Berihulay, H., Li, Y., Liu, X., Gebreselassie, G., Islam, R., Liu, W., Jiang, L., and Ma, Y.: Genetic diversity and population structure in multiple Chinese goat populations using a SNP panel, Animal Genetics, 50, 242–249, https://doi.org/10.1111/age.12776, 2019.
Biabani, P., Yeganeh, H. M., Shahrbabak, H. M., and Mokhber, M.: Detection of genetic differences betwee
n Holstein and Iranian north-west indigenous hybrid cattle using genomic data, Res. Anim. Prod., 13, 175–186, https://doi.org/10.52547/rap.13.37.175, 2022.
Browning, B. L., Tian, X., Zhou, Y., and Browning, S. R.: Fast two-stage phasing of large-scale sequence data, Am. J. Hum. Genet., 108, 1880–1890, https://doi.org/10.1016/j.ajhg.2021.08.005, 2021.
Colli, L., Milanesi, M., Vajana, E., Iamartino, D., Bomba, L., Puglisi, F., and Ajmone-Marsan, P.: New insights on water buffalo genomic diversity and post-domestication migration routes from medium density SNP chip data, Front. Genet., 9, 53, https://doi.org/10.3389/fgene.2018.00053, 2018.
Decker, J. E., McKay, S. D., Rolf, M. M., Kim, J., Molina Alcala, A., Sonstegard, T. S., Hanotte, O., Götherström, A., Seabury, C. M., Praharani, L., Babar, M. E., Regitano, L. C. A., Yildiz, M. A., Heaton, M. P., Liu, W. S., Lei, C. Z., Reecy, J. M., Saif-Ur-Rehman, M., Schnabel, R. D., and Taylor, J. F.: Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle, PLoS Genet., 10, e1004254, https://doi.org/10.1371/journal.pgen.1004254, 2014.
Doekes, H. P., Veerkamp, R. F., Bijma, P., Hiemstra, S. J., and Windig, J. J.: Trends in genome-wide and region-specific genomic diversity in the Dutch-Flemish Holstein–Friesian breeding program from 1986 to 2015, Genet. Sel. Evol., 50, 1–16, https://doi.org/10.1186/s12711-018-0385-y, 2018.
Elhaik, E.: Principal Component Analyses (PCA)-based findings in population genetic studies are highly biased and must be reevaluated, Scientific Reports, 12, 14683, https://doi.org/10.1038/s41598-022-14395-4, 2022.
Gaspar, H. A. and Breen, G.: Probabilistic ancestry maps: a method to assess and visualize population substructures in genetics, BMC Bioinformatics, 20, 116, https://doi.org/10.1186/s12859-019-2680-1, 2019.
Gautier, M., Laloë, D., and Moazami-Goudarzi, K.: Insights into the Genetic History of French Cattle from Dense SNP Data on 47 Worldwide Breeds, PLoS ONE, 5, e13038, https://doi.org/10.1371/journal.pone.0013038, 2010.
Giovannini, S., Chessari, G., Riggio, S., Marletta, D., Sardina, M. T., Mastrangelo, S., and Sarti, F. M.: Insight into the current genomic diversity, conservation status and population structure of Tunisian Barbarine sheep breed, Front. Genet., 15, 1379086, https://doi.org/10.3389/fgene.2024.1379086, 2024.
Jombart, T. and Ahmed, I.: adegenet 1.3-1: new tools for the analysis of genome-wide SNP data, Bioinformatics, 27, 3070–3071, https://doi.org/10.1093/bioinformatics/btr521, 2011.
Jombart, T., Devillard, S., and Balloux, F.: Discriminant analysis of principal components: a new method for the analysis of genetically structured populations, BMC Genetics, 11, 94, https://doi.org/10.1186/1471-2156-11-94, 2010.
Kalinowski, S. T.: Counting alleles with rarefaction: private alleles and hierarchical sampling designs, Conserv. Genet, 5, 539–543, 2004.
Karimi, K., Strucken, E. M., Moghaddar, N., Ferdosi, M. H., Esmailizadeh, A., and Gondro, C.: Local and global patterns of admixture and population structure in Iranian native cattle, BMC Genetics, 17, 1–14, https://doi.org/10.1186/s12863-016-0335-9, 2016.
