{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T10:06:27Z","timestamp":1789553187561,"version":"build-2803163510"},"reference-count":98,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T00:00:00Z","timestamp":1789516800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biology"],"abstract":"<jats:p>This study aimed to characterize the genomic diversity, population structure, and candidate regions consistent with selection in Hamdani (HAM) sheep using high-density SNP generated by double-digest restriction site-associated DNA sequencing (ddRADseq). A total of 20 animals were sampled, and after quality filtering, 310,663 SNPs from 18 individuals were retained for downstream analyses. Genetic diversity parameters indicated a relatively high level of genomic variation within the breed (HO = 0.323 \u00b1 0.01 and HE = 0.326 \u00b1 0.01) and low levels of inbreeding (FHOM = 0.029 \u00b1 0.02 and FROH = 0.008 \u00b1 0.01), suggesting that the population has maintained substantial genetic diversity and has not experienced recent intensive inbreeding. Population structure analyses revealed that HAM sheep form a distinct genetic cluster separated from Turkish fat-tailed breeds, reflecting their unique genetic background and breeding history. Footprints of selection analyses based on runs of homozygosity (ROH) and integrated haplotype score (iHS) identified preliminary candidate genomic regions consistent with selection. After FDR correction, 12 of the 34 trait\u2013chromosome combinations tested for the iHS-derived regions and three of the eight combinations tested for the ROH-derived regions were significantly enriched. Functional annotation highlighted biologically relevant candidate genes involved in reproductive performance (TSHR, FSHR, and LHCGR), lipid metabolism (ABCG1 and LPIN1), and environmental adaptation (LACC1 and MBOAT7). This ddRADseq-based genome-wide characterization provides preliminary information on genetic variability and candidate genomic regions consistent with selection in HAM sheep. Therefore, further studies focusing on a larger sampling strategy across multiple different sheep breeds are needed to design conservation, breeding, and future genomic selection programs.<\/jats:p>","DOI":"10.3390\/biology15181630","type":"journal-article","created":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T09:06:37Z","timestamp":1789549597000},"page":"1630","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic Diversity and Footprints of Selection in Hamdani Sheep"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-7758-9323","authenticated-orcid":false,"given":"Ebru","family":"Demir","sequence":"first","affiliation":[{"name":"Department of Agricultural Biotechnology, Faculty of Agriculture, Eski\u015fehir Osmangazi University, Eski\u015fehir 26160, T\u00fcrkiye"},{"name":"Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesco","family":"Perini","sequence":"additional","affiliation":[{"name":"Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4507-7426","authenticated-orcid":false,"given":"Eymen","family":"Demir","sequence":"additional","affiliation":[{"name":"Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya 07070, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2725-2921","authenticated-orcid":false,"given":"Emiliano","family":"Lasagna","sequence":"additional","affiliation":[{"name":"Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"\u00dcmit","family":"Bilginer","sequence":"additional","affiliation":[{"name":"Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53705, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5933-349X","authenticated-orcid":false,"given":"Sarp","family":"Kaya","sequence":"additional","affiliation":[{"name":"Department of Medical Services and Techniques, Vocational School of Burdur Health Services, Burdur Mehmet Akif Ersoy University, Burdur 15100, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7183-0170","authenticated-orcid":false,"given":"Beste","family":"G\u00f6neci Fidan","sequence":"additional","affiliation":[{"name":"Department