Genomic structure of a crossbred Landrace pig population

Abstract

Single nucleotide polymorphism (SNP) markers are used to study population structure and conservation genetics, which permits assessing similarities regarding the linkage disequilibrium and information about the relationship among individuals. To investigate the population genomic structure of 300 females and 25 males from a commercial maternal pig line we analyzed linkage disequilibrium extent, inbreeding coefficients using genomic and conventional pedigree data, and population stratification. The average linkage disequilibrium (r 2 ) was 0.291 ± 0.312 for all adjacent SNPs, distancing less than 100 Kb (kilobase) between markers. The average inbreeding coefficients obtained from runs of homozygosity (ROH) and pedigree analyses were 0.119 and 0.0001, respectively. Low correlation was observed between the inbreeding coefficients possibly as a result of genetic recombination effect accounted for the ROH estimates or caused by pedigree identification errors. A large number of long ROHs might indicate recent inbreeding events in the studied population. A total of 36 homozygous segments were found in more than 30% of the population and these ROH harbor genes associated with reproductive traits. The population stratification analysis indicated that this population was possibly originated from two distinct populations, which is a result from crossings between the eastern and western breeds used in the formation of the line. Our findings provide support to understand the genetic structure of swine populations and may assist breeding companies to avoid a high level of inbreeding coefficients to maintain genetic diversity, showing the effectiveness of using genome-wide SNP information for quantifying inbreeding when the pedigree was incomplete or incorrect.

Genetic Variability in Local and Imported Germplasm Chicken Populations as Revealed by Analyzing Runs of Homozygosity

“…Small local and imported conserved populations bred inter se had a greater (>20) number of ROHs (e.g., BMF, BB, BL, RW1 and C), meaning a reduced genetic diversity similar to what was shown in small livestock populations kept by individual breeders or in local breeds [ 2 , 27 , 28 , 29 , 30 , 31 ]. In contrast, the genomes of two- and three-breed F 1 crossbred progenies contained a lesser (<6) number of ROHs ( Table 1 ; Figure 1 ), which was consistent with lower ROH metrics observed in other studies on crossbred animals (e.g., [ 3 , 32 ]).…”

“…Assessment of the genome-wide diversity plays a significant role in conserving local and imported genetic resources and maintaining an effective program for breeding commercial populations (e.g., [ 1 , 2 , 3 ]). Previously, in the framework of a poultry germplasm conservation and utilization research project, we assessed a broad spectrum of the world’s chicken germplasm populations for genetic variation at economically important loci [ 4 , 5 ] and multiple single nucleotide polymorphisms (SNP) loci [ 6 , 7 , 8 , 9 ].…”

“…A comparative genetic evaluation of livestock populations of different origin, population history, and size is an important source of information for genetic changes in their genome, including degree of homozygosity across genome-wide regions [ 2 , 3 , 10 ]. This is especially desirable when breeding small conserved groups and evaluating crossbreeding/inbreeding effects [ 11 , 12 ].…”

Runs of homozygosity analysis of South African sheep breeds from various production systems investigated using OvineSNP50k data

“…Runs of homozygosity (ROH) are contiguous segments of homozygous genotypes that are present in an individual due to parents transmitting identical haplotypes to their offspring [ 5 ]. The extent and frequency of ROHs are useful in providing information about the ancestry of an individual and its population [ 5 , 6 ] with longer ROHs associated with more recent inbreeding within a pedigree while short ROHs are associated with ancient common ancestors [ 7 , 8 ]. Shorter ROH can also be used to infer ancient relationships, information which in livestock is often missing due to limited recording.…”

Estrutura populacional e acurácia da predição genômica em populações de aves: um estudo de simulação

“…A gestão da diversidade genética de uma raça doméstica é essencial para o uso sustentável de recursos genéticos e seu melhoramento (Falconer e Mackay, 1996). Por isso, um dos parâmetros a serem trabalhados seria o controle da endogamia, que é fundamental para a produção e conservação genética animal, pois induz à redução da diversidade genética (Joaquim et al, 2019).…”