Ecological geneticsEcological geneticsЭкологическая генетика1811-09322411-9202Eco-Vector69046810.17816/ecogen690468KWRQRPGenetic basis of ecosystems evolutionГенетические основы эволюции экосистемResearch ArticleSearch for traces of selection for meat productivity in Cornish chickensПоиск следов селекции мясной продуктивности у кур породы корнишhttps://orcid.org/0000-0002-5087-64449897-0884SmaragdovMichael G.СмарагдовМихаил Григорьевич
Russian Federation

Cand. Sci. (Biology)

канд. биол. наук

mik7252@yandex.ruhttps://orcid.org/0000-0003-0210-93448768-8906DementievaNatalia V.ДементьеваНаталия Викторовна
Russian Federation

Cand. Sci. (Biology)

канд. биол. наук

dementevan@mail.ruhttps://orcid.org/0000-0001-6434-62873547-1009ShcherbakovYuri S.ЩербаковЮрий Сергеевич
Russian Federation

Cand. Sci. (Biology)

канд. биол. наук

yura.10.08.94.94@mail.ruResearch Institute of Farm Animal Genetics and Breeding—Branch of the Academician L.K. Ernst Federal Research Center for Animal HusbandryВсероссийский научно-исследовательский институт генетики и разведения сельскохозяйственных животных — филиал Федерального исследовательского центра животноводства — ВИЖ им. акад. Л.К. Эрнста26112025020720262421051161809202526112025Copyright ©; 2026, Eco-VectorCopyright ©; 2026, Эко-Вектор2026Eco-VectorЭко-Векторhttps://eco-vector.com/for_authors.php#07https://journals.eco-vector.com/ecolgenet/article/view/690468

BACKGROUND: One approach to identify the “traces” of selection is to search for extended homozygous (ROH) and heterozygous-enriched (HRR) regions in the animal genome. ROH islands are thought to result from directional selection, while HRR islands are thought to result from balanced selection.

AIM: This study aimed to perfrom a genome-wide SNP analysis of the genotype of cross-selected Cornish chickens to identify ROH and HRR islands on their chromosomes and to annotate the genes within them.

METHODS: For this study, biological materials of the Cornish Hubbard cross were obtained from the biobank of the RRIFAGB institute. The chickens were genotyped with a 60K SNP array.

RESULTS: The HRR segments were an order of magnitude shorter than the ROH segments. The data indicate the removal of monomorphic SNPs from the chicken genome, since SNPs with a minor allele frequency (MAF) < 0.01 were removed. The localization of the ROH islands was completely altered by the removal of SNPs with a MAF < 0.01, whereas the localization of the HRR islands was only partially altered. Genes in the ROH islands identified while retaining SNPs with a MAF < 0.01 are responsible for chicken weight and their feed consumption. Removal of SNPs with a MAF < 0.01 identified ROH islands containing genes associated with the regulation of intramuscular fat content and the number of eggs laid. The HRR islands that were found contain genes responsible for chicken body weight, feed intake, and embryonic development.

CONCLUSIONS: Genes located in ROH islands are responsible for the consumer traits of the Cornish meat breed bred by directional selection, while genes located in HRR islands are most likely not targets of balanced selection.

Обоснование. Один из подходов к выявлению «следов» селекции — поиск протяжённых гомозиготных (ROH) и обогащённых гетерозиготностью (HRR) регионов в геноме животных. Считается, что ROH-острова являются результатом направленного отбора, тогда как HRR-участки — результатом сбалансированного отбора.

Цель исследования. Полногеномный SNP-анализ генотипа кроссов кур мясного направления породы корниш для выявления ROH- и HRR-острова в хромосомах и аннотирования генов в их пределах.

Методы. Для целей данного исследования биологический материал корниш кросса Хаббард был получен из биобанка Всероссийского научно-исследовательского института генетики и разведения сельскохозяйственных животных. Цыплят генотипировали с использованием ДНК-чипа плотностью 60K.

Результаты. Сегменты HRR были на порядок короче сегментов ROH. Данные указывают на удаление мономорфных однонуклеотидных замен (SNP) в геноме кур, поскольку SNP с частотой минорного аллеля (MAF) < 0,01 были исключены. Локализация ROH-островов полностью изменилась после удаления SNP с MAF < 0,01, тогда как локализация HRR-островов изменилась лишь частично. Гены в ROH-островах при сохранении SNP с MAF < 0,01 связаны с массой птиц и конверсией корма. Удаление SNP с MAF < 0,01 позволило идентифицировать ROH-острова, содержащие гены, ассоциированные с регуляцией содержания внутримышечного жира и количеством снесённых яиц. Обнаруженные HRR-острова содержат гены, ответственные за живую массу цыплят, потребление корма и эмбриональное развитие.