of Agricultural Biotechnology, Faculty of Agriculture, Eski\u015fehir Osmangazi University, Eski\u015fehir 26160, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sezai","family":"Alkan","sequence":"additional","affiliation":[{"name":"Department of Animal Technology, Faculty of Agriculture, Ordu University, Ordu 52200, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2413-1713","authenticated-orcid":false,"given":"Taki","family":"Karsl\u0131","sequence":"additional","affiliation":[{"name":"Department of Animal Science, Faculty of Agriculture, Eski\u015fehir Osmangazi University, Eski\u015fehir 26160, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bahar Argun","family":"Karsl\u0131","sequence":"additional","affiliation":[{"name":"Department of Agricultural Biotechnology, Faculty of Agriculture, Eski\u015fehir Osmangazi University, Eski\u015fehir 26160, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,16]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"11597","DOI":"10.1073\/pnas.0801317105","article-title":"Domestication and early agriculture in the Mediterranean basin: Origins, diffusion, and impact","volume":"105","author":"Zeder","year":"2008","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1146\/annurev-ecolsys-110512-135813","article-title":"The evolution of animal domestication","volume":"45","author":"Larson","year":"2014","journal-title":"Annu. Rev. Ecol. Evol. Syst."},{"key":"ref_3","unstructured":"FAO (2026, July 20). FAOSTAT, Food and Agriculture Organization of the United Nations, Food and Agriculture Data, Available online: https:\/\/www.fao.org\/faostat\/en\/#data\/QCL."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"20518","DOI":"10.1038\/s41598-024-71617-7","article-title":"Genome-wide discovery of selection signatures in four Anatolian sheep breeds revealed by ddRADseq","volume":"14","author":"Demir","year":"2024","journal-title":"Sci. Rep."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Aydin, K.B., Bi, Y., Brito, L.F., Uluta\u015f, Z., and Morota, G. (2024). Review of sheep breeding and genetic research in T\u00fcrkiye. Front. Genet., 15.","DOI":"10.3389\/fgene.2024.1308113"},{"key":"ref_6","first-page":"161","article-title":"A Study on the Technical and Structural Characteristics of Nomadic Sheep Breeding Enterprises: Diyarbak\u0131r Province Example","volume":"65","author":"Ayan","year":"2024","journal-title":"J. Anim. Prod."},{"key":"ref_7","first-page":"161","article-title":"Some growth, reproduction and lactation characteristics of hamdani sheep","volume":"28","year":"2018","journal-title":"Yuz. Yil Univ. J. Agric. Sci."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"e70584","DOI":"10.1002\/vms3.70584","article-title":"Analysis of Population Structure and Selection Signatures in Two Iraqi Fat-Tailed Sheep Breeds","volume":"11","author":"Bayraktar","year":"2025","journal-title":"Vet. Med. Sci."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"10","DOI":"10.64362\/zjse.36","article-title":"Performance of Hamdani Sheep in Iraq: A Review","volume":"1","author":"Alkass","year":"2025","journal-title":"Zanin J. Sci. Eng."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"264","DOI":"10.21608\/avmj.2024.308004.1325","article-title":"Comparative Analysis of Sheep Growth Traits in Karakul, Al-Naimi, and Hamdani Breeds","volume":"71","author":"Aljubouri","year":"2025","journal-title":"Assiut Vet. Med. J."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1590\/S1415-47572014000300004","article-title":"Identification of selection signatures in livestock species","volume":"37","author":"Gouveia","year":"2014","journal-title":"Genet. Mol. Biol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"104257","DOI":"10.1016\/j.livsci.2020.104257","article-title":"Selection signatures in livestock genome: A review of concepts, approaches and applications","volume":"241","author":"Saravanan","year":"2020","journal-title":"Livest. Sci."