<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Publishing DTD v1.3 20210610//EN" "JATS-journalpublishing1-3.dtd">
<article article-type="research-article" dtd-version="1.3" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xml:lang="ru"><front><journal-meta><journal-id journal-id-type="publisher-id">vavilov</journal-id><journal-title-group><journal-title xml:lang="ru">Вавиловский журнал генетики и селекции</journal-title><trans-title-group xml:lang="en"><trans-title>Vavilov Journal of Genetics and Breeding</trans-title></trans-title-group></journal-title-group><issn pub-type="epub">2500-3259</issn><publisher><publisher-name>Institute of Cytology and Genetics of Siberian Branch of the RAS</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="doi">10.18699/vjgb-24-13</article-id><article-id custom-type="elpub" pub-id-type="custom">vavilov-4061</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="section-heading" xml:lang="ru"><subject>ГЕНЕТИКА ЖИВОТНЫХ</subject></subj-group><subj-group subj-group-type="section-heading" xml:lang="en"><subject>ANIMAL GENETICS</subject></subj-group></article-categories><title-group><article-title>Сравнительные особенности геномного разнообразия кур Gallus gallus domesticus с декоративным фенотипом оперения «баки и борода»</article-title><trans-title-group xml:lang="en"><trans-title>Comparative peculiarities of genomic diversity in Gallus gallus domesticus chickens with decorative plumage: the muffs and beard phenotype</trans-title></trans-title-group></title-group><contrib-group><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0003-0210-9344</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Дементьева</surname><given-names>Н. В.</given-names></name><name name-style="western" xml:lang="en"><surname>Dementieva</surname><given-names>N. V.</given-names></name></name-alternatives><bio xml:lang="ru"><p>пос. Тярлево, Санкт-Петербург</p></bio><bio xml:lang="en"><p>Tyarlevo, St. Petersburg</p></bio><xref ref-type="aff" rid="aff-1"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0001-6434-6287</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Щербаков</surname><given-names>Ю. С.</given-names></name><name name-style="western" xml:lang="en"><surname>Shcherbakov</surname><given-names>Y. S.</given-names></name></name-alternatives><bio xml:lang="ru"><p>пос. Тярлево, Санкт-Петербург</p></bio><bio xml:lang="en"><p>Tyarlevo, St. Petersburg</p></bio><xref ref-type="aff" rid="aff-1"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0003-2362-2892</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Рябова</surname><given-names>А. Е.</given-names></name><name name-style="western" xml:lang="en"><surname>Ryabova</surname><given-names>A. E.</given-names></name></name-alternatives><bio xml:lang="ru"><p>пос. Тярлево, Санкт-Петербург</p></bio><bio xml:lang="en"><p>Tyarlevo, St. Petersburg</p></bio><xref ref-type="aff" rid="aff-2"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0001-5166-979X</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Вахрамеев</surname><given-names>А. Б.</given-names></name><name name-style="western" xml:lang="en"><surname>Vakhrameev</surname><given-names>A. B.</given-names></name></name-alternatives><bio xml:lang="ru"><p>пос. Тярлево, Санкт-Петербург</p></bio><bio xml:lang="en"><p>Tyarlevo, St. Petersburg</p></bio><xref ref-type="aff" rid="aff-2"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0002-3281-4581</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Макарова</surname><given-names>А. В.</given-names></name><name name-style="western" xml:lang="en"><surname>Makarova</surname><given-names>A. V.</given-names></name></name-alternatives><bio xml:lang="ru"><p>пос. Тярлево, Санкт-Петербург</p></bio><bio xml:lang="en"><p>Tyarlevo, St. Petersburg</p></bio><xref ref-type="aff" rid="aff-1"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0003-3828-1111</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Николаева</surname><given-names>О. А.</given-names></name><name name-style="western" xml:lang="en"><surname>Nikolaeva</surname><given-names>O. A.