Genetic diversity analysis of two commercial breeds of pigs using genomic and pedigree data

Abstract

Background: Genetic improvement in livestock populations can be achieved without significantly affecting genetic diversity if mating systems and selection decisions take genetic relationships among individuals into consideration. The objective of this study was to examine the genetic diversity of two commercial breeds of pigs. Genotypes from 1168 Landrace (LA) and 1094 Large White (LW) animals from a commercial breeding program in Brazil were obtained using the Illumina PorcineSNP60 Beadchip. Inbreeding estimates based on pedigree (F x) and genomic information using runs of homozygosity (F ROH) and the single nucleotide polymorphisms (SNP) by SNP inbreeding coefficient (F SNP) were obtained. Linkage disequilibrium (LD), correlation of linkage phase (r) and effective population size (N e ) were also estimated.

Results: Estimates of inbreeding obtained with pedigree information were lower than those obtained with genomic data in both breeds. We observed that the extent of LD was slightly larger at shorter distances between SNPs in the LW population than in the LA population, which indicates that the LW population was derived from a smaller N e . Estimates of N e based on genomic data were equal to 53 and 40 for the current populations of LA and LW, respectively. The correlation of linkage phase between the two breeds was equal to 0.77 at distances up to 50 kb, which suggests that genome-wide association and selection should be performed within breed. Although selection intensities have been stronger in the LA breed than in the LW breed, levels of genomic and pedigree inbreeding were lower for the LA than for the LW breed.

Conclusions: The use of genomic data to evaluate population diversity in livestock animals can provide new and more precise insights about the effects of intense selection for production traits. Resulting information and knowledge can be used to effectively increase response to selection by appropriately managing the rate of inbreeding, minimizing negative effects of inbreeding depression and therefore maintaining desirable levels of genetic diversity.

Fig. 1

Decay of average pairwise linkage disequilibrium (r ²) over distance between SNPs in Landrace and Large White populations

Fig. 2

Correlation of linkage phase between breeds for SNP pairs grouped by distance in 100 kb intervals across the genome

Fig. 3

Effective population size (N _e) of the Landrace and Large White populations

Fig. 4

Inbreeding estimates based on pedigree information (F _x)

Fig. 5

Relationship between the number of ROH and the average length of each ROH for the Landrace and Large White populations. Each point represents the number and average length of ROH of one animal. Red circles represent Landrace and green triangles represent Large White animals