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1111\/j.1365-2052.2010.02038.x","article-title":"Genetic diversity in farm animals\u2013a review","volume":"41","author":"Groeneveld","year":"2010","journal-title":"Anim. Genet."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"255","DOI":"10.3390\/ruminants2020017","article-title":"Conservation and selection of genes related to environmental adaptation in native small ruminant breeds: A review","volume":"2","author":"Demir","year":"2022","journal-title":"Ruminants"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1080\/09291016.2019.1642650","article-title":"Advanced software programs for the analysis of genetic diversity in livestock genomics: A mini review","volume":"53","author":"Saravanan","year":"2022","journal-title":"Biol. Rhythm Res."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"107570","DOI":"10.1016\/j.smallrumres.2025.107570","article-title":"Unveiling genomic diversity and population structure in three Anatolian goats at genome-wide level","volume":"251","author":"Bilginer","year":"2025","journal-title":"Small Rumin. Res."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"147950","DOI":"10.1016\/j.gene.2023.147950","article-title":"Revelation of genetic diversity and genomic footprints of adaptation in Indian pig breeds","volume":"893","author":"Vani","year":"2024","journal-title":"Gene"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"161","DOI":"10.5194\/aab-68-161-2025","article-title":"Genome-wide genetic characterization and selection signatures in Anatolian Merino sheep","volume":"68","author":"Karsli","year":"2025","journal-title":"Arch. Anim. Breed."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"105193","DOI":"10.1016\/j.psj.2025.105193","article-title":"Genome-wide comparative analysis of variability and population structure between autochthonous Turkish chicken breeds and commercial hybrid lines","volume":"104","author":"Demir","year":"2025","journal-title":"Poult. Sci."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1707","DOI":"10.1007\/s11250-019-02180-x","article-title":"Genome-wide discovery of SNPs in candidate genes related to production and fertility traits in Sahiwal cattle","volume":"52","author":"Vineeth","year":"2020","journal-title":"Trop. Anim. Health Prod."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"17283","DOI":"10.1038\/s41598-023-44402-1","article-title":"Genome-wide identification of candidate copy number polymorphism genes associated with complex traits of Tibetan-sheep","volume":"13","author":"Tian","year":"2023","journal-title":"Sci. Rep."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1173","DOI":"10.1007\/s00335-025-10164-6","article-title":"Genomic scans for diversity and selection signatures in Indian Red Sindhi cattle","volume":"36","author":"Nayak","year":"2025","journal-title":"Mamm. Genome"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"107285","DOI":"10.1016\/j.smallrumres.2024.107285","article-title":"Genetic diversity and population structure of four Anatolian sheep revealed by genome-wide ddRADseq data","volume":"235","author":"Karsli","year":"2024","journal-title":"Small Rumin. Res."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Peterson, B.K., Weber, J.N., Kay, E.H., Fisher, H.S., and Hoekstra, H.E. (2012). Double digest RADseq: An inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0037135"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"4737","DOI":"10.1111\/mec.15253","article-title":"Stacks 2: Analytical methods for paired-end sequencing improve RADseq-based population genomics","volume":"28","author":"Rochette","year":"2019","journal-title":"Mol. Ecol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: An ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"iab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"Gigascience"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Chang, C.C., Chow, C.C., Tellier, L.C., Vattikuti, S., Purcell, S.M., and Lee, J.J. (2015). Second-generation PLINK: Rising to the challenge of larger and richer datasets. Gigascience, 4.","DOI":"10.1186\/s13742-015-0047-8"},{"key":"ref_30","unstructured":"Rambaut, A. (2026, July 20). FigTree v.1.4.4. Available online: https:\/\/github.com\/rambaut\/figtree."