Investigation of a Short Interspersed Nuclear Element Polymorphic Site in the PorcineVertninGene: Allele Frequencies and Association Study With Meat Quality, Carcass and Production Traits in Italian Large White pigs

Abstract

A 291 bp short interspersed nuclear element (SINE) insertion in the porcine vertnin (VRTN) gene on porcine chromosome 7 was shown to affect vertebral number and several production traits: allele Q (with the insertion) increases vertebral number compared to the wild type allele (WT, without insertion). In this study we genotyped this polymorphism in eight pig breeds (Italian Large White, Italian Duroc, Italian Landrace, Cinta Senese, Mora Romagnola, Casertana, Apulo Calabrese, and Nero Siciliano) and in Italian wild boars to evaluate allele frequency distribution of the two alleles. Allele Q was the most frequent in Italian Landrace and Italian Duroc (0.738 and 0.545, respectively) whereas it was the less frequent in all other breeds and was absent in wild boars. Association study was carried out in two Italian Large White samples. These two groups of animals were constituted by performance tested pigs for which estimated breeding values (EBV) and random residuals (RR) for several traits (average daily gain, back fat thickness, feed:gain ratio, lean cuts and ham weight) were calculated: i) 270 pigs chosen without any criteria (random group), that were also measured for several meat quality traits; ii) 560 gilts with extreme and divergent EBV for back fat thickness. For these animals vertebral number was not available. Results of the association analyses indicated that allele Q was associated with a lower ham weight, confirming indirectly, the negative correlation reported by other studies between vertebral number and this trait. No other trait was associated with the analysed VRTN polymorphism.

A retrospective analysis of allele frequency changes of major genes during 20 years of selection in the Italian Large White pig breed

“…Allele Q (with the insertion) is associated with increased vertebrae number (Mikawa et al 2011) that, in turn, should positively affect other traits such as lean meat production and reproduction parameters (Borchers et al 2004;Duijvesteijn et al 2014). We showed that allele Q was mildly associated with lower HW in Italian Large White pigs (Fontanesi et al 2014). Ham weight is relevant for the production of dry-cured hams, and although the Italian pig breeders association calculates an estimated breeding value (EBV) for this trait, this parameter is not included in the general selection index of the boars.…”

“…In a previous study on Italian Large White performance‐tested pigs, we identified a mild association between allele Q and lower HW (Fontanesi et al . ). As HW increased during the last 20 years of selection in the Italian Large White breed (Figure ), probably because of its correlation with lean meat content that is part of the general selection index of the breed, one should expect a decrease, not an increase in the frequency of VRTN Q allele.…”

“…As vertebral number is correlated with body length that, in turn, is correlated with other productive and reproductive traits (Borchers et al 2004), it appears that the observed increase of approximately 20% of allele Q in the investigated boars might be derived by indirect selection due to the existing correlations between vertebrae number and other traits under selection in this population. In a previous study on Italian Large White performancetested pigs, we identified a mild association between allele Q and lower HW (Fontanesi et al 2014). As HW increased during the last 20 years of selection in the Italian Large White breed (Figure 1), probably because of its correlation with lean meat content that is part of the general selection index of the breed, one should expect a decrease, not an increase in the frequency of VRTN Q allele.…”

“…We showed that allele Q was mildly associated with lower HW in Italian Large White pigs (Fontanesi et al . ). Ham weight is relevant for the production of dry‐cured hams, and although the Italian pig breeders association calculates an estimated breeding value (EBV) for this trait, this parameter is not included in the general selection index of the boars.…”

Twenty years of artificial directional selection have shaped the genome of the Italian Large White pig breed

“…Moreover, SNPs with P < 0.001 in two previous genome‐wide association (GWA) studies for BFT and ADG carried out in the Italian Large White breed (Fontanesi et al . , ) were used to identify overlapping regions (using median haploblock size, defined above) containing SNPs with the same significant values as in this study.…”