</given-names></name></name-alternatives><bio xml:lang="ru"><p>пос. Тярлево, Санкт-Петербург</p></bio><bio xml:lang="en"><p>Tyarlevo, St. Petersburg</p></bio><xref ref-type="aff" rid="aff-2"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0002-4468-0365</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Дысин</surname><given-names>А. П.</given-names></name><name name-style="western" xml:lang="en"><surname>Dysin</surname><given-names>A. P.</given-names></name></name-alternatives><bio xml:lang="ru"><p>пос. Тярлево, Санкт-Петербург</p></bio><bio xml:lang="en"><p>Tyarlevo, St. Petersburg</p></bio><xref ref-type="aff" rid="aff-2"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0002-2963-378X</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Азовцева</surname><given-names>А. И.</given-names></name><name name-style="western" xml:lang="en"><surname>Azovtseva</surname><given-names>A. I.</given-names></name></name-alternatives><bio xml:lang="ru"><p>пос. Тярлево, Санкт-Петербург</p></bio><bio xml:lang="en"><p>Tyarlevo, St. Petersburg</p></bio><xref ref-type="aff" rid="aff-2"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0001-6193-5617</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Рейнбах</surname><given-names>Н. Р.</given-names></name><name name-style="western" xml:lang="en"><surname>Reinbah</surname><given-names>N. R.</given-names></name></name-alternatives><bio xml:lang="ru"><p>пос. Тярлево, Санкт-Петербург</p></bio><bio xml:lang="en"><p>Tyarlevo, St. Petersburg</p></bio><xref ref-type="aff" rid="aff-2"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0003-4702-2736</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Митрофанова</surname><given-names>О. В.</given-names></name><name name-style="western" xml:lang="en"><surname>Mitrofanova</surname><given-names>O. V.</given-names></name></name-alternatives><bio xml:lang="ru"><p>пос. Тярлево, Санкт-Петербург</p></bio><bio xml:lang="en"><p>Tyarlevo, St. Petersburg</p></bio><email xlink:type="simple">mo1969@mail.ru</email><xref ref-type="aff" rid="aff-2"/></contrib></contrib-group><aff-alternatives id="aff-1"><aff xml:lang="ru">Всероссийский научно-­исследовательский институт генетики и разведения сельскохозяйственных животных – филиал Федерального исследовательского центра животноводства – ВИЖ им. академика Л.К. Эрнста<country>Россия</country></aff><aff xml:lang="en">Russian Research Institute of Farm Animal Genetics and Breeding – Branch of the L.K. Ernst Federal Research Center for Animal Husbandry<country>Russian Federation</country></aff></aff-alternatives><aff-alternatives id="aff-2"><aff xml:lang="ru">Всероссийский научно­-исследовательский институт генетики и разведения сельскохозяйственных животных – филиал Федерального исследовательского центра животноводства – ВИЖ им. академика Л.К. Эрнста<country>Россия</country></aff><aff xml:lang="en">Russian Research Institute of Farm Animal Genetics and Breeding – Branch of the L.K. Ernst Federal Research Center for Animal Husbandry<country>Russian Federation</country></aff></aff-alternatives><pub-date pub-type="collection"><year>2024</year></pub-date><pub-date pub-type="epub"><day>02</day><month>03</month><year>2024</year></pub-date><volume>28</volume><issue>1</issue><fpage>108</fpage><lpage>116</lpage><permissions><copyright-statement>Copyright &amp;#x00A9; Дементьева Н.В., Щербаков Ю.С., Рябова А.Е., Вахрамеев А.Б., Макарова А.В., Николаева О.А., Дысин А.П., Азовцева А.И., Рейнбах Н.Р., Митрофанова О.В., 2024</copyright-statement><copyright-year>2024</copyright-year><copyright-holder xml:lang="ru">Дементьева Н.В., Щербаков Ю.С., Рябова А.Е., Вахрамеев А.Б., Макарова А.В., Николаева О.А., Дысин А.П., Азовцева А.И., Рейнбах Н.Р., Митрофанова О.В.</copyright-holder><copyright-holder xml:lang="en">Dementieva N.V., Shcherbakov Y.S., Ryabova A.E., Vakhrameev A.B., Makarova A.V., Nikolaeva O.A., Dysin A.P., Azovtseva A.I., Reinbah N.R., Mitrofanova O.V.