Выводы. Гены, расположенные в ROH-островах, отвечают за потребительские признаки мясной породы корниш, выведенной методом направленного отбора, тогда как гены, расположенные в HRR-островах, с высокой вероятностью не являются целью сбалансированного отбора.

single nucleotide polymorphismruns of homozygosityheterozygosity rich regionschickensоднонуклеотидный полиморфизмпротяжённые гомозиготные участкирегионы, обогащённые гетерозиготностьюкуры породы корнишMinistry of Science and Higher Education of the Russian FederationМинистерство науки и высшего образования Российской Федерации124020200114-7This research was supported by the Ministry of Science and Higher Education of the Russian Federation (State Assignment Program), theme No. 124020200114-7Исследование выполнено при поддержке Министерства науки и высшего образования Российской Федерации (программа государственного задания, тема № 124020200114-7)Egorova AV, Efimov DN, Emanuylova ZhV. The method for the selection of males of broiler parental flock. Poultry. 2019;(7–8):8–12. doi: 10.33845/0033-3239-2019-68-7-8-8-12 EDN: ZJUFMMCeballos F, Joshi P, Clark D, et al. Runs of homozygosity: windows into population history and trait architecture. Nat Rev Genet. 2018;19:220–234. doi: 10.1038/nrg.2017.109Curtis D, Vine AE, Knight J. Study of regions of extended homozygosity provides a powerful method to explore haplotype structure of human populations. Ann Hum Genet. 2008;72(2):261–278. doi: 10.1111/j.1469-1809.2007.00411.xChessari G, Criscione A, Marletta D, et al. Characterization of heterozygosity-rich regions in Italian and worldwide goat breeds. Sci Rep. 2024;14(1):3. doi: 10.1038/s41598-023-49125-xFijarczyk A, Babik W. Detecting balancing selection in genomes: limits and prospects. Mol Ecol. 2015;24(14):3529–3545. doi: 10.1111/mec.13226Purcell S, Neale B, Todd-Brown K, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81(3):559–575. doi: 10.1086/519795Biscarini F, Cozzi P, Gaspa G, Marras G. detectRUNS: an R package to detect runs of homozygosity and heterozygosity in diploid genomes. CRAN. 2024. doi: 10.32614/CRAN.package.detectRUNSSmaragdov MG. Identification of homozygosity-rich regions in the Holstein genome. Vavilov Journal of Genetics and Breeding. 2023;27(5):471–479. doi: 10.18699/vjgb-23-57 EDN: XSDGWAPsifidi A, Banos G, Matika O, et al. Genome-wide association studies of immune, disease and production traits in indigenous chicken ecotypes. Genet Sel Evol. 2016;48(1):74. doi: 10.1186/s12711-016-0252-7Tall GG. Ric-8 regulation of heterotrimeric G proteins. J Recept Signal Transduct. 2013;33(3):139–143 doi: 10.3109/10799893.2013.763828Machado CF, Nagai MH, Lyra CS, et al. Conditional deletion of Ric-8b in olfactory sensory neurons leads to olfactory impairment. J Neurosci. 2017;37(50):12202–12213. doi: 10.1523/JNEUROSCI.0943-17.2017Choi W, Choe MS, Kim SM, et al. RFX4 is an intrinsic factor for neuronal differentiation through induction of proneural genes POU3F2 and NEUROD1. Cell Mol Life Sci. 2024;81:99. doi: 10.1007/s00018-024-05129-yWu Z, Derks MFL, Dibbits B, et al. A novel loss-of-function variant in transmembrane Protein 263 (TMEM263) of autosomal dwarfism in chicken. Front Genet. 2018;9:193. doi: 10.3389/fgene.2018.00193Yang L, Du X, Wei S, et al. Genome-wide association analysis identifies potential regulatory genes for eumelanin pigmentation in chicken plumage. Anim Genet. 2017;48(5):611–614. doi: 10.1111/age.12573Courtland JL, Bradshaw TWA, Waitt G, et al. Genetic disruption of WASHC4 drives endo-lysosomal dysfunction and cognitive-movement impairments in mice and humans. eLife. 