Analysis of Homozygous-by-Descent (HBD) Segments for Purebred and Crossbred Pigs in Russia

Abstract

Intensive selection raises the efficiency of pig farming considerably, but it also promotes the accumulation of homozygosity, which can lead to an increase in inbreeding and the accumulation of deleterious variation. The analysis of segments homozygous-by-descent (HBD) and non-HBD segments in purebred and crossbred pigs is of great interest. Research was carried out on 657 pigs, of which there were Large White (LW, n = 280), Landrace (LR, n = 218) and F1 female (♂LR × ♀LW) (F1, n = 159). Genotyping was performed using the GeneSeek® GGP Porcine HD Genomic Profiler v1 (Illumina Inc., USA). To identify HBD segments and estimate autozygosity (inbreeding coefficient), we used the multiple HBD classes model. LW pigs exhibited 50,420 HBD segments, an average of 180 per animal; LR pigs exhibited 33,586 HBD segments, an average of 154 per animal; F1 pigs exhibited 21,068 HBD segments, an average of 132 per animal. The longest HBD segments in LW were presented in SSC1, SSC13 and SSC15; in LR, in SSC1; and in F1, in SSC15. In these segments, 3898 SNPs localized in 1252 genes were identified. These areas overlap with 441 QTLs (SSC1—238 QTLs; SSC13—101 QTLs; and SSC15—102 QTLs), including 174 QTLs for meat and carcass traits (84 QTLs—fatness), 127 QTLs for reproduction traits (100 QTLs—litter traits), 101 for production traits (69 QTLs—growth and 30 QTLs—feed intake), 21 QTLs for exterior traits (9 QTLs—conformation) and 18 QTLs for health traits (13 QTLs—blood parameters). Thirty SNPs were missense variants. Whilst estimating the potential for deleterious variation, six SNPs localized in the NEDD4, SEC11C, DCP1A, CCT8, PKP4 and TENM3 genes were identified, which may show deleterious variation. A high frequency of potential deleterious variation was noted for LR in DCP1A, and for LW in TENM3 and PKP4. In all cases, the genotype frequencies in F1 were intermediate between LR and LW. The findings presented in our work show the promise of genome scanning for HBD as a strategy for studying population history, identifying genomic regions and genes associated with important economic traits, as well as deleterious variation.

Genetic Diversity, Admixture and Analysis of Homozygous-by-Descent (HBD) Segments of Russian Wild Boar

“…When compared with domestic pigs, the level of autozygosity of wild boar was lower. The studies of Landrace and Large White pig showed that total autozygosity (inbreeding coefficient) was approximately 0.23 (0.15–0.34) [ 52 ], for different populations of wild boar was in the range of 0.025–0.168. Short segments are practically absent in Russian wild boar.…”

Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array

“…Hence, crossbreeding is still an important method to expand the genetic variation of modern cattle breeds [ 4 ]. High-intensity artificial selection might promote genetic progress, but it could lead to an increase in the population inbreeding level [ 52 ]. Huaxi cattle have undergone generations of artificial selection in the breeding process in recent years.…”

Investigation of the Genetic Architecture of Pigs Subjected to Breeding Intensification

“…Selection signatures can also be localized in homozygous areas of various lengths [ 1 ]. When creating breeds of farm animals, the accumulation of homozygosity allows pure-bred animals to possess certain qualities and steadily pass them on to their offspring [ 18 ]. The use of homozygosity patterns of ROH (Runs Of Homozygosity) makes it possible to reveal long homozygous areas in a genome [ 19 ].…”