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

Abstract

In this study, we investigated whether a selection programme based on boar genetic evaluation obtained with a classical BLUP animal model can change allele frequencies in a pig population. All Italian Large White boars born from 1992 to 2012 with estimated breeding value reliability >0.85 (n = 200) were selected among all boars of this breed. Boars were genotyped with markers in major genes (IGF2 intron3-g.3072G>A, MC4R p.D298N, VRTN PRE1 insertion, PRKAG3 p.I199V and FTO g.276T>G). Genotyping data were analysed grouping boars in eight classes according to their year of birth. To evaluate the influence of time on allele frequencies of the genotyped markers, multinomial logistic regression models were computed. Four of five polymorphic sites (IGF2, MC4R, VRTN and FTO) showed significant (p < 0.01) changes in allele frequencies over time due to a progressive and continuous increase of one allele (associated with higher lean meat content, higher average daily gain and favourable feed: gain ratio) and, consequently, decrease of the other one, following the directional selection of the selection programme of this pig breed. The retrospective analysis that was carried out in Italian Large White boars suggests that selection based on methodologies assuming the infinitesimal model is able to modify in a quite short period of time allele frequencies in major genes, increasing the frequency of alleles explaining a relevant (non-infinitesimal) fraction of the overall genetic variability for production traits.

A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits

“…This mechanism could be responsible for the allele frequency differences between the AQUA and founder population at the consistent outlier GCR_cBin27732_Ctg1_177 which is located near melanocortin receptor 4 (Table 4). Melanocortin peptides affect motivation to feed in rainbow trout (Schjolden, Schiöth, Larhammar, Winberg, & Larson, 2009) and have previously found to be associated with weight gain and feed intake in pigs (Fontanesi et al., 2015). Two other consistent outlier loci are located near candidate genes associated with growth and metabolism.…”

“…In contrast, the similar selection differentials applied to classic quantitative traits like growth are assumed to cause only minor changes in allele frequencies (Falconer & Mackay, 1996) that would be undetectable using outlier locus methodology (Wellenreuther & Hansson, 2016), but see Fontanesi et al (2015). Both single locus and quantitative traits might show rapid genetic divergence between aquaculture strains and wild populations of Atlantic salmon.…”

“…(2015). Both single locus and quantitative traits might show rapid genetic divergence between aquaculture strains and wild populations of Atlantic salmon.…”

Evolution of the additive genetic variance–covariance matrix under continuous directional selection on a complex behavioural phenotype

“…However, changes in allele frequency under directional selection have been shown in a few livestock populations [24] and in the current experiment. Specifically, we previously showed, in two of the four HR lines, dramatic changes in the frequency of a Mendelian recessive 'mini-muscle' allele that causes a 50% reduction in hind limb muscle mass, as well as many pleiotropic effects that are apparently conducive to supporting high levels of rspb.royalsocietypublishing.org Proc.…”

“…Thus, the animal model inferred G back to the hypothetical parental population of the time period given the data provided. Obviously, in finite populations (with drift) and especially in populations under selection (the HR lines) in which allele frequencies change [24], some assumptions of the infinitesimal model do not hold. In this case, the animal model may not yield a strict estimate of G in the base parental population, but one that is 'biased' towards subsequent generations for which data are included.…”