Kijas, J. W., Ortiz, J. S., McCulloch, R., James, A., Brice, B., Swain, B., and International Goat Genome Consortium: Genomic diversity and investigation of polledness in divergent goat populations using 52,088 SNPs, Anim. Genet., 44, 285–289, https://doi.org/10.1111/age.12035, 2013.
Kukučková, V., Moravčíková, N., Ferenčaković, M., Simčič, M., Mészáros, G., Sölkner, J., Trakovická, A., Kadlečík, O., Curik, I., and Kasarda, R.: Genomic characterization of Pinzgau cattle: genetic conservation and breeding perspectives, Conserv. Genet., 18, 893–910, https://doi.org/10.1007/s10592-017-0935-9, 2017.
Kusza, S., Badaoui, B., and Wanjala, G.: Insights into the genomic homogeneity of Moroccan indigenous sheep breeds though the lens of runs of homozygosity, Sci. Rep., 14, 16515, https://doi.org/10.1038/s41598-024-67558-w, 2024.
Luikart, G., England, P. R., Tallmon, D., Jordan, S., and Taberlet, P.: The power and promise of population genomics: from genotyping to genome typing, Nat. Rev. Genet., 4, 981–994, 2013.
Ma, J., and Amos, C. I.: Principal components analysis of population admixture, PLoS ONE, 7, e40115, https://doi.org/10.1371/journal.pone.0040115, 2012.
Makgahlela, M. L., Knürr, T., Aamand, G. P., Strandén, I., and Mäntysaari, E. A.: Single step evaluations using haplotype segments, Interbull Bulletin, 47, 217–221, 2013.
Makina, S. O., Muchadeyi, F. C., van Marle-Köster, E., MacNeil, M. D., and Maiwashe, A.: Genomic diversity and population structure among six cattle breeds in South Africa using a whole genome SNP panel, Front. Genet., 5, 333, https://doi.org/10.3389/fgene.2014.00333, 2014.
Mastrangelo, S., Sardina, M. T., Tolone, M., Di Gerlando, R., Sutera, A. M., Fontanesi, L., and Portolano, B.: Genome-wide identification of runs of homozygosity islands and associated genes in local dairy cattle breeds, Animal, 12, 2480–2488, https://doi.org/10.1017/S1751731118000629, 2018.
Matukumalli, L. K., Lawley, C. T., Schnabel, R. D., Taylor, J. F., Allan, M. F., Heaton, M. P., O'Connell, J., Moore, S. S., Smith, T. P. L., Sonstegard, T. S., and Van Tassell, C. P.: Development and Characterization of a High Density SNP Genotyping Assay for Cattle, PLoS ONE, 4, e5350, https://doi.org/10.1371/journal.pone.0005350, 2009.
Moradi Shahrebabak, H., Biabani, P., Mehrbani Yeganeh, H., and Mokhber, M.: Investigating the genomic diversity of Iranian native and Holstein cattle breeds using genomic data, Research Journal of Livestock Science, 36, 87–98, https://doi.org/10.22092/asj.2022.357456.2201, 2023.
Nei, M.: Genetic distance between populations, Am. Nat., 106, 283–292, 1972.
Papachristou, D., Koutsouli, P., Laliotis, G. P., Kunz, E., Upadhyay, M., Seichter, D., Russ, I., Götz, K.-U., and Medugorac, I.: Genomic diversity and population structure of the indigenous Greek and Cypriot cattle populations, Genet. Sel. Evol., 52, 43, https://doi.org/10.1186/s12711-020-00560-8, 2020.
Price, A. L., Patterson, N. J., Plenge, R. M., Weinblatt, M. E., Shadick, N. A., and Reich, D.: Principal components analysis corrects for stratification in genome-wide association studies, Nat. Genet., 38, 904–909, https://doi.org/10.1038/ng1847, 2006.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., and Sham, P. C.: PLINK: a toolset for whole-genome association and population-based linkage analysis, Am. J. Hum. Genet., 81, 559–575, https://doi.org/10.1086/519795, 2007.
Rahimmadar, S., Ghaffari, M., Mokhber, M., and Williams, J. L.: Linkage disequilibrium and effective population size of buffalo populations of Iran, Turkey, Pakistan, and Egypt using a medium density SNP array, Front. Genet., 12, 608186, https://doi.org/10.3389/fgene.2021.608186, 2021.