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1655","DOI":"10.1101\/gr.094052.109","article-title":"Fast model-based estimation of ancestry in unrelated individuals","volume":"19","author":"Alexander","year":"2009","journal-title":"Genome Res."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Milanesi, M., Capomaccio, S., Vajana, E., Bomba, L., Garcia, J.F., Ajmone-Marsan, P., and Colli, L. (2017). BITE: An R package for biodiversity analyses. bioRxiv.","DOI":"10.1101\/181610"},{"key":"ref_33","unstructured":"Biscarini, F., Cozzi, P., Gaspa, G., and Marras, G. (2026, July 20). Detect Runs of Homozygosity and Runs of Heterozygosity in Diploid Genomes. Available online: https:\/\/cran.r-project.org\/web\/packages\/detectRUNS\/vignettes\/detectRUNS.vignette.html."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1186\/s40104-021-00608-9","article-title":"Estimates of genomic inbreeding and identification of candidate regions that differ between Chinese indigenous sheep breeds","volume":"12","author":"Liu","year":"2021","journal-title":"J. Anim. Sci. Biotechnol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1111\/1755-0998.12634","article-title":"rehh 2.0: A reimplementation of the R package rehh to detect positive selection from haplotype structure","volume":"17","author":"Gautier","year":"2017","journal-title":"Mol. Ecol. Resour."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1880","DOI":"10.1016\/j.ajhg.2021.08.005","article-title":"Fast two-stage phasing of large-scale sequence data","volume":"108","author":"Browning","year":"2021","journal-title":"Am. J. Hum. Genet."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Voight, B.F., Kudaravalli, S., Wen, X., and Pritchard, J.K. (2006). A Map of Recent Positive Selection in the Human Genome. PLoS Biol., 4.","DOI":"10.1371\/journal.pbio.0040154"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"giaa149","DOI":"10.1093\/gigascience\/giaa149","article-title":"GALLO: An R package for genomic annotation and integration of multiple data sources in livestock for positional candidate loci","volume":"9","author":"Fonseca","year":"2020","journal-title":"Gigascience"},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Kominakis, A., Tarsani, E., Hager-Theodorides, A.L., Mastranestasis, I., Gkelia, D., and Hadjigeorgiou, I. (2021). Genetic differentiation of mainland-island sheep of Greece: Implications for identifying candidate genes for long-term local adaptation. PLoS ONE, 16.","DOI":"10.1371\/journal.pone.0257461"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Wolf, M.J., Yin, T., Neumann, G.B., Korku\u0107, P., Brockmann, G.A., K\u00f6nig, S., and May, K. (2021). Genome-wide association study using whole-genome sequence data for fertility, health indicator, and endoparasite infection traits in German black pied cattle. Genes, 12.","DOI":"10.3390\/genes12081163"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1016\/j.livsci.2017.10.014","article-title":"Identification of artificial selection signatures in Caracu breed lines selected for milk production and meat production","volume":"206","author":"Campos","year":"2017","journal-title":"Livest. Sci."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Abousoliman, I., Reyer, H., Oster, M., Murani, E., Mohamed, I., and Wimmers, K. (2021). Genome-wide analysis for early growth-related traits of the locally adapted Egyptian Barki sheep. Genes, 12.","DOI":"10.3390\/genes12081243"},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Zhang, L., Zhang, S., Yuan, M., Zhan, F., Song, M., Shang, P., Yang, F., Li, X., Qiao, R., and Han, X. (2023). Genome-wide association studies and runs of homozygosity to identify reproduction-related genes in Yorkshire pig population. Genes, 14.","DOI":"10.3390\/genes14122133"},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Qiao, L., Ma, K., Yao, Q., Zhang, S., Pang, Z., Wang, W., Cai, K., and Liu, W. (2025). Whole-Genome Sequencing of Dorper\u00d7 Hu Hybrid Sheep for Screening Selection Signatures Associated with Litter Size. Animals, 15.","DOI":"10.3390\/ani15233505"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"25","DOI":"10.5194\/aab-69-25-2026","article-title":"Runs of homozygosity reveal candidate genes for economic traits in Danish Large White pigs","volume":"69","author":"Ding","year":"2026","journal-title":"Arch. Anim. Breed."