Identification of candidate genes and SNPs associated with growth traits by genome-wide association study (GWAS) in sea cucumber (Apostichopus japonicus)

Abstract

Growth traits are considered the most important production traits for aquatic animals. The genetic enhancement of growth traits has the potential to boost productivity, shorten breeding periods and reduce costs. We constructed four full-sib families of the same age to monitor the growth parameters of A. japonicus and observed a growth variation coefficient exceeding 50 %. To investigate the causes of significant growth variation between individuals, we performed genome-wide association analyses on 271 randomly selected A. japonicus. We identified 3 single nucleotide polymorphisms (SNPs) that showed a significant (−log₁₀(P-value) = 7.65) association and 368 suggestively (−log₁₀(P-value) = 5) association SNPs with growth using a linear mixed model (LMM). A total of 447 candidate genes linked to these SNPs were identified, some of which show a direct relationship with neuroimmunity, transcriptional regulation, signal transduction, substance metabolism, cell differentiation and development processes. These genes differ from growth axis hormone genes in fish, suggesting that the growth trait regulation mechanism of A. japonicus may be species-specific. Furthermore, we validated the differential expression of six genes between high-growth (H) group and low-growth (L) group, which may play crucial roles in the growth of A. japonicus. The results provide not only molecular markers for genetic improvement but also new insights into the regulatory mechanisms of the economically traits in A. japonicus.