Single nucleotide polymorphisms of the SIF gene and their association with growth traits in swimming crab (Portunus trituberculatus)

Abstract

The swimming crab (Portunus trituberculatus) is an economically important aquaculture species in China. Mining candidate single nucleotide polymorphisms (SNPs) and genes associated with growth traits of P. trituberculatus is of great importance for the genetic breeding of this species. Among the genes associated with growth traits, “protein still life, isoforms C/SIF type 2 (SIF)” is thought to be an important gene affecting animal growth and development. In the current study, we investigated the SIF gene from P. trituberculatus to better understand its biological function. The full-length cDNA of SIF was 6185 bp, with a 5208 bp open reading frame encoding 1735 amino acids. Homology analysis showed that SIF shared 90.07% identity with Procambarus clarkii and 40.25–86.95% with other species. Expression pattern analysis of SIF in fast- and slow-growing groups revealed a significantly higher expression level in the former than in the latter (P < 0.05). qPCR studies revealed the ubiquitous expression of SIF in seven tissues tested, but most abundantly in the heart compared with muscle, testis, ovary, seminal vesicle, gill, and hepatopancreas (P < 0.05). A total of 38 SNPs in the UTRs and exons of SIF were screened and genotyped in 184 individuals of swimming crabs by targeted resequencing. Association analysis showed that four SNPs were significantly associated with growth traits (full carapace width, carapace length, body height, and body weight; P < 0.05). Two SNPs out of the four SNPs were shaped as a haploblock containing three haplotypes (GC, TA, and TC), and the TA haplotype showed significantly higher growth traits than the GC haplotype. Overall, the results provided potential candidate genes and SNP markers for the genetic improvement of growth traits in P. trituberculatus breeding.

Keywords

• Portunus trituberculatus
• SIF
• SNP
• Haplotype
• Growth traits