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Zhao, F., Deng, T., Shi, L., Wang, W., Zhang, Q., Du, L., and Wang, L. (2020). Genomic scan for selection signature reveals fat deposition in Chinese indigenous sheep with extreme tail types. Animals, 10.","DOI":"10.3390\/ani10050773"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1111\/age.13138","article-title":"Combined approaches identify known and novel genes associated with sheep litter size and non-seasonal breeding","volume":"52","author":"Tao","year":"2021","journal-title":"Anim. Genet."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1186\/s12711-024-00880-z","article-title":"Whole-genome resequencing of Chinese indigenous sheep provides insight into the genetic basis underlying climate adaptation","volume":"56","author":"Jin","year":"2024","journal-title":"Genet. Sel. Evol."},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Wu, X., Pei, J., Xiong, L., Ge, Q., Bao, P., Liang, C., Yan, P., and Guo, X. (2025). Genome-wide scan for selection signatures reveals novel insights into the adaptive capacity characteristics in three Chinese cattle breeds. BMC Genom., 26.","DOI":"10.1186\/s12864-025-11328-z"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"106396","DOI":"10.1016\/j.psj.2026.106396","article-title":"Genome-wide association study reveals candidate genes associated with key egg production traits in Langya chickens","volume":"105","author":"Zhang","year":"2026","journal-title":"Poult. Sci."},{"key":"ref_51","first-page":"117","article-title":"Identification of genes related to the trait of litter size in prolificacy breeds using Genome-wide Association Studies (GWAS)","volume":"13","author":"Hamadalahmad","year":"2025","journal-title":"J. Rumin. Res."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"106836","DOI":"10.1016\/j.smallrumres.2022.106836","article-title":"Genome-wide association study of live body weight and body conformation traits in young Karachai goats","volume":"216","author":"Selionova","year":"2022","journal-title":"Small Rumin. Res."},{"key":"ref_53","first-page":"1","article-title":"Weighted Single-Step Genome-Wide Association Study of Milk Production Traits in the Russian Black-and-White cattle","volume":"4","author":"Abdulrahman","year":"2025","journal-title":"J. Biotechnol. Its App."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"625","DOI":"10.1111\/jbg.70048","article-title":"Genetic Parameters and Genome-Wide Association Studies for Fertility and Reproduction Traits in US Katahdin Sheep Based on the Single-Step GBLUP Methodology","volume":"143","author":"Ospina","year":"2026","journal-title":"J. Anim. Breed. Genet."},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Li, Y., Chen, Z., Fang, Y., Cao, C., Zhang, Z., Pan, Y., and Wang, Q. (2022). Runs of homozygosity revealed reproductive traits of Hu sheep. Genes, 13.","DOI":"10.3390\/genes13101848"},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Tsartsianidou, V., Otapasidis, A., Papakostas, S., Karaiskou, N., Vouraki, S., and Triantafyllidis, A. (2024). Genome-Wide patterns of homozygosity and heterozygosity and candidate genes in Greek insular and Mainland native goats. Genes, 16.","DOI":"10.3390\/genes16010027"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/s40104-025-01155-3","article-title":"Genome-wide landscape of genetic diversity, runs of homozygosity, and runs of heterozygosity in five Alpine and Mediterranean goat breeds","volume":"16","author":"Pegolo","year":"2025","journal-title":"J. Anim. Sci. Biotechnol."