated with body weight and muscle unsaturated fatty acids in grass carp (Ctenopharyngodon idella) through GWAS analysis

Grass carp ( Ctenopharyngodon idella ) has an important economic value in the world. In order to meet increasing high quality nutritional demands, there is an urgent need for genetic selection in breeding programs to improve fish muscle quality. Body weight (BW) and muscle unsaturated fatty acid (UFA) content are economically important traits in fish. In this study, we conducted a genome-wide association study (GWAS) based on whole-genome resequencing to identify single nucleotide polymorphisms (SNPs) and candidate genes potentially associated with BW and muscle UFA content in grass carp. A total of 4315,253 high-quality SNPs were identified and mapped onto 24 chromosomes. We identified 9, 4, 7 and 6 SNPs significantly associated with BW, UFA, polyunsaturated fatty acids (PUFA), and docosahexaenoic acid (DHA) content of fish muscle, respectively. Within the 100 kb upstream and downstream range of these significant SNPs, 51 candidate genes were associated with BW, while 48, 88 and 113 candidate genes were linked to muscle UFA, PUFA, and DHA content, respectively. Notably, nfatc 2 a , mylk 4 a , ext 2 associated growth, st 6 galnac 5, hmgcra , Rab 8 a and ptges 3 a associated with lipid metabolism. The findings of this study will facilitate the breeding of higher muscle UFA content new varieties of grass carp in the future. • We conducted GWAS based on whole-genome resequencing to identify SNPs in grass carp. • We identified 21, 3, 37, and 57 SNPs associated with BW, UFA, PUFA, and DHA. • The genes ppp 1 r 18, antxr 1 a may be involved in the growth of fish. • The genes cygb 2, sema 3 e , dusp 22 a may be involved in lipid metabolism process. • The results will facilitate the breeding of higher muscle UFA content new varieties.