Investigation of SNPs in the ATP1A2, CA3and DECR1 genes mapped to porcine chromosome 4: analysis in groups of pigs divergent for meat production and quality traits

Abstract

Three genes (ATPase, Na+/K+transporting, α2(+) polypeptide, ATP1A2; carbonic anhydrase III, CA3; 2,4- dienoyl CoA reductase 1, mitochondrial, DECR1), isolated from a porcine skeletal muscle cDNA library and mapped on porcine chromosome 4 (SSC4), were investigated. A new single nucleotide polymorphism (SNP) was identified in the 3’-untranslated region of the CA3 gene and used to genetically map this locus on SSC4 together with the ATP1A2and DECR1loci for which SNPs were already reported. Allele frequencies of the three loci were reported for 11 pig breeds (Italian Large White, Italian Landrace, Italian Duroc, Belgian Landrace, Hampshire, Piétrain, Meishan, Cinta Senese, Casertana, Calabrese and Nero Siciliano). Radiation hybrid mapping of these genes confirmed the linkage mapping results as well as mapping information reported by other authors. Then, the SNPs identified in the ATP1A2, CA3and DECR1genes were genotyped in Italian Large White and Italian Duroc animal groups with extreme and divergent estimated breeding value for several production traits. For CA3significant differences in allele frequencies (P< 0.05) were observed between the extreme groups of pigs for the lean cuts (Italian Large White) and visible intermuscular fat (Italian Duroc) traits. For DECR1, a significant difference in allele frequencies was observed only for the vis- ible intermuscular fat trait. ATP1A2, which maps close to the FAT1locus, did not show any significant dif- ference. A very high linkage disequilibrium (D’= 0.967; P< 0.0001) was identified between CA3and DECR1 in the Italian Duroc population. Further investigations are needed to evaluate the effect of CA3and DECR1 on the considered traits.

Keywords

• ATP1A2, CA3, DECR1, Meat production traits, Pig chromosome 4