Genomic data reveals large similarities among Canadian and French maternal pig lines

Abstract

Combining reference populations from different countries and breeds could be an affordable way to enlarge the size of the reference populations for genomic prediction of breeding values. Therefore, the main objectives of this study were to assess the genetic diversity within and between two Canadian and French pig breeds (Landrace and Yorkshire) and the genomic relatedness among populations to evaluate the feasibility of an across-country reference population for pig genomic selection. A total of 14 756 pigs were genotyped on two single nucleotide polymorphism (SNP) chip panels (∼65K SNPs). A principal component analysis clearly discriminated Landrace and Yorkshire breeds, and also, but to a lesser extent, the Canadian and French purebred pigs of each breed. Linkage disequilibrium (LD) between adjacent SNPs was similar within Yorkshire populations. However, levels of LD were slightly different for Landrace populations. The consistency of gametic phase was very high between Yorkshire populations (0.96 at 0.05 Mb) and high for Landrace (0.88 at 0.05 Mb). Based on consistency of gametic phase, Canadian and French pig maternal lines are genetically close to each other. These results are promising, as they indicate that the accuracy of estimated genomic breeding values may increase by combining reference populations from the two countries.

Purebred and Crossbred Genomic Evaluation and Mate Allocation Strategies To Exploit Dominance in Pig Crossbreeding Schemes

“…The LD decay was measured for increasing distances between markers by calculating the mean r 2 within each distance interval. The resulting average over replicates of LD of SNP with an interval distance, assuming a 1Mbp:1cM ratio, of 0.9 to 1 Mbp, was the same for both parental breeds, r 2 ¼ 0.15, close to values observed in real data in Landrace and Yorkshire breeds at the same distance (Boré et al 2018).…”

Investigating the impact of non-additive genetic effects in the estimation of variance components and genomic predictions for heat tolerance and performance traits in crossbred and purebred pig populations

“…The findings from this study suggest that the gene actions for heat stress-related traits in this population are mainly additive, or at least most of the non-additive genetic effects are captured by the additive genetic component. Although the dataset used in this study came only from crossbred animals, the pure breeds used for crossbreeding are both considered maternal breeds (Large White and Landrace) and genetically related [ 57 – 59 ]. Thus, in crossings between lines or breeds with high genetic distance it would be expected higher heterosis and greater non-additive genetic variance estimates [ 21 ] in comparison to the present study.…”