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

Abstract

BackgroundGenetic 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 (Fx) and genomic information using runs of homozygosity (FROH) and the single nucleotide polymorphisms (SNP) by SNP inbreeding coefficient (FSNP) were obtained. Linkage disequilibrium (LD), correlation of linkage phase (r) and effective population size (Ne) were also estimated.ResultsEstimates 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 Ne. Estimates of Ne 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.ConclusionsThe 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.

Characterization and management of long runs of homozygosity in parental nucleus lines and their associated crossbred progeny

“…Identification of shared haplotypes also highlights the fact that portions of the genome have shared haplotypes across populations, which cannot be determined when the population is characterized at the genome-wide level. Previous work on a different population by Zanella et al [8] also showed that shared haplotypes exist between the LW and LA breeds, although the frequency at which they occurred in the crossbred genome was not investigated. The LW breed originated in England as a cross between Cumberland, Leicecstershire, Middle and Small White breeds, with early registration records dating back to 1884 [59].…”

“…With genomic information, it is possible to better understand how frequent long haplotypes are shared across the parental breeds in a swine breeding system. Previous work by Zanella et al [8] showed that haplotypes are shared across Large White (LW) and Landrace (LA) breeds based on a 50-SNP (single nucleotide polymorphism) run of homozygosity (ROH) metric. A ROH is generated when an individual receives a haplotype that is identical by descent from each parent [9].…”

Genetic characteristics and diversity of Korean Jeju Black cattle by whole genome SNP markers

“…Inbreeding coefficient can be calculated both from pedigree and genomic data but in general, pedigree data information gives lower value than those obtained with genomic data. However, better accuracies of inbreeding coefficient (F SNP ) could be estimated from the genome wide SNP data [8]. Effective population size (N E ) is one of the important genetic parameters that used to determine the amount of genetic variation, genetic drift, and linkage disequilibrium (LD) in both cattle and human population [9,10].…”

Weighted likelihood inference of genomic autozygosity patterns in dense genotype data

“…Studies of ROA in the genomes of ancient hominins [29][30][31] and early Europeans [32] have provided unique insights into the mating patterns and effective population sizes of our early forbearers. In non-humans, ROA patterns have provided insights into the differential histories of woolly mammoth [33], great ape [34,35], cat [36], canid [37][38][39][40][41][42], and bird [43] populations, while in livestock breeds they have provided insights into their origins, relationships, and recent management [42,[44][45][46][47][48][49][50][51][52][53][54][55][56][57][58][59][60][61] and the lasting effects of artificial section [58,[61][62][63][64][65][66][67][68][69][70][71][72]…”