Association Analysis between Single Nucleotide Polymorphisms in the Promoter Region of LEP, MYF6, MYOD1, OPN, SCD Genes and Carcass Traits in Heavy Pigs

Abstract

The purpose of the study was to evaluate associations between average daily gain (ADG) and DNA variability in the regulatory region of candidate genes in Italian Large White, Italian Duroc and Italian Landrace breeds for heavy pig production. The ADG of pigs was available as Estimated Breeding Values (EBVs) and Random Residuals (RRs). Within each breed, 200 individuals were sampled, 100 in the higher and 100 in the lower 5% tail of the normal distribution curve according to the EBVs for ADG of the populations (600 pigs overall). Six SNPs in promoter regions of 5 candidate genes (MYF6, MYOD1, OPN, SCD and two for LEP) were analysed. Allele frequencies were calculated and the SNPs for LEP, MYF6 and MYOD1 segregated in the 3 breeds, while polymorphisms in the OPN and SCD genes did not segregate in Italian Large White and Italian Landrace, and Italian Landrace respectively. Fisher’s exact test (two-tailed) for the distribution of allele frequencies in minus and plus variant groups was significant for LEP_1 and MYOD1 in Italian Large White, for LEP_1, LEP_2, MYOD1, OPN and SCD in Italian Duroc and for LEP_1, LEP_2 and MYOD1 in Italian Landrace. Several putative binding sites were detected in the promoter regions using MATINSPECTOR software. Analysed mutations may affect putative core sequences of binding sites for transcription factors involved in muscle and fat tissues deposition. However, variations in binding affinities of the sequences related to the SNPs and the expected differential gene expression require to be evaluated.