},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Onzima, R.B., Upadhyay, M.R., Doekes, H.P., Brito, L.F., Bosse, M., Kanis, E., Groenen, M.A., and Crooijmans, R.P. (2018). Genome-wide characterization of selection signatures and runs of homozygosity in Ugandan goat breeds. Front. Genet., 9.","DOI":"10.3389\/fgene.2018.00318"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1007\/s11250-025-04726-8","article-title":"Genome scan for runs of homozygosity in Saanen goats selected under tropical environments reveals candidate genes for adaptive and production traits","volume":"57","author":"Lobo","year":"2025","journal-title":"Trop. Anim. Health Prod."},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Deniskova, T.E., Dotsev, A.V., Koshkina, O.A., Solovieva, A.D., Churbakova, N.A., Petrov, S.N., Frolov, A.N., Platonov, S.A., Abdelmanova, A.S., and Vladimirov, M.A. (2025). Examination of runs of homozygosity distribution patterns and relevant candidate genes of potential economic interest in Russian goat breeds using whole-genome sequencing. Genes, 16.","DOI":"10.3390\/genes16060631"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"854","DOI":"10.1111\/age.13474","article-title":"Genomic responses to climatic challenges in beef cattle: A review","volume":"55","author":"Colombi","year":"2024","journal-title":"Anim. Genet."},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Peng, W., Zhang, Y., Gao, L., Wang, S., Liu, M., Sun, E., Lu, K., Zhang, Y., Li, B., and Li, G. (2025). Investigation of selection signatures of dairy goats using whole-genome sequencing data. BMC Genom., 26.","DOI":"10.1186\/s12864-025-11437-9"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"giae099","DOI":"10.1093\/gigascience\/giae099","article-title":"Near telomere-to-telomere genome assembly of Mongolian cattle: Implications for population genetic variation and beef quality","volume":"13","author":"Su","year":"2024","journal-title":"Gigascience"},{"key":"ref_64","doi-asserted-by":"crossref","unstructured":"Kanlisi, R.A., Amuzu-Aweh, E.N., Naazie, A., Otsyina, H.R., Kelly, T.R., Gallardo, R.A., Lamont, S.J., Zhou, H., Dekkers, J., and Kayang, B.B. (2024). Genetic architecture of body weight, carcass, and internal organs traits of Ghanaian local chickens. Front. Genet., 15.","DOI":"10.3389\/fgene.2024.1297034"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"327","DOI":"10.5713\/ajas.17.0276","article-title":"Genome\u2013wide association study of carcass weight in commercial Hanwoo cattle","volume":"31","author":"Edea","year":"2018","journal-title":"Asian-Australas. J. Anim. Sci."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/j.theriogenology.2021.08.012","article-title":"Genome-wide association studies reveals polygenic genetic architecture of litter traits in Duroc pigs","volume":"173","author":"Ding","year":"2021","journal-title":"Theriogenology"},{"key":"ref_67","doi-asserted-by":"crossref","unstructured":"Ramos, Z., Garrick, D.J., Blair, H.T., Vera, B., Ciappesoni, G., and Kenyon, P.R. (2023). Genomic regions associated with wool, growth and reproduction traits in Uruguayan Merino sheep. Genes, 14.","DOI":"10.3390\/genes14010167"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1007\/s12041-025-01520-1","article-title":"Genomewide signatures revealing new evidence for selection of important traits in indigenous cattle breeds of Tamil Nadu, India","volume":"105","author":"Vani","year":"2026","journal-title":"J. Genet."},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Kudinov, A.A., Dementieva, N.V., Mitrofanova, O.V., Stanishevskaya, O.I., Fedorova, E.S., Larkina, T.A., Mishina, A.O., Plemyashov, K.V., Griffin, D.K., and Romanov, M.N. (2019). Genome-wide association studies targeting the yield of extraembryonic fluid and production traits in Russian White chickens. BMC Genom., 20.","DOI":"10.1186\/s12864-019-5605-5"},{"key":"ref_70","doi-asserted-by":"crossref","unstructured":"Zhao, Y., He, S., Huang, J., and Liu, M. (2023). Genome-wide association analysis of muscle pH in Texel Sheep\u00d7 Altay Sheep F2 resource population. Animals, 13.","DOI":"10.3390\/ani13132162"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"2586262","DOI":"10.1080\/10495398.2025.2586262","article-title":"Single-step genome-wide association study of milk somatic cell scores across multi-cattle breeds in Ethiopia","volume":"36","author":"Chernet","year":"2025","journal-title":"Anim. Biotechnol."