R Core Team: R: A language and environment for statistical computing, R Foundation for Statistical Computing, Vienna, Austria,
https://www.r-project.org/ (last access: 26 August 2024), 2024.
Rodríguez-Ramilo, S. T., Fernández, J., Toro, M. A., Hernández, D., and Villanueva, B.: Genome-wide estimates of coancestry, inbreeding and effective population size in the Spanish Holstein population, PLoS ONE, 10, e0124157, https://doi.org/10.1371/journal.pone.0124157, 2015.
Salehi, R., Javanmard, A., Mokhber, M., and Alijani, S.: Analysis of genomic diversity in worldwide Holstein populations based on genomic array information, in: Proceedings of the 10th National and 2nd International Animal Science Congress of Iran, Karaj, Iran, 30–31 August 2023a.
Salehi, R., Javanmard, A., Mokhber, M., and Alijani, S.: Genomic Selection Signatures in Two French and Swedish Holstein Cattle Breeds Provide Evidence for Several Potential Candidate Genes Linked to Economic Traits, Iran. J. Appl. Anim. Sci., 13, 677–684, 2023b.
Sempéré, G., Moazami-Goudarzi, K., Eggen, A., Laloë, D., Gautier, M., and Flori, L.: WIDDE: a Web-Interfaced next-generation database for genomic diversity exploration, with a first application in cattle, BMC Genomics, 16, 940, https://doi.org/10.1186/s12864-015-2181-1, 2015.
Shakeri, R., Javanmard, A., Hasanpur, K., Abbasi, M., Khansefid, M., and Rahimi Varposhti, M.: Assessment of genetic diversity within Holstein population using bovine SNP chip data, Res. Anim. Prod., 12, 140–149, 2021.
Sharma, A., Lee, S. H., Lim, D., Chai, H. H., Choi, B. H., and Cho, Y.: A genome-wide assessment of genomic diversity and population structure of Korean native cattle breeds, BMC Genet., 17, 1–9, https://doi.org/10.1186/s12863-017-0472-z, 2016.
Toro-Ospina, A. M., Herrera Rios, A. C., Pimenta Schettini, G., Vallejo Aristizabal, V. H., Bizarria dos Santos, W., Zapata, C. A., and Ortiz Morea, E. G.: Identification of runs of homozygosity islands and genomic estimated inbreeding values in Caqueteño Creole cattle (Colombia), Genes, 13, 1232, https://doi.org/10.3390/genes13071232, 2022.
Villanueva, B., Fernández, A., Saura, M., Caballero, A., Fernández, J., Morales-González, E., Toro, M. A., and Pong-Wong, R.: The value of genomic relationship matrices to estimate levels of inbreeding, Genet. Sel. Evol., 53, 42, https://doi.org/10.1186/s12711-021-00635-0, 2021.
Vostry, L., Vostra-Vydrova, H., Moravcikova, N., Kasarda, R., Cubric-Curik, V., Brzakova, M., Sölkner, J., Shihabi, M., Hidalgo Moreno, J. A., and Spehar, M.: Genomic diversity and population structure of the Czech Holstein cattle, Livest. Sci., 273, 105261, https://doi.org/10.1016/j.livsci.2023.105261, 2023.
Weir, B. S. and Cockerham, C. C.: Estimating F-statistics for the analysis of population structure, Evolution, 38, 1358–1370, https://doi.org/10.2307/2408641, 1984.
Wright, S.: Evolution and the genetics of populations, in: Variability Within and Among Natural Populations, Vol. 4, University of Chicago Press, Chicago, IL, USA, ISBN: 978-0-226-91052-9, 1978.
Wultsch, C., Caragiulo, A., Dias-Freedman, I., Quigley, H., Rabinowitz, S., and Amato, G.: Genetic diversity and population structure of Mesoamerican jaguars (
Panthera onca): implications for conservation and management, PLoS ONE, 11, e0162377, https://doi.org/10.1371/journal.pone.0162377, 2016.
Yue, X. P., Dechow, C., and Liu, W. S.: A limited number of Y chromosome lineages is present in North American Holsteins, J. Dairy Sci., 98, 2738–2745, https://doi.org/10.3168/jds.2014-8601, 2015.