</copyright-holder><license license-type="creative-commons-attribution" xlink:href="https://creativecommons.org/licenses/by/4.0/" xlink:type="simple"><license-p>This work is licensed under a Creative Commons Attribution 4.0 License.</license-p></license></permissions><self-uri xlink:href="https://vavilov.elpub.ru/jour/article/view/4061">https://vavilov.elpub.ru/jour/article/view/4061</self-uri><abstract><p>На протяжении истории взаимодействия с домашними животными человек стремился усилить не только их продуктивные качества, но и различные декоративные особенности. У кур ряда пород сформировались пучки удлиненных перьев, выступающих сбоку и снизу от клюва, образуя фенотип, описываемый как «баки и борода» (англ. muffs and beard). Это неполный аутосомно-­доминантный фенотип, кодируемый локусом Mb, локализованным на хромосоме GGA27. Цель нашей работы – проанализировать генетическое разнообразие пород кур, определенное с помощью полногеномного генотипирования с использованием чипов Chicken 60K BeadChip. Всего в анализе учитывалось 53 313 однонуклеотидных полиморфных замен (SNP). ДНК получена от пород, обладающих маркерным признаком «баки и борода»: фавероль (n = 20), украинская ушанка (n = 18), орловская (n = 20), новопавловская белая (n = 20) и новопавловская цветная (n = 15). В качестве альтернативной породы, не имеющей фенотипа «баки и борода», использовалась русская белая (n = 20). Птица содержалась в ЦКП «Генетическая коллекция редких и исчезающих пород кур» (г. Санкт­-Петербург, Пушкин), входящем в состав Сетевой биоресурсной коллекции животных и птиц. Методом многомерного шкалирования установлено, что отдельную группировку образовали популяции новопавловская белая и новопавловская цветная. В самостоятельную группу объединились породы украинская ушанка и орловская. С помощью кластерного анализа с учетом ошибки кросс­валидации и наиболее вероятным числом кластеров K = 4 орловская порода выделена в отдельную группу. Украинская ушанка в этом случае продемонстрировала значительное сходство с орловской породой. При K = 5 разделились новопавловская белая и новопавловская цветная популяции. И только при K = 6 явный отдельный кластер образовала украинская ушанка. У кур русской белой породы отмечено наибольшее количество коротких (1–2 Mб) гомозиготных районов. В месте расположения гена HOXB8 в регионе 3.402–3.404 Мб на хромосоме GGA27 у представителей пород c фенотипом «баки и борода» гомозиготные районы встречаются редко. Сканирование генома кур с использованием чипа Chicken 60K BeadChip позволяет получить достаточно информации о генетическом разнообразии пород кур для понимания особенностей формирования у них декоративного фенотипа «баки и борода».</p></abstract><trans-abstract xml:lang="en"><p>Throughout history, humans have been attempting to develop the ornamental features of domestic animals in addition to their productive qualities. Many chicken breeds have developed tufts of elongated feathers that jut out from the sides and bottom of the beak, leading to the phenotype known as muffs and beard. It is an incomplete autosomal dominant phenotype determined by the Mb locus localised on chromosome GGA27. This project aimed to analyse the genetic diversity of chicken breeds using full genomic genotyping with the Chicken 60K BeadChip. A total of 53,313 Single Nucleotide Polymorphisms were analysed. DNA was obtained from breeds with the muffs and beard as a marker phenotype: Faverolles (n = 20), Ukrainian Muffed (n = 18), Orloff (n = 20), Novopavlov White (n = 20), and Novopavlov Coloured (n = 15). The Russian White (n = 20) was selected as an alternative breed without the muffs and beard phenotype. The chickens are owned by the Centre of Collective Use “Genetic Collection of Rare and Endangered Breeds of Chickens” (St. Petersburg region, Pushkin), and are also included in the Core Shared Research Facility (CSRF) and/or Large­Scale Research Facility (LSRF). Multidimensional scaling revealed that the Novopavlov White and the Novopavlov Coloured populations formed a separate group. The Ukrainian Muffed and the Orloff have also been combined into a separate group. Based on cluster analysis, with the