danДоклады Национальной академии наук БеларусиDoklady of the National Academy of Sciences of Belarus1561-83232524-2431The Republican Unitary Enterprise Publishing House "Belaruskaya Navuka"10.29235/1561-8323-2022-66-3-301-309dan-1068Research ArticleБИОЛОГИЯBIOLOGYДифференциация пород домашних свиней c использованием расширенного биоинформатического анализа SNPBreed differentiation of domestic pigs using SNP – extended bioinformatical analysishttps://orcid.org/0000-0002-7822-0746КипеньВ. Н.KipenV. N.

Кипень Вячеслав Николаевич – канд. биол. наук, вед. науч. сотрудник

ул. Академическая, 27, 220072, Минск

Kipen Viachaslau N. – Ph. D. (Biology), Leading Researcher

27, Akademicheskaya Str., 220072, Minsk

v.kipen@igc.byhttps://orcid.org/0000-0001-7961-1952СнытковЕ. В.SnytkovE. V.

Снытков Евгений Владимирович – мл. науч. сотрудник

ул. Академическая, 27, 220072, Минск

Snytkov Evgenij V. – Junior Researcher

27, Akademicheskaya Str., 220072, Minsk

evsnytkov@gmail.comhttps://orcid.org/0000-0001-6087-5069МихайловаМ. Е.MikhailovaM. E.

Михайлова Мария Егоровна – канд. биол. наук, заведующий лабораторией

ул. Академическая, 27, 220072, Минск

Mikhailova Mariya E. – Ph. D. (Biology), Head of the Laboratory

27, Akademicheskaya Str., 220072, Minsk

M.Mikhailova@igc.byhttps://orcid.org/0000-0001-5442-566XШейкоР. И.SheykoR. I.

Шейко Руслан Иванович – член-корреспондент, д-р с.-х. наук, профессор, директор

ул. Академическая, 27, 220072, Минск

Sheyko Ruslan I. – Corresponding Member, D. Sc. (Agrarian), Professor

27, Akademicheskaya Str., 220072, Minsk

R.I.Sheyko@igc.byИнститут генетики и цитологии Национальной академии наук БеларусиInstitute of Genetics and Cytology of the National Academy of Sciences of Belarus202201072022663301309Copyright © Кипень В.Н., Снытков Е.В., Михайлова М.Е., Шейко Р.И., 20222022Кипень В.Н., Снытков Е.В., Михайлова М.Е., Шейко Р.И.Kipen V.N., Snytkov E.V., Mikhailova M.E., Sheyko R.I.Данная работа распространяется под лицензией Creative Commons Attribution 4.0.This work is licensed under a Creative Commons Attribution 4.0 License.https://doklady.belnauka.by/jour/article/view/1068

С использованием методов биоинформатики проведен анализ данных по секвенированию геномов особей вида Sus scrofa domesticus, которые расположены в базе Sequence Read Archive (NCBI-SRA). Определены in silico генотипы для пяти пород домашних свиней – дюрок, ландрас, пьетрен, крупная белая и йоркшир с помощью алгоритма, разработанного на языке программирования Python. На основании двухстадийного биоинформатического анализа определен широкий перечень SNP c высоким потенциалом для дифференциации. Полученные результаты будут использованы при создании экспресс-методов для определения чистопородности свиней данных пород. Расши ренный биоинформатический анализ, который включал в себя определение генотипа по 7451 SNP для 248 геномов Sus scrofa domesticus, позволил выявить суммарно 393 SNP для всех пород, для которых имеется существенная разница в частоте альтернативных аллелей у пород свиней дюрок, ландрас, пьетрен, крупная белая и йоркшир. Обозначены кластеры в пределах хромосом, в которых плотность SNP с высоким дифференцирующим потенциалом наиболее высока. Для свиней породы дюрок нами выявлены 184 SNP, имеющие дифференцирующий потенциал, для 24 из которых показан высокий дифференцирующий потенциал, для свиней породы ландрас – 52 SNP и 7, для свиней породы пьетрен – 39 и 9, для свиней породы крупная белая – 104 и 22, для свиней породы йоркшир – 14 и 5 соответственно.

Using the methods of bioinformatics, the analysis of data on sequencing of the genomes of individuals of the species Sus scrofa domesticus, which are located in the Sequence Read Archive (NCBI-SRA) database, was carried out. Genotypes were determined in silico for five breeds of domestic pigs – Duroc, Landrace, Pietrain, Large White and Yorkshire using an algorithm developed in the Python programming language. Based on a two-stage bioinformatics analysis, a wide range of SNPs with a high potential for differentiation was identified. The results obtained will be used to create express methods for determining the purity of pigs of these breeds. Extended bioinformatics analysis, which included genotyping by 7451 SNPs for 248 Sus scrofa domesticus genomes, revealed a total of 393 SNPs for all breeds for which there is a significant difference in the frequency of alternative alleles in Duroc, Landrace, Pietrain, Large White and Yorkshire pig breeds. Clusters within chromosomes are indicated, in which the density of SNPs with a high differentiating potential is the highest. For Duroc pigs, we identified 184 SNPs with differentiating potential, 24 of which showed a high differentiating potential, for Landrace pigs – 52 SNPs and 7, for Pietrain pigs – 39 and 9, for Large White pigs – 104 and 22, for Yorkshire pigs – 14 and 5, respectively.

Sus scrofa domesticusдифференциацияоднонуклеотидный полиморфизмпородоспеци фичностьдюрокландраспьетренкрупная белаяйоркширROC-анализin silicoSus scrofa domesticusdifferentiationsingle nucleotide polymorphismbreed specificityDurocLandracePietrainLarge WhiteYorkshireROC analysisin silicoИсследование выполнено в рамках ГПНИ «Биотехнологии-2» (2021–2025 гг.), подпрограмма «Геномика, эпигеномика, биоинформатика», НИР «Разра ботка системы генетического анализа для опреде ления чистопородности свиней на основе изучения SNPлокусов».The study was carried out within the framework of the State Scientific Research Program “Biotech nology-2” (2021–2025), subprogram “Genomics, epigeno mics, bioinformatics”, research work “Development of a genetic analysis system for determining the purity of pigs based on the study of SNP loci”.ReferencesБиоинформатический анализ геномов коммерческих пород домашних свиней для идентификации породоспецифичных SNP / В. Н. Кипень [и др.] // Вес. 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The authors declare that there are no conflicts of interest present.