},{"key":"ref_72","doi-asserted-by":"crossref","unstructured":"Shen, Z., Yang, L., Xue, Y., Chang, X., Shen, J., Sun, W., Zeng, Y., Meng, J., and Yao, X. (2026). Machine Learning-Based Genome-Wide Association Study Reveals Genetic Loci Associated with Body Measurement Traits in Yili Horses. Animals, 16.","DOI":"10.3390\/ani16091373"},{"key":"ref_73","doi-asserted-by":"crossref","unstructured":"Pedrosa, V.B., Schenkel, F.S., Chen, S.Y., Oliveira, H.R., Casey, T.M., Melka, M.G., and Brito, L.F. (2021). Genomewide association analyses of lactation persistency and milk production traits in Holstein cattle based on imputed whole-genome sequence data. Genes, 12.","DOI":"10.3390\/genes12111830"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1016\/j.ygeno.2021.02.009","article-title":"Genomic scans for selection signatures revealed candidate genes for adaptation and production traits in a variety of cattle breeds","volume":"113","author":"Saravanan","year":"2021","journal-title":"Genomics"},{"key":"ref_75","doi-asserted-by":"crossref","unstructured":"Hollmann, A.K., Bleyer, M., Tipold, A., Ne\u00dfler, J.N., Wemheuer, W.E., Sch\u00fctz, E., and Brenig, B. (2017). A genome-wide association study reveals a locus for bilateral iridal hypopigmentation in Holstein Friesian cattle. BMC Genet., 18.","DOI":"10.1186\/s12863-017-0496-4"},{"key":"ref_76","doi-asserted-by":"crossref","unstructured":"Mastrangelo, S., Cendron, F., Sottile, G., Niero, G., Portolano, B., Biscarini, F., and Cassandro, M. (2020). Genome-wide analyses identifies known and new markers responsible of chicken plumage color. Animals, 10.","DOI":"10.3390\/ani10030493"},{"key":"ref_77","doi-asserted-by":"crossref","unstructured":"Melo-Rojas, C., Bravo-Matheus, P.W., Amaht Araoz, C., and Zapata-Coacalla, C. (2023). Identification of polymorphisms in TYRP1, DCT and RAB38 genes and their association with coat color in alpacas. Front. Anim. Sci., 4.","DOI":"10.3389\/fanim.2023.1236582"},{"key":"ref_78","doi-asserted-by":"crossref","unstructured":"Bayraktar, M., Durmu\u015f, M., Uyguner, \u00d6., Turan, M., \u00d6zcan, B.D., and Koluman, N. (2026). Comprehensive analysis of population structure and genomic diversity in fifteen Anatolian sheep breeds. BMC Vet. Res., 22.","DOI":"10.1186\/s12917-026-05544-2"},{"key":"ref_79","doi-asserted-by":"crossref","unstructured":"Dzomba, E.F., Chimonyo, M., Pierneef, R., and Muchadeyi, F.C. (2021). Runs of homozygosity analysis of South African sheep breeds from various production systems investigated using OvineSNP50k data. BMC Genom., 22.","DOI":"10.1186\/s12864-020-07314-2"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"604","DOI":"10.1111\/age.12173","article-title":"Genetic diversity in nine native Turkish sheep breeds based on microsatellite analysis","volume":"45","author":"Yilmaz","year":"2014","journal-title":"Anim. Genet."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/j.smallrumres.2019.10.009","article-title":"Determination of genetic diversity of the Akkaraman sheep breed from Turkey","volume":"182","author":"Ozmen","year":"2020","journal-title":"Small Rumin. Res."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1038\/nrg.2017.109","article-title":"Runs of homozygosity: Windows into population history and trait architecture","volume":"19","author":"Ceballos","year":"2018","journal-title":"Nat. Rev. Genet."},{"key":"ref_83","doi-asserted-by":"crossref","unstructured":"Li, R., Zhao, Y., Liang, B., Pu, Y., Jiang, L., and Ma, Y. (2023). Genome-wide signal selection analysis revealing genes potentially related to sheep-milk-production traits. Animals, 13.","DOI":"10.3390\/ani13101654"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"e73665","DOI":"10.1002\/ece3.73665","article-title":"Putative Genomic Signatures of Local Adaptation in Five Local Indonesian Sheep Reveal Selection on Immunity, Reproduction, and Production Traits","volume":"16","author":"Astuti","year":"2026","journal-title":"Ecol. Evol."