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Kostyunina O.V., Abdelmanova A.S., Martynova E.U., Zinovieva N.A. Search for genomic regions carrying the lethal genetic variants in the Duroc pigs. Sel'skokhozyaistvennaya Biologiya [Agricultural Biology], 2020, Vol. 55, № 2, p. 275-284.
(how to cite this article)

doi: 10.15389/agrobiology.2020.2.275eng

UDC: 636.4:636.082:575.22:577.21

The equipment of the Center for Biological Resources and Bioengineering of Farm Animals (Ernst Federal Science Center for Animal Husbandry) was used for the study. Supported financially within the frame of GZ 0445-2019-0026, No. АААА-А18-118021590138-1

 

SEARCH FOR GENOMIC REGIONS CARRYING THE LETHAL GENETIC VARIANTS IN THE DUROC PIGS

O.V. Kostyunina1, A.S. Abdelmanova1, E.U. Martynova2, N.A. Zinovieva1

1Ernst Federal Science Center for Animal Husbandry,60, pos. Dubrovitsy, Podolsk District, Moscow Province, 142132 Russia, e-mail kostolan@mail.ru (✉ corresponding author), preevetic@mail.ru, n_zinovieva@mail.ru;
2Center of Life Sciences, Skolkovo Institute of Science and Technology, 3, ul. Nobelya, Moscow, 143026 Russia, e-mail elenamartynovaster@gmail.com

ORCID:
Kostyunina O.V. orcid.org/0000-0001-8206-3221
Martynova E.U. orcid.org/0000-0003-0802-0236
Abdelmanova A.S. orcid.org/0000-0003-4752-0727
Zinovieva N.A. orcid.org/0000-0003-4017-6863

Received October 31, 2019

 

The necessity to address the problem of reducing embryonic losses, which in pigs are estimated at the level up to 30 %, is not in doubt. LoF (Loss of Function) mutations, which in the homozygous state can lead to the termination of synthesis or synthesis of non-functional proteins, are considered as one of the genetic factors that cause embryonic mortality. While in cattle, an intensive search for LoF mutations is carried out, in pigs, studies of such mutations are still performed on a smaller scale. Whole-genome analysis using medium- and high-density SNP chips which are uniformly covering the entire genome allows researchers to apply new approaches to identify positional candidates for lethal recessive variants. One of such approaches is the analysis of the level of the linkage disequilibrium (LD) of alleles of SNP markers. The aim of our research was to search for genomic regions that carry presumed lethal recessive variants in Duroc pigs, based on the analysis of the linkage disequilibrium of alleles in SNP loci. Studies were carried out with 715 Duroc boars bred in JSC Top Gen (Voronezh region) in 2017-2019. Whole-genome genotyping was carried out using Porcine GGP HD DNA chips (Neogene/Illumina Inc., USA) containing about 70 thousand SNP. After the quality control, 42981 polymorphic SNP were selected for analysis. Search of reference sequences (rs) and clarification of their localization was carried out using the Ensembl database (http://www.ensembl.org). Functional gene annotations were performed using the GeneCards database (http://www.genecards.org/). Analysis of the maintenance of genetic equilibrium showed the presence of 990 SNPs with the absence of one of the homozygous genotypes (2.30 % of the total number of polymorphic SNPs), which were distributed among all pig chromosomes, including 205 SNPs, which were in the linkage disequilibrium (0.48 %). Chromosomes SSC9 (0.8 %), SSC5 (0.77 %), SSC7 (0.68 %) and SSC2 (0.68 %) were characterized by the highest ratio of SNPs in linkage disequilibrium, while chromosomes SSC13 (0.28 %), SSC4 (0.29 %) and SSC10 (0.30 %) were the lowest. For 52 SNPs, of which 25 SNPs were localized within genes, differences in observed and expected heterozygosity frequencies were statistically significant (p < 0.01). Among SNPs located in intergenic regions, two SNPs (rs81350198 and rs81337222) are associated with important phenotypes from earlier GWAS studies. For 12 of the 25 identified positional candidate genes (OR4C45, EPHB4, EML4, SLC4A1AP, ZFAT, CELSR2, NEGR1, LRRC32, MYOCD, HUNK, RPH3A,and DOCK1), we obtained the information on their role in various processes in organisms of mammals, including nervous system development, angiogenesis, cardiogenesis, cell differentiation, apoptosis and many others. The integration of DNA markers associated with lethal phenotypes into breeding programs, in addition to DNA markers identified by GWAS studies, will significantly improve the efficiency of marker and genomic breeding programs in pigs.

Keywords: pigs, linkage disequilibrium, lethal variants, LoF (loss of function), single nucleotide polymorphisms.

 

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