2021;10:e61590. doi: 10.7554/eLife.61590Nemoto T, Tagashira H, Kita T, et al. Functional characteristics and therapeutic potential of SLC41 transporters. J Pharmacol Sci. 2023;151(2):88–92. doi: 10.1016/j.jphs.2022.12.003Dadousis C, Somavilla A, Ilska JJ, et al. A genome-wide association analysis for body weight at 35 days measured on 137,343 broiler chickens. Genet Sel Evol. 2021;53:70. doi: 10.1186/s12711-021-00663-wMonteiro Moreira GC, Poleti MD, Pértille F, et al. Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach. BMC Genet. 2019;20:83. doi: 10.1186/s12863-019-0783-3Lin S, Luo W, Jiang M, et al. Chicken CCDC152 shares an NFYB-regulated bidirectional promoter with a growth hormone receptor antisense transcript and inhibits cells proliferation and migration. Oncotarget. 2017;8(48): 84039–84053. doi: 10.18632/oncotarget.21091Barreto Sánchez AL, Wang Q, Thiam M, et al. Liver transcriptome response to heat stress in Beijing you chickens and Guang Ming broilers. Genes. 2022;13(3):416. doi: 10.3390/genes13030416Gopalan L, Sebastian A, Praul CA, et al. Metformin affects the transcriptomic profile of chicken ovarian cancer cells. Genes. 2021;13(1):30. doi: 10.3390/genes13010030Bian LH, Wang SZ, Wang QG, et al. Variation at the insulin-like growth factor 1 gene and its association with body weight traits in the chicken. J Anim Breed Genet. 2008;125(4):265–270. doi: 10.1111/j.1439-0388.2008.00739.xOgunpaimo OJ, Ojoawo HT, Wheto MY, et al. Association of insulin-like growth factor 1 (IGF1) gene polymorphism with the reproductive performance of three dual-purpose chicken breeds. Translational Anim Sci. 2021;5(4):txab215. doi: 10.1093/tas/txab215Fujita S, Honda K, Yamaguchi M, et al. Role of Insulin-like growth factor-1 in the central regulation of feeding behavior in chicks. J Poultry Sci. 2019;56(4):270–276. doi: 10.2141/jpsa.0180127Piórkowska K, Żukowski K, Połtowicz K, et al. Identification of candidate genes and regulatory factors related to growth rate through hypothalamus transcriptome analyses in broiler chickens. BMC Genomics. 2020;21:509. doi: 10.1186/s12864-020-06884-5Sun J, Tan X, Yang X, et al. Identification of candidate genes for meat color of chicken by combing selection signature analyses and differentially expressed genes. Genes. 2022;13(2):307. doi: 10.3390/genes13020307Abdalla EAE, Makanjuola BO, Wood BJ, Baes CF. Genome-wide association study reveals candidate genes relevant to body weight in female turkeys (Meleagris gallopavo). PloS One. 2022;17(3):e0264838. doi: 10.1371/journal.pone.0264838Li D, Pan Z, Zhang K, et al. Identification of the differentially expressed genes of muscle growth and intramuscular fat metabolism in the development stage of yellow broilers. Genes. 2020;11(3):244. doi: 10.3390/genes11030244Petroli Marchesi JA, Ono RK, Cantão ME, et al. Exploring the genetic architecture of feed efficiency traits in chickens. Sci Rep. 2021;11(1):4622. doi: 10.1038/s41598-021-84125-9Liao R, Zhang X, Chen Q, et al. Genome-wide association study reveals novel variants for growth and egg traits in Dongxiang blue-shelled and White Leghorn chickens. Anim Genet. 2016;47(5):588–596. doi: 10.1111/age.12456Ghafouri F, Sadeghi M, Bahrami A, et al. Identification of genes affecting the amount of abdominal fat in broiler chickens using microarray and RNA sequencing data. Iranian J Anim Sci. 2020;50(4):259–269. doi: 10.22059/ijas.2019.281245.653703Fu W, Lee WR, Abasht B. Detection of genomic signatures of recent selection in commercial broiler chickens. BMC Genet. 2016;17:122. doi: 10.1186/s12863-016-0430-1Niu X, Tyasi TL, Qin N, et al. Sequence variations in estrogen receptor 1 and 2 genes and their association with egg production traits in Chinese Dagu chickens. J Vet Med Sci. 2017;79(5):927–934. doi: 10.1292/jvms.17-0014Liu Y, Katoh H, Sekizuka T, et al. SNARE protein USE1 is involved in the glycosylation and the expression of mumps virus fusion protein and important for viral propagation. PLoS Pathogens. 