Genome-wide association study reveals growth-related markers and candidate genes for selection in Chinese longsnout catfish (Leiocassis longirostris)

Abstract

Growth-related traits are economically important in fish because they directly affect fish production. The Chinese longsnout catfish (Leiocassis longirostris) is an important aquaculture species and its consumption is growing in China. In this study, using 200 individuals and high-throughput SNP genotyping technology, we performed the first genome-wide association study (GWAS) in L. longirostris to identify putative genomic regions and candidate genes associated with growth traits (including body mass, total length, standard length, head width, snout length, and caudal peduncle depth). The morphometrics of these traits were highly correlated (Pearson's correlation coefficients = 0.88–0.96, p < 0.05). GWAS detected 12, 5, 6, 9, 4, and 8 SNPs loci that were significantly associated (-log10P ≥ 5.21) with body mass, total length, standard length, head width, snout length, and caudal peduncle depth, respectively. Subsequently, within the 100 kb upstream and downstream regions surrounding these significant SNPs, 96, 31, 39, 61, 22, and 36 candidate genes for the 6 growth traits, respectively, were detected. Interestingly, chromosome (Chr) 16 had the most SNPs significantly associated with growth traits, and the majority of those were shared among multiple growth-related traits. In addition, multiple candidate genes surrounding these SNPs have been shown to serve essential functions in biological processes closely-related to growth, such as enox2, ky, and coma1. These results indicated that Chr16 may be central to growth characteristics. Other Chrs had genes involved in bone development, cell proliferation, and fatty acid metabolism, including matn1, sdc3, if2b3, kif3a, h1b, cadh7, rerg, and fabph. Our findings not only help understand the genetic architecture of growth traits in fish, but facilitate the identification of candidate genes for marker-assisted selection towards breeding faster growing L. longirostris in the future.