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

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 purebr...

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Autores principales: Bakoev, Siroj, Kolosov, Anatoly, Bakoev, Faridun, Kostyunina, Olga, Bakoev, Nekruz, Romanets, Timofey, Koshkina, Olga, Getmantseva, Lyubov
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8400874/
https://www.ncbi.nlm.nih.gov/pubmed/34440604
http://dx.doi.org/10.3390/life11080861
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author Bakoev, Siroj
Kolosov, Anatoly
Bakoev, Faridun
Kostyunina, Olga
Bakoev, Nekruz
Romanets, Timofey
Koshkina, Olga
Getmantseva, Lyubov
author_facet Bakoev, Siroj
Kolosov, Anatoly
Bakoev, Faridun
Kostyunina, Olga
Bakoev, Nekruz
Romanets, Timofey
Koshkina, Olga
Getmantseva, Lyubov
author_sort Bakoev, Siroj
collection PubMed
description 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.
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spelling pubmed-84008742021-08-29 Analysis of Homozygous-by-Descent (HBD) Segments for Purebred and Crossbred Pigs in Russia Bakoev, Siroj Kolosov, Anatoly Bakoev, Faridun Kostyunina, Olga Bakoev, Nekruz Romanets, Timofey Koshkina, Olga Getmantseva, Lyubov Life (Basel) Article 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. MDPI 2021-08-22 /pmc/articles/PMC8400874/ /pubmed/34440604 http://dx.doi.org/10.3390/life11080861 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Bakoev, Siroj
Kolosov, Anatoly
Bakoev, Faridun
Kostyunina, Olga
Bakoev, Nekruz
Romanets, Timofey
Koshkina, Olga
Getmantseva, Lyubov
Analysis of Homozygous-by-Descent (HBD) Segments for Purebred and Crossbred Pigs in Russia
title Analysis of Homozygous-by-Descent (HBD) Segments for Purebred and Crossbred Pigs in Russia
title_full Analysis of Homozygous-by-Descent (HBD) Segments for Purebred and Crossbred Pigs in Russia
title_fullStr Analysis of Homozygous-by-Descent (HBD) Segments for Purebred and Crossbred Pigs in Russia
title_full_unstemmed Analysis of Homozygous-by-Descent (HBD) Segments for Purebred and Crossbred Pigs in Russia
title_short Analysis of Homozygous-by-Descent (HBD) Segments for Purebred and Crossbred Pigs in Russia
title_sort analysis of homozygous-by-descent (hbd) segments for purebred and crossbred pigs in russia
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8400874/
https://www.ncbi.nlm.nih.gov/pubmed/34440604
http://dx.doi.org/10.3390/life11080861
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