Identification of SNPs and candidate genes associated with growth using GWAS and transcriptome analysis in Coilia nasus

The improvement of growth trait can foster the sustained and stable development of the aquaculture industry and is generally regarded as a primary objective in the breeding projects for economic fish. Coilia nasus, a migratory fish species naturally inhabiting in the middle and lower reaches of the Yangtze River and offshore waters of China, exhibits significant culturing potential and economic value. However, due to genetic degradation, there is a pronounced trend towards miniaturization and exaggerated growth variations within the cultured population. In order to facilitate the healthy development of the aquaculture industry of C. nasus, whole-genome association analysis (GWAS) and transcriptome analysis (RNA-seq) have been employed to identify molecular markers associated with growth traits and elucidate genetic foundations. A total of 234 individuals of C. nasus were subjected to whole-genome resequencing for genotyping, resulting in the identification of 2,306,254 high-quality SNPs. Fourteen SNPs were proved to have suggestive association with body length (BL) or body weight (BW), with the explained phenotypic variation ranging from 2.21% to 2.71%. We obtained two shared significant SNP peaks for BL and BW on LG6 and LG9, and bmp8a and uqcrfs1 were identified as their causal genes. Comparative transcriptome analysis based on extreme body size obtained 54 and 20 overlapping differentially expressed genes (DEGs) between different sexes in brain and muscle, respectively. Combining the results of GWAS and RNA-seq, we identified five candidate genes and one pathway associated with growth, including uqcrfs1, bmp8a, gabrb4, tshz3a, ahcyl1, and the mTORC1 signaling pathway. Our research findings provide molecular markers for genetic selection in C. nasus growth, and contribute to understand the molecular mechanisms of population growth variations.