Polymorphisms in the FOXO gene are associated with growth traits in the Sanmen breeding population of the razor clam Sinonovacula constricta

Abstract

We identified the FOXO gene and five single-nucleotide polymorphisms (SNPs) in its coding region in the Sanmen breeding population of the razor clam Sinonovacula constricta. The ScFOXO gene encodes a protein of 625 amino acids in length that contains a conserved DNA-binding domain. Real-time polymerase chain reaction analysis showed that ScFOXO mRNA is widely expressed in adult tissues, with higher expression in the siphons and gills. Of the SNPs, c.879G > C (Val293Val) and c.1725A > G (Ser575Ser) are synonymous mutations, and c.543C > T (Phe181Leu), c.848A > G (Tyr283Cys), and c.1625G > C (Gly542Phe) are non-synonymous mutations. The SNPs all show significant associations with total body weight, shell length, shell width, and shell height (SH) in this population. Polymorphic parameter analysis showed that all SNPs except c.848A > G (Tyr283Cys) exhibit complete linkage. The SNP c.1625G > C (Gly542Phe) was used for genetic linkage mapping and demonstrates the strongest linkage (logarithm of the odds [LOD] value: 41.46) with the marker 96616 (37.02 cM) in the linkage group 9. The LOD value of this marker in relation to growth traits ranges from 1.04 to 1.53; only markers with a LOD value ≥ 3 were considered to be linked with growth traits in the razor clam linkage map. In summary, ScFOXO may be a growth trait-related gene and may represent a marker for Sanmen breeding group selection. Keywords: Sinonovacula constricta, Single-nucleotide polymorphism (SNP), FOXO, Growth traits