cross­validation error and the most probable number of clusters K = 4 taken into account, the Orloff was singled out as a separate group. The Ukrainian Muffed exhibited a notable similarity with the Orloff under the same conditions. At K = 5, the populations of the Novopavlov White and the Novopavlov Coloured diverged. Only at K = 6, a distinct and separate cluster was formed by the Ukrainian Muffed. The Russian White had the greatest number of short (1–2 Mb) homozygous regions. If the HOXB8 gene is located between 3.402 and 3.404 Mb on chromosome GGA27, homozygous regions are rarely found in the chickens with the muffs and beard phenotype. Scanning the chicken genome with the Chicken 60K BeadChip provided enough information about the genetic diversity of the chicken breeds for the peculiarities of the development of the ornamental muffs and beard phenotypes in them to be understood. For example, Phoenix bantams, whose tail feathers grow throughout their lives, require greater consideration of husbandry conditions.</p></trans-abstract><kwd-group xml:lang="ru"><kwd>полногеномное генотипирование</kwd><kwd>SNP-­маркер</kwd><kwd>фенотип</kwd><kwd>генотип</kwd><kwd>генетическое разнообразие</kwd><kwd>полиморфизм</kwd><kwd>гетерозиготность</kwd><kwd>ДНК</kwd><kwd>породы кур</kwd></kwd-group><kwd-group xml:lang="en"><kwd>whole­-genome genotyping</kwd><kwd>SNP marker</kwd><kwd>phenotype</kwd><kwd>genotype</kwd><kwd>genetic diversity</kwd><kwd>polymorphism</kwd><kwd>heterozygosity</kwd><kwd>DNA</kwd><kwd>chicken breeds</kwd></kwd-group><funding-group xml:lang="en"><funding-statement>We are thankful for the support of this work provided by the Centre of Collective Use, the owner of Genetic Collection of Rare and Endangered Breeds of Chickens. This work was financially supported by the Ministry of Science and Higher Education of the Russian Federation, Grant No. 075-15-2021-1037 (Internal No. 15.BRK.21.0001).</funding-statement></funding-group></article-meta></front><back><ref-list><title>References</title><ref id="cit1"><label>1</label><citation-alternatives><mixed-citation xml:lang="ru">Alexander D.H., Novembre J., Lange K. Fast model­based estimation of ancestryin unrelated individuals. Genome Res. 2009;19(9):1655-1664. DOI 10.1101/gr.094052.109</mixed-citation><mixed-citation xml:lang="en">Alexander D.H., Novembre J., Lange K. Fast model­based estimation of ancestryin unrelated individuals. Genome Res. 2009;19(9):1655-1664. DOI 10.1101/gr.094052.109</mixed-citation></citation-alternatives></ref><ref id="cit2"><label>2</label><citation-alternatives><mixed-citation xml:lang="ru">Anderson C., Pettersson F., Clarke G., Cardon L.R., Morris A.P., Zondervan K.T. Data quality control in genetic case­control association studies. Nat. Protoc. 2010;5:1564-­1573. DOI 10.1038/nprot.2010.116</mixed-citation><mixed-citation xml:lang="en">Anderson C., Pettersson F., Clarke G., Cardon L.R., Morris A.P., Zondervan K.T. Data quality control in genetic case­control association studies. Nat. Protoc. 2010;5:1564-­1573. DOI 10.1038/nprot.2010.116</mixed-citation></citation-alternatives></ref><ref id="cit3"><label>3</label><citation-alternatives><mixed-citation xml:lang="ru">Biscarini F., Cozzi P., Orozco­ter Wengel P. Lessons learnt on the analysis of large sequence data in animal genomics. Anim. Genet. 2018;49(3):147-­158. DOI 10.1111/age.12655</mixed-citation><mixed-citation xml:lang="en">Biscarini F., Cozzi P., Orozco­ter Wengel P. Lessons learnt on the analysis of large sequence data in animal genomics. Anim. Genet. 2018;49(3):147-­158. DOI 10.1111/age.12655</mixed-citation></citation-alternatives></ref><ref id="cit4"><label>4</label><citation-alternatives><mixed-citation xml:lang="ru">Bryant D., Moulton V. Neighbor­net: an agglomerative method for the construction of phylogenetic networks. Mol. Biol. Evol. 2004;21(2): 255­-265. DOI.10.1093/molbev/msh018</mixed-citation><mixed-citation xml:lang="en">Bryant D., Moulton V. Neighbor­net: an agglomerative method for the construction of phylogenetic networks. Mol. Biol. Evol. 2004;21(2): 255­-265. DOI.10.1093/molbev/msh018</mixed-citation></citation-alternatives></ref><ref id="cit5"><label>5</label><citation-alternatives><mixed-citation xml:lang="ru">Dementeva N.V., Romanov M.N., Kudinov A.A., Mitrofanova O.V., Stanishevskaya O.I., Terletsky V.P., Fedorova E.S., Nikitkina E.V., Plemyashov K.V. Studying the structure of a gene pool population of the Russian White chicken breed by genome­wide SNP scan. Selskokhozyaystvennaya Biologiya = Agricultural Biology. 