Meta-Analysis of SNPs Determining Litter Traits in Pigs.

Nearly 2000 SNPs associated with pig litter size traits have been reported based on genome-wide association studies (GWASs). The aims of this study were to gather and integrate previously reported associations between SNPs and five litter traits: total number born (TNB), number born alive (NBA), number of stillborn (SB), litter birth weight (LWT), and corpus luteum number (CLN), in order to evaluate their common genetic background and to perform a meta-analysis (MA) of GWASs for total number born (TNB) recorded for animals from five pig populations. In this study, the genes with the largest number of associations with evaluated litter traits were GABRG3, RBP7, PRKD1, and STXBP6. Only 21 genes out of 233 associated with the evaluated litter traits were reported in more than one population or for more than one trait. Based on this evaluation, the most interesting candidate gene is PRKD1, which has an association with SB and TNB traits. Based on GO term analysis, PRKD1 was shown to be involved in angiogenesis as well. As a result of the MA, two new genomic regions, which have not been previously reported, were found to be associated with the TNB trait. One SNP was located on Sus scrofa chromosome (SSC) 14 in the intron of the FAM13C gene. The second SNP was located on SSC9 within the intron of the AGMO gene. Functional analysis revealed a strong candidate causal gene underlying the QTL on SSC9. The third best hit and the most promising candidate gene for litter size was found within the SOSTDC1 gene, associated with lower male fertility in rats. We showed that litter traits studied across pig populations have only a few genomic regions in common based on candidate gene comparison. PRKD1 could be an interesting candidate gene with a wider association with fertility. The MA identified new genomic regions on SSC9 and SSC14 associated with TNB. Further functional analysis indicated the most promising gene was SOSTDC1, which was confirmed to affect male fertility in other mammals. This is an important finding, as litter traits are by default linked with females rather than males.

Estimation of litter size variability phenotypes in Large White sows.

The objective of this study was to obtain new phenotypes of phenotypic variability for the total number born (TNB) in pigs using the residual variance of TNB. The analysis was based on 246,799 Large White litter observations provided by Topigs Norsvin. Three animal models were used to obtain estimates of residual variance for TNB: the basic model (BM) containing fixed effects of farm-year and season and random effects of animal and permanent environmental sow, the basic model with an additional fixed effect of parity (BMP) and a random regression model (RRM). The within-individual variance of the residuals was calculated and log-transformed to obtain three new variability traits: LnVarBM, LnVarBMP and LnVarRRM. Then, (co)variance components, heritability, the genetic coefficient of variation at the standard deviation level (GCVSDe ) and genetic correlations between the three LnVar's and between the LnVar's and mean total number born (mTNB) were estimated with uni-, bi- and trivariate models. Results indicated that genetically LnVar's are the same trait and are positively correlated with the mTNB (~0.60). Thus, both traits should be included in breeding programmes to avoid an increase in TNB variability while selecting for increased TNB. Heritability of the LnVar's was estimated at 0.021. The GCVSDe for LnVar's showed that a change of 8% in residual standard deviation of TNB could be obtained per generation. Those results indicate that phenotypic variability of litter size is under genetic control, thus it may be improved by selection.