Genome-wide analysis of genetic diversity and artificial selection in Large White pigs in Russia

Bakoev, Siroj; Getmantseva, Lyubov; Kostyunina, Olga; Bakoev, Nekruz; Prytkov, Yuri; Усатов, А. В.; Tatarinova, Tatiana V.

doi:10.7717/peerj.11595

Cited by 6 publications

(2 citation statements)

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“…Thereby an assessment of genetical differentiation between the pigs that have undergone and have not undergone selection intensification is of particular interest. In this aspect, we conducted research using pigs raised on the territory of the Russian Federation at different periods of time and identified the signatures of selection in pigs due to trends in different socio-economic conditions [ 22 ]. However, studying modern livestock of Large White pigs has shown that formations of selection signatures are influenced by selection centers themselves since each of them implements its own breeding strategy.…”

Section: Introductionmentioning

confidence: 99%

Investigation of the Genetic Architecture of Pigs Subjected to Breeding Intensification

Kolosov

Getmantseva

Kolosova

et al. 2022

Genes

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Pigs are strategically important animals for the agricultural industry. An assessment of genetic differentiation between pigs, undergone and not undergone to selection intensification, is of particular interest. Our research was conducted on two groups of Large White pigs grown on the same farm but in different years. A total of 165 samples were selected with 78 LW_А (n = 78, the Russian selection) and LW_B (n = 87, a commercial livestock). For genotyping, we used GeneSeek® GGP Porcine HD Genomic Profiler v1 (Illumina Inc, San Diego, CA, USA). To define breeding characteristics of selection, we used smoothing FST and segment identification of HBD (Homozygous-by-Descent). The results of smoothing FST showed 20 areas of a genome with strong ejection regions of the genome located on all chromosomes except SSC2, SSC3, and SSC8. The average realized autozygosity in Large White pigs of native selection was in (LW_A)—0.21, in LW_В—0.29. LW_А showed 13,338 HBD segments, 171 per one animal, and LW_B—15,747 HBD segments, 181 per one animal. The ejections found by the smoothing FST method were partially localized in the HBD regions. In these areas, the genes ((NCBP1, PLPPR1, GRIN3A, NBEA, TRPC4, HS6ST3, NALCN, SMG6, TTC3, KCNJ6, IKZF2, OBSL1, CARD10, ETV6, VWF, CCND2, TSPAN9, CDH13, CEP128, SERPINA11, PIK3CG, COG5, BCAP29, SLC26A4) were defined. The revealed genes can be of special interest for further studying their influence on an organism of an animal since they can act as candidate genes for selection-significant traits.

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Section: Introductionmentioning

confidence: 99%

Investigation of the Genetic Architecture of Pigs Subjected to Breeding Intensification

Kolosov

Getmantseva

Kolosova

et al. 2022

Genes

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“…An accumulation of homozygosity can lead to an increase in inbreeding and the accumulation of deleterious variants, presenting an economical problem in farming. Using sequencing technology this group recently studied mitochondrial DNA and genome diversity in Large White pigs in Russia [19,20].…”

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confidence: 99%

Life: Computational Genomics Applications in Life Sciences

Orlov

Anashkina

2021

Life

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Genetic diversity and autozygosity estimates in wild european boars and domesticated pigs

Bakoev,

Romanets,

Korobeinikova

et al. 2024

Ecological genetics

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Pigs are one of the most widely distributed domestic animals. The study of their genetic diversity and selection loci is of great interest both in the field of genetics and animal breeding, and in the aspect of conservation and development of breeding resources and food security. The aim of the presented work is to evaluate the autozygosity and distribution of autozygosity segments (HBD) in wild boars and pigs of the main commercial breeds: Large White, Landrace and Duroc, and to search for selection loci related to adaptation to habitat conditions and selection pressure. Based on the results of the genome scan, the average autozygosity values in boars and pigs were in the range of 0.23 - 0.29, but in boars about 0.08 of the genome share is covered by HBD segments, presumably originating from ancestors who lived about 206 years ago; in pigs - originating from ancestors who lived about 64 years ago. Only 3 segments met the criteria for top-HBD (frequency of at least 60% and at least 10 SNPs) in boars. In Large White, Landrace and Duroc pigs, 18, 9 and 35 segments were identified, respectively. In general, the analysis of HBD segments showed that they reflect the main breeding strategies aimed at developing commercial pigs.

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Genome-wide analysis of genetic diversity and artificial selection in Large White pigs in Russia

Cited by 6 publications

References 45 publications

Investigation of the Genetic Architecture of Pigs Subjected to Breeding Intensification

Investigation of the Genetic Architecture of Pigs Subjected to Breeding Intensification

Life: Computational Genomics Applications in Life Sciences

Genetic diversity and autozygosity estimates in wild european boars and domesticated pigs

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