2017; 52(6):1166-­1174. DOI 10.15389/agrobiology.2017.6.1166eng</mixed-citation><mixed-citation xml:lang="en">Dementeva N.V., Romanov M.N., Kudinov A.A., Mitrofanova O.V., Stanishevskaya O.I., Terletsky V.P., Fedorova E.S., Nikitkina E.V., Plemyashov K.V. Studying the structure of a gene pool population of the Russian White chicken breed by genome­wide SNP scan. Selskokhozyaystvennaya Biologiya = Agricultural Biology. 2017; 52(6):1166-­1174. DOI 10.15389/agrobiology.2017.6.1166eng</mixed-citation></citation-alternatives></ref><ref id="cit6"><label>6</label><citation-alternatives><mixed-citation xml:lang="ru">Dementieva N.V., Kudinov A.A., Larkina T.A., Mitrofanova O.V., Dysin A.P., Terletsky V.P., Tyshchenko V.I., Griffin D.K., Romanov M.N. Genetic variability in local and imported germplasm chicken populations as revealed by analyzing runs of homozygosity. Animals (Basel). 2020;10(10):1887. DOI 10.3390/ani10101887</mixed-citation><mixed-citation xml:lang="en">Dementieva N.V., Kudinov A.A., Larkina T.A., Mitrofanova O.V., Dysin A.P., Terletsky V.P., Tyshchenko V.I., Griffin D.K., Romanov M.N. Genetic variability in local and imported germplasm chicken populations as revealed by analyzing runs of homozygosity. Animals (Basel). 2020;10(10):1887. DOI 10.3390/ani10101887</mixed-citation></citation-alternatives></ref><ref id="cit7"><label>7</label><citation-alternatives><mixed-citation xml:lang="ru">Dementieva N.V., Mitrofanova O.V., Dysin A.P., Kudinov A.A., Stanishevskaya O.I., Larkina T.A., Plemyashov K.V., Griffin D.K., Romanov M.N., Smaragdov M.G. Assessing the effects of rare alleles and linkage disequilibrium on estimates of genetic diversity in the chicken populations. Animal. 2021;15(3):100-171. DOI 10.1016/j.animal.2021.100171</mixed-citation><mixed-citation xml:lang="en">Dementieva N.V., Mitrofanova O.V., Dysin A.P., Kudinov A.A., Stanishevskaya O.I., Larkina T.A., Plemyashov K.V., Griffin D.K., Romanov M.N., Smaragdov M.G. Assessing the effects of rare alleles and linkage disequilibrium on estimates of genetic diversity in the chicken populations. Animal. 2021;15(3):100-171. DOI 10.1016/j.animal.2021.100171</mixed-citation></citation-alternatives></ref><ref id="cit8"><label>8</label><citation-alternatives><mixed-citation xml:lang="ru">Fedorova E.S., Dementieva N.V., Shcherbakov Y.S., Stanishevskaya O.I. Identification of key candidate genes in runs of homozygosity of the genome of two chicken breeds, associated with cold adaptation. Biology (Basel). 2022;11(4):547. DOI 10.3390/biology11040547</mixed-citation><mixed-citation xml:lang="en">Fedorova E.S., Dementieva N.V., Shcherbakov Y.S., Stanishevskaya O.I. Identification of key candidate genes in runs of homozygosity of the genome of two chicken breeds, associated with cold adaptation. Biology (Basel). 2022;11(4):547. DOI 10.3390/biology11040547</mixed-citation></citation-alternatives></ref><ref id="cit9"><label>9</label><citation-alternatives><mixed-citation xml:lang="ru">Ferenčaković M., Sölkner J., Curik I. Estimating autozygosity from high­throughput information: effects of SNP density and genotyping errors. Genet. Sel. Evol. 2013;45:42. DOI 10.1186/1297­-9686-45-42</mixed-citation><mixed-citation xml:lang="en">Ferenčaković M., Sölkner J., Curik I. Estimating autozygosity from high­throughput information: effects of SNP density and genotyping errors. Genet. Sel. Evol. 2013;45:42. DOI 10.1186/1297­-9686-45-42</mixed-citation></citation-alternatives></ref><ref id="cit10"><label>10</label><citation-alternatives><mixed-citation xml:lang="ru">Fisinin V.I., Selionova M.I., Shinkarenko L.A., Shcherbakova N.G. Study of microsatellites in the Russian breeds of turkey. Selskokhozyaystvennaya Biologiya = Agricultural Biology. 