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

Siroj Bakoev,Lyubov Getmantseva,Anatoly Kolosov,Faridun Bakoev,Olga Kostyunina,Nekruz Bakoev,Timofey Romanets,Olga Koshkina

doi:10.3390/life11080861

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.

Highlights

IntroductionImproving the efficiency of livestock production is associated with intensive selection and different breeding strategies
The assessments of each class in autozygosity are difficult to interpret as inbreeding coefficients, since they have variability in an individual, and in this case, to obtain an inbreeding coefficient, we summarized the autozygosity for all HBD classes
The estimates of each class in autozygosity are difficult to interpret as inbreeding coefficients, since they have individual variability, and in this case, to obtain inbreeding coefficients, since they have individual variability, and in this case, to obtain the inbreeding coefficient, we summarized the autozygosity for all HBD classes

Summary

Introduction

Improving the efficiency of livestock production is associated with intensive selection and different breeding strategies. High-intensity selection promotes genetic progress, but it can lead to an undesirable increase in the level of inbreeding in purebred livestock [1,2]. In creating breeds of farm animals, the accumulation of homozygosity is the main goal, which allows the purebred animals to possess certain qualities, and to steadily pass them on to their offspring. The intensive selection of highly productive animals leads to an increase in the frequency of homozygotes for deleterious variation [3]

Objectives

Methods

Results

Discussion

Conclusion