2022;18(12):e1010949. doi: 10.1371/journal.ppat.1010949Sakai H, Sawada Y, Tokunaga N, et al. Uhrf1 governs the proliferation and differentiation of muscle satellite cells. iScience. 2022;25(3):103928. doi: 10.1016/j.isci.2022.103928Evseev D, Magor KE. Innate immune responses to avian influenza viruses in ducks and chickens. Vet Sci. 2019;6(1):5. doi: 10.3390/vetsci6010005Dong R, Li X, Lai K-O. Activity and Function of the PRMT8 Protein Arginine Methyltransferase in Neurons. Life. 2021;11(11):1132. doi: 10.3390/life11111132Alvarez-Rodriguez M, Ntzouni M, Wright D, et al. Chicken seminal fluid lacks CD9- and CD44-bearing extracellular vesicles. Reprod Domestic Anim. 2020;55(3):293–300. doi: 10.1111/rda.13617Abdelmanova AS, Dotsev AV, Romanov MN, et al. Unveiling comparative genomic trajectories of selection and key candidate genes in egg-type Russian white and meat-type white cornish chickens. Biology. 2021;10(9):876. doi: 10.3390/biology10090876Zhao X, Nie C, Zhang J, et al. Identification of candidate genomic regions for chicken egg number traits based on genome-wide association study. BMC Genom. 2021;22(1):610. doi: 10.1186/s12864-021-07755-3Huang S, He Y, Ye S, et al. Genome-wide association study on chicken carcass traits using sequence data imputed from SNP array. J Appl Genet. 2018;59(3):335–344. doi: 10.1007/s13353-018-0448-3Yu P, Song S, Zhang X, et al. Downregulation of apoptotic repressor AVEN exacerbates cardiac injury after myocardial infarction. PNAS USA. 2023;20(42):e2302482120. doi: 10.1073/pnas.2302482120Wu P, Zhou K, Zhang J, et al. Transcriptome integration analysis at different embryonic ages reveals key lncRNAs and mRNAs for chicken skeletal muscle. Front Vet Sci. 2022;9:908255. doi: 10.3389/fvets.2022.9082552Li G-S, Liu W-W, Zhang F, et al. Genome-wide association study of bone quality and feed efficiency-related traits in Pekin ducks. Genomics. 2020;112(6):5021–5028. doi: 10.1016/j.ygeno.2020.09.023Priyanka PP, Yenugu S. Coiled-Coil Domain-containing (CCDC) proteins: functional roles in general and male reproductive physiology. Reprod Sci. 2021;28:2725–2734. doi: 10.1007/s43032-021-00595-2Bai F-R, Wu Q-Q, Wu Y-J, et al. Germline FOXJ2 overexpression causes male infertility via aberrant autophagy activation by LAMP2A upregulation. Cell Death Dis. 2022;13(7):665. doi: 10.1038/s41419-022-05116-wHuang X, Otecko NO, Peng M, et al. Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds. BMC Genom. 2020;21:316. doi: 10.1186/s12864-020-6736-4Nihashi Y, Umezawa K, Shinji S, et al. Distinct cell proliferation, myogenic differentiation, and gene expression in skeletal muscle myoblasts of layer and broiler chickens. Sci Rep. 2019;9:16527. doi: 10.1038/s41598-019-52946-4Chai Y, Liu Z, Fu S, et al. Effects of exogenous melatonin on expressional differences of immune-related genes in cashmere goats. Front Genet. 2022;13:967402. doi: 10.3389/fgene.2022.967402Romanov MN, Shakhin AV, Abdelmanova AS, et al. Dissecting selective signatures and candidate genes in grandparent lines subject to high selection pressure for broiler production and in a local Russian chicken breed of Ushanka. Genes. 2024;15(4):524. doi: 10.3390/genes15040524Fedorova ES, Dementieva NV, Shcherbakov YuS, Stanishevskaya OI. 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/biology11040547Romanov MN, Abdelmanova AS, Fisinin VI, et al. Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds. J Anim Sci Biotechnol. 2023;14(1):35. doi: 10.1186/s40104-022-00813-0Gao C, Wang K, Hu X, et al. Conservation priority and run of homozygosity pattern assessment of global chicken genetic resources. Poult Sci. 2023;102(11):103030. doi: 10.1016/j.psj.2023.103030