2017;52(4):739-748. DOI 10.15389/agrobiology.2017.4.739eng</mixed-citation><mixed-citation xml:lang="en">Fisinin V.I., Selionova M.I., Shinkarenko L.A., Shcherbakova N.G. Study of microsatellites in the Russian breeds of turkey. Selskokhozyaystvennaya Biologiya = Agricultural Biology. 2017;52(4):739-748. DOI 10.15389/agrobiology.2017.4.739eng</mixed-citation></citation-alternatives></ref><ref id="cit11"><label>11</label><citation-alternatives><mixed-citation xml:lang="ru">Francis R.M. Pophelper: an R package and web app to analyse and visualize population structure. Mol. Ecol. Resour. 2017;17(1):27­32. DOI 10.1111/1755­0998.12509</mixed-citation><mixed-citation xml:lang="en">Francis R.M. Pophelper: an R package and web app to analyse and visualize population structure. Mol. Ecol. Resour. 2017;17(1):27­32. DOI 10.1111/1755­0998.12509</mixed-citation></citation-alternatives></ref><ref id="cit12"><label>12</label><citation-alternatives><mixed-citation xml:lang="ru">Guo H.W., Li C., Wang X.N., Li Z.J., Sun G.R., Li G.X., Liu X.J., Kang X.T., Han R.L. Genetic diversity of mtDNA D­loop sequences in four native Chinese chicken breeds. Br. Poult. Sci. 2017;58(5): 490­-497. DOI 10.1080/00071668.2017.1332403</mixed-citation><mixed-citation xml:lang="en">Guo H.W., Li C., Wang X.N., Li Z.J., Sun G.R., Li G.X., Liu X.J., Kang X.T., Han R.L. Genetic diversity of mtDNA D­loop sequences in four native Chinese chicken breeds. Br. Poult. Sci. 2017;58(5): 490­-497. DOI 10.1080/00071668.2017.1332403</mixed-citation></citation-alternatives></ref><ref id="cit13"><label>13</label><citation-alternatives><mixed-citation xml:lang="ru">Guo Y., Gu X., Sheng Z., Wang Y., Luo C., Liu R., Qu H., Shu D., Wen J., Crooijmans R.P., Carlborg Ö., Zhao Y., Hu X., Li N. A complex structural variation on chromosome 27 leads to the ectopic expression of HOXB8 and the muffs and beard phenotype in chickens. PLoS Genet. 2016;12(6):e1006071. DOI 10.1371/journal.pgen.1006071</mixed-citation><mixed-citation xml:lang="en">Guo Y., Gu X., Sheng Z., Wang Y., Luo C., Liu R., Qu H., Shu D., Wen J., Crooijmans R.P., Carlborg Ö., Zhao Y., Hu X., Li N. A complex structural variation on chromosome 27 leads to the ectopic expression of HOXB8 and the muffs and beard phenotype in chickens. PLoS Genet. 2016;12(6):e1006071. DOI 10.1371/journal.pgen.1006071</mixed-citation></citation-alternatives></ref><ref id="cit14"><label>14</label><citation-alternatives><mixed-citation xml:lang="ru">Huson D., Bryant D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 2006;23(2):254-­267. DOI 10.1093/molbev/msj030</mixed-citation><mixed-citation xml:lang="en">Huson D., Bryant D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 2006;23(2):254-­267. DOI 10.1093/molbev/msj030</mixed-citation></citation-alternatives></ref><ref id="cit15"><label>15</label><citation-alternatives><mixed-citation xml:lang="ru">Keenan K., McGinnity P., Cross T.F., Crozier W.W., Prodöhl P.A. diveRsity: an R package for the estimation and exploration of population genetics parameters and their associated errors. Methods Ecol. Evol. 2013;4(8):782-­788. DOI 10.1111/2041­210X.12067</mixed-citation><mixed-citation xml:lang="en">Keenan K., McGinnity P., Cross T.F., Crozier W.W., Prodöhl P.A. diveRsity: an R package for the estimation and exploration of population genetics parameters and their associated errors. Methods Ecol. Evol. 2013;4(8):782-­788. DOI 10.1111/2041­210X.12067</mixed-citation></citation-alternatives></ref><ref id="cit16"><label>16</label><citation-alternatives><mixed-citation xml:lang="ru">Krivoruchko A.Y., Skokova A.V., Yatsyk O.A., Kanibolotskaya A.A. Modern approaches to the genetic identification of farm animal breeds (review). Agrarnaya Nauka Evro-Severo-Vostoka = Agricultural Science Euro-North-East. 2021;22(3):317-­328. DOI 10.30766/2072­-9081.2021.22.3.317-­328 (in Russian)</mixed-citation><mixed-citation xml:lang="en">Krivoruchko A.Y., Skokova A.V., Yatsyk O.A., Kanibolotskaya A.A. Modern approaches to the genetic identification of farm animal breeds (review). Agrarnaya Nauka Evro-Severo-Vostoka = Agricultural Science Euro-North-East. 2021;22(3):317-­328. DOI 10.30766/2072­-9081.2021.22.3.317-­328 (in Russian)</mixed-citation></citation-alternatives></ref><ref id="cit17"><label>17</label><citation-alternatives><mixed-citation xml:lang="ru">Lawal R.A., Hanotte O. Domestic chicken diversity: origin, distribution, and adaptation. Anim. Genet. 