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1042\/bse0500265","article-title":"Lipid transport by mammalian ABC proteins","volume":"50","author":"Quazi","year":"2011","journal-title":"Essays Biochem."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"107","DOI":"10.3390\/biology2010107","article-title":"PRDM proteins: Molecular mechanisms in signal transduction and transcriptional regulation","volume":"2","author":"Abbondanza","year":"2013","journal-title":"Biology"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.lfs.2014.04.007","article-title":"Phosphodiesterase 9: Insights from protein structure and role in therapeutics","volume":"106","author":"Singh","year":"2014","journal-title":"Life Sci."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"893","DOI":"10.1007\/s10815-022-02456-6","article-title":"Regulation of antral follicular growth by an interplay between gonadotropins and their receptors","volume":"39","author":"Casarini","year":"2022","journal-title":"J. Assist. Reprod. Genet."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"1513","DOI":"10.1016\/S0022-2275(20)32205-7","article-title":"Role of ABCG1 and other ABCG family members in lipid metabolism","volume":"42","author":"Schmitz","year":"2001","journal-title":"J. Lipid Res."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1111\/age.13299","article-title":"RNAseq reveals modulation of genes involved in fatty acid biosynthesis in chicken liver according to genetic background, sex, and diet","volume":"54","author":"Perini","year":"2023","journal-title":"Anim. Genet."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1016\/j.metabol.2010.04.021","article-title":"The role of JAZF1 on lipid metabolism and related genes in vitro","volume":"60","author":"Li","year":"2011","journal-title":"Metabolism"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1016\/j.tem.2013.06.003","article-title":"Metabolic actions of Rho-kinase in periphery and brain","volume":"24","author":"Huang","year":"2013","journal-title":"Trends Endocrinol. Metab."},{"key":"ref_93","doi-asserted-by":"crossref","unstructured":"Porto-Neto, L.R., Reverter, A., Prayaga, K.C., Chan, E.K., Johnston, D.J., Hawken, R.J., Fordyce, G., Garcia, J.F., Sonstegard, T.S., and Bolormaa, S. (2013). The genetic architecture of climatic adaptation of tropical cattle. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0113284"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1007\/s00335-026-10203-w","article-title":"Candidate genes related to growth and milk production in three Anatolian goats revealed by GWAS","volume":"37","author":"Demir","year":"2026","journal-title":"Mamm. Genome"},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"1053","DOI":"10.1007\/s00535-024-02157-0","article-title":"Immunological dynamics in MASH: From landscape analysis to therapeutic intervention","volume":"59","author":"Rabiu","year":"2024","journal-title":"J. Gastroenterol."},{"key":"ref_96","doi-asserted-by":"crossref","unstructured":"Li, F., Cui, X., Yang, Q., Nie, Y., Wang, J., and Sun, S. (2025). The research progress of LACC1. Front. Immunol., 16.","DOI":"10.3389\/fimmu.2025.1698702"},{"key":"ref_97","doi-asserted-by":"crossref","unstructured":"Wang, Y., Niu, Z., Zeng, Z., Jiang, Y., Jiang, Y., Ding, Y., Tang, S., Shi, H., and Ding, X. (2020). Using high-density SNP array to reveal selection signatures related to prolificacy in Chinese and Kazakhstan sheep breeds. Animals, 10.","DOI":"10.3390\/ani10091633"},{"key":"ref_98","doi-asserted-by":"crossref","unstructured":"S\u00e1nchez-Ramos, R., Trujano-Chavez, M.Z., Gallegos-S\u00e1nchez, J., Becerril-P\u00e9rez, C.M., Cadena-Villegas, S., and Cortez-Romero, C. (2023). Detection of candidate genes associated with fecundity through genome-wide selection signatures of Katahdin ewes. 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