Characterization of single nucleotide polymorphism in IGF1 and IGF1R genes associated with growth traits in striped catfish (Pangasianodon hypophthalmus Sauvage, 1878)

Abstract

Development of molecular markers for growth trait in striped catfish (Pangasianodon hypophthalmus) is of importance to the aquaculture industry in the Mekong river delta. This study aims to analyze the genetic variation and the effects of the Insulin-like growth factor 1 (IGF1) and Insulin-like growth factor 1 receptor (IGF1R) genes on growth traits in striped catfish. We sequenced fragments of IGF1 and IFG1R genes from 10 individuals of fast-growing fish and 10 individuals of slow-growing fish to discover single nucleotide polymorphisms (SNPs). Among the discovered SNPs, one SNP (13,680 A > T in intron 2) of IGF1 gene, three SNPs (13,357 T > C, 15392 T > A in intron 1 and 83,894 A > G in intron 15) in IGF1R gene were filtered and further validated by individual genotyping in 70 fast-growing fish and 70 slow-growing fish using the multiplex SNaPshot method (single base extension method). Our analyses showed that two SNPs (IGF1:13680 A > T and IGF1R:13357 T > C) were significantly associated with the growth trait (p < 0.01 and p < 0.05, respectively) and therefore considered as candidate SNP markers for growth trait in P. hypophthalmus. In addition, a haplotype analysis was carried out to confirm the association between three SNPs in IGF1R gene with growth traits. Moreover, the combination of the two candidate SNP markers was further analyzed to examine their cumulative effect on the growth traits. The result showed that the combination of genotype AA of IGF1:13680 A > T and genotype TT of IGF1R:13357 T > C led to the positive cumulative effect on the growth (p < 0.01). The variations identified in this study have a potential to be marker candidates for assisted selection in genetic breeding of the striped catfish.