2021;52(4):385­-394. DOI 10.1111/age.13091</mixed-citation><mixed-citation xml:lang="en">Lawal R.A., Hanotte O. Domestic chicken diversity: origin, distribution, and adaptation. Anim. Genet. 2021;52(4):385­-394. DOI 10.1111/age.13091</mixed-citation></citation-alternatives></ref><ref id="cit18"><label>18</label><citation-alternatives><mixed-citation xml:lang="ru">Letunic I., Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021; 49(W1):W293-­W296. DOI 10.1093/nar/gkab301</mixed-citation><mixed-citation xml:lang="en">Letunic I., Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021; 49(W1):W293-­W296. DOI 10.1093/nar/gkab301</mixed-citation></citation-alternatives></ref><ref id="cit19"><label>19</label><citation-alternatives><mixed-citation xml:lang="ru">Malomane D.K., Simianer H., Weigend A., Reimer C., Schmitt A.O., Weigend S. The SYNBREED chicken diversity panel: a global resource to assess chicken diversity at high genomic resolution. BMC Genomics. 2019;20(1):345. DOI 10.1186/s12864-­019­5727­-9</mixed-citation><mixed-citation xml:lang="en">Malomane D.K., Simianer H., Weigend A., Reimer C., Schmitt A.O., Weigend S. The SYNBREED chicken diversity panel: a global resource to assess chicken diversity at high genomic resolution. BMC Genomics. 2019;20(1):345. DOI 10.1186/s12864-­019­5727­-9</mixed-citation></citation-alternatives></ref><ref id="cit20"><label>20</label><citation-alternatives><mixed-citation xml:lang="ru">Mulim H.A., Brito L.F., Pinto L.F.B., Ferraz J.B.S., Grigoletto L., Silva M.R., Pedrosa V.B. Characterization of runs of homozygosity, heterozygosity-enriched regions, and population structure in cattle populations selected for different breeding goals. BMC Genomics. 2022;23(1):209. DOI 10.1186/s12864­-022­-08384-­0</mixed-citation><mixed-citation xml:lang="en">Mulim H.A., Brito L.F., Pinto L.F.B., Ferraz J.B.S., Grigoletto L., Silva M.R., Pedrosa V.B. Characterization of runs of homozygosity, heterozygosity-enriched regions, and population structure in cattle populations selected for different breeding goals. BMC Genomics. 2022;23(1):209. DOI 10.1186/s12864­-022­-08384-­0</mixed-citation></citation-alternatives></ref><ref id="cit21"><label>21</label><citation-alternatives><mixed-citation xml:lang="ru">Paronyan I.A., Jurchenko O.P., Vakhrameev A.B., Makarova A.V. Breeding of indigenous and rare breeds of chickens. Genetika i Razvedenie Životnyh = Animal Genetics and Breeding. 2016;4:62-66 (in Russian)</mixed-citation><mixed-citation xml:lang="en">Paronyan I.A., Jurchenko O.P., Vakhrameev A.B., Makarova A.V. Breeding of indigenous and rare breeds of chickens. Genetika i Razvedenie Životnyh = Animal Genetics and Breeding. 2016;4:62-66 (in Russian)</mixed-citation></citation-alternatives></ref><ref id="cit22"><label>22</label><citation-alternatives><mixed-citation xml:lang="ru">Pembleton L.W., Cogan N.O., Forster J.W. StAMPP: an R package for calculation of genetic differentiation and structure of mixed­ploidy level populations. Mol. Ecol. Resour. 2013;13(5):946-­952. DOI 10.1111/1755-­0998.12129</mixed-citation><mixed-citation xml:lang="en">Pembleton L.W., Cogan N.O., Forster J.W. StAMPP: an R package for calculation of genetic differentiation and structure of mixed­ploidy level populations. Mol. Ecol. Resour. 2013;13(5):946-­952. DOI 10.1111/1755-­0998.12129</mixed-citation></citation-alternatives></ref><ref id="cit23"><label>23</label><citation-alternatives><mixed-citation xml:lang="ru">Price A.L., Patterson N.J., Plenge R.M., Weinblatt M.E., Shadick N.A., Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 2006;38(8):904­-909. DOI 10.1038/ng1847</mixed-citation><mixed-citation xml:lang="en">Price A.L., Patterson N.J., Plenge R.M., Weinblatt M.E., Shadick N.A., Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 2006;38(8):904­-909. DOI 10.1038/ng1847</mixed-citation></citation-alternatives></ref><ref id="cit24"><label>24</label><citation-alternatives><mixed-citation xml:lang="ru">Purfield D.C., Berry D.P., McParland S., Bradley D.G. Runs of homozygosity and population history in cattle. BMC Genet. 2012;13:70. DOI 10.1186/1471-­2156­-13­-70</mixed-citation><mixed-citation xml:lang="en">Purfield D.C., Berry D.P., McParland S., Bradley D.G. Runs of homozygosity and population history in cattle. BMC Genet. 2012;13:70. DOI 10.1186/1471-­2156­-13­-70</mixed-citation></citation-alternatives></ref><ref id="cit25"><label>25</label><citation-alternatives><mixed-citation xml:lang="ru">Restoux G., Rognon X., Vieaud A., Guemene D., Petitjean F., Rouger R., Brard­Fudulea S., Lubac­Paye S., Chiron G., Tixier­Boichard M. Managing genetic diversity in breeding programs of small populations: the case of French local chicken breeds. Genet. Sel. Evol. 2022;54:56. DOI 10.1186/s12711-­022-­00746-­2</mixed-citation><mixed-citation xml:lang="en">Restoux G., Rognon X., Vieaud A., Guemene D., Petitjean F., Rouger R., Brard­Fudulea S., Lubac­Paye S., Chiron G., Tixier­Boichard M. Managing genetic diversity in breeding programs of small populations: the case of French local chicken breeds. Genet. Sel. Evol. 2022;54:56. DOI 10.1186/s12711-­022-­00746-­2</mixed-citation></citation-alternatives></ref><ref id="cit26"><label>26</label><citation-alternatives><mixed-citation xml:lang="ru">Strillacci G., Cozzi M.C., Gorla E., Mosca F., Schiavini F., Román-Ponce S.I., Ruiz López F.J., Schiavone A., Marzoni M., Cerolini S., Bagnato A. Genomic and genetic variability of six chicken populations using single nucleotide polymorphism and copy number variants as markers. Animal. 2017;11(5):737­-745. DOI 10.1017/S1751731116002135</mixed-citation><mixed-citation xml:lang="en">Strillacci G., Cozzi M.C., Gorla E., Mosca F., Schiavini F., Román-Ponce S.I., Ruiz López F.J., Schiavone A., Marzoni M., Cerolini S., Bagnato A. Genomic and genetic variability of six chicken populations using single nucleotide polymorphism and copy number variants as markers. Animal. 2017;11(5):737­-745. DOI 10.1017/S1751731116002135</mixed-citation></citation-alternatives></ref><ref id="cit27"><label>27</label><citation-alternatives><mixed-citation xml:lang="ru">Yang K.X., Zhou H., Ding J.M., He C., Niu Q., Gu C.J., Zhou Z.X., Meng H., Huang Q.Z. Copy number variation in HOXB7 and HOXB8 involves in the formation of beard trait in chickens. Anim. Genet. 2020;51(6):958­-963. DOI 10.1111/age.13011</mixed-citation><mixed-citation xml:lang="en">Yang K.X., Zhou H., Ding J.M., He C., Niu Q., Gu C.J., Zhou Z.X., Meng H., Huang Q.Z. Copy number variation in HOXB7 and HOXB8 involves in the formation of beard trait in chickens. Anim. Genet. 2020;51(6):958­-963. DOI 10.1111/age.13011</mixed-citation></citation-alternatives></ref><ref id="cit28"><label>28</label><citation-alternatives><mixed-citation xml:lang="ru">Yuan J., Li S., Sheng Z., Zhang M., Liu X., Yuan Z., Yang N., Chen J. Genome-wide run of homozygosity analysis reveals candidate genomic regions associated with environmental adaptations of Tibetan native chickens. BMC Genomics. 2022;23(1):91. DOI 10.1186/s12864-­021-­08280­-z</mixed-citation><mixed-citation xml:lang="en">Yuan J., Li S., Sheng Z., Zhang M., Liu X., Yuan Z., Yang N., Chen J. Genome-wide run of homozygosity analysis reveals candidate genomic regions associated with environmental adaptations of Tibetan native chickens. BMC Genomics. 2022;23(1):91. DOI 10.1186/s12864-­021-­08280­-z</mixed-citation></citation-alternatives></ref></ref-list><fn-group><fn fn-type="conflict"><p>The authors declare that there are no conflicts of interest present.</p></fn></fn-group></back></article>
