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Research Articles

Genome-wide genetic variation and population structure of native and cosmopolitan cattle breeds reared in Türkiye

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References

  • Zeder MA, Emshwiller E, Smith BD, Bradley DG. Documenting domestication: the intersection of genetics and archaeology. Trends Genet. 2006;22(3):139–155.
  • Demir E, Moravčíková N, Argun Karsli B, et al. Mitochondrial DNA diversity of D-loop region in three native Turkish cattle breeds. Arch Anim Breed. 2023;66(1):31–40.
  • Demir E, Balcioglu MS. Genetic diversity and population structure of four cattle breeds raised in Turkey using microsatellite markers. Czech J Anim Sci. 2019;64(10):411–419.
  • Introduction Catalogue of Domestic Animals Resources in Türkiye 2009. https://www.tarimorman.gov.tr/TAGEM/Belgeler/yayin/Katalog%20Türkçe.pdf. Last accessed on 20-03-2023.
  • Soysal Mİ, Ünal EÖ, Gürcan EK. Conservation and sustainable use of farm animal genetic resource. J Anim Sci Prod. 2020;3(2):210–227.
  • Frankham R, Ballou SEJD, Briscoe DA, Ballou JD. Introduction to Conservation Genetics. Cambridge, United Kingdom: Cambridge University Press. 2002.
  • Demir E, Bilginer U, Balcioglu MS, Karsli T. Direct and indirect contributions of molecular genetics to farm animal welfare: a review. Anim Health Res Rev. 2021;22(2):177–186.
  • Boettcher PJ, Tixier-Boichard M, Toro MA, et al. Objectives, criteria and methods for using molecular genetic data in priority setting for conservation of animal genetic resources. Anim Genet. 2010;41(s1):64–77.
  • Bilginer U, Ergin M, Demir E, Yolcu Hİ. Argun Karsli B. Detection of genetic diversity in cattle by microsatellite and SNP markers-a review. Anim Sci Pap Rep. 2022;40(4):375–392.
  • Kumar H, Panigrahi M, Chhotaray S, et al. Comparative analysis of five different methods to design a breed-specific SNP panel for cattle. Anim Biotechnol. 2021;32(1):130–136.
  • Panigrahi M, Kumar H, Saravanan KA, et al. Trajectory of livestock genomics in South Asia: a comprehensive review. Gene. 2022;843:146808.
  • Malik AA, Sharma R, Ahlawat S, Deb R, Negi MS, Tripathi SB. Analysis of genetic relatedness among Indian cattle (Bos indicus) using genotyping‐by‐sequencing markers. Anim Genet. 2018;49(3):242–245.
  • Geibel J, Reimer C, Weigend S, Weigend A, Pook T, Simianer H. How array design creates SNP ascertainment bias. PLOS One. 2021;16(3):e0245178.
  • De Donato M, Peters SO, Mitchell SE, Hussain T, Imumorin IG. Genotyping-by-sequencing (GBS): a novel, efficient and cost-effective genotyping method for cattle using next-generation sequencing. PLOS One. 2013;8(5):e62137.
  • Vineeth MR, Surya T, Sivalingam J, et al. Genome-wide discovery of SNPs in candidate genes related to production and fertility traits in Sahiwal cattle. Trop Anim Health Prod. 2020;52(4):1707–1715.
  • Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLOS One. 2012;7(5):e37135.
  • Tyagi SK, Mehrotra A, Singh A, et al. Comparative signatures of selection analyses identify loci under positive selection in the Murrah Buffalo of India. Fron Genet. 1915;2021;12:673697.
  • Simon SE, Radhika G, Aravindakshan TV, Thomas M, Raji K. Double digest restriction associated DNA sequencing for identification of single nucleotide polymorphisms in goats. J Vet Anim Sci. 2019;50(2):108–113.
  • Li Y, Li B, Yang M, et al. Genome-wide association study and fine mapping reveals candidate genes for birth weight of Yorkshire and Landrace pigs. Front Genet. 2020;11:183.
  • Bateson ZW, Hammerly SC, Johnson JA, Morrow ME, Whittingham LA, Dunn PO. Specific alleles at immune genes, rather than genome‐wide heterozygosity, are related to immunity and survival in the critically endangered Attwater’s prairie‐chicken. Mol Ecol. 2016;25(19):4730–4744.
  • Öner Y, Yılmaz O, Eriş C, Ata N, Ünal C, Koncagül S. Genetic diversity and population structure of Turkish native cattle breeds. SA J Anim Sci. 2019;49(4):628–635.
  • Boğa Kuru B, Kırmızıbayrak T, Özşensoy Y. Zavot cattle genetic characterization using microsatellites. Trop Anim Health Prod. 2022;54(6):363.
  • Demir E, Moravčíková N, Karsli T, Kasarda R. Future perspective of NGS data for evaluation of population genetic structure in Turkish cattle. Acta Fytotech Zootech. 2022;25(2):1336–9245.
  • TSI. The number of animals per species and breed. https://data.tuik.gov.tr/Bulten/Index?p=Hayvansal-Uretim-Istatistikleri-2022-49682. Last accessed on 25-06-2023.
  • Rochette NC, Rivera‐Colón AG, Catchen JM. Stacks 2: analytical methods for paired‐end sequencing improve RADseq‐based population genomics. Mol Ecol. 2019;28(21):4737–4754.
  • Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34(17):i884–i890.
  • Li H, Durbin R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics. 2009;25(14):1754–1760.
  • Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. Gigascience. 2021;10(2):giab008.
  • Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. 2015;4(1):7.
  • Weir BS, Cockerham CC. Estimating F-statistics for the analysis of population structure. Evol. 1984;38(6):1358–1370.
  • Nei M. Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci U S A. 1973;70(12):3321–3323.
  • De Jong MJ, De Jong JF, Hoelzel AR, Janke A. SambaR: an R package for fast, easy and reproducible population‐genetic analyses of biallelic SNP data sets. Mol Ecol Resour. 2021;21(4):1369–1379.
  • Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 2006;23(2):254–267.
  • Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 2009;19(9):1655–1664.
  • Pickrell J, Pritchard J. Inference of population splits and mixtures from genome-wide allele frequency data. PLOS Genet. 2012;8(11):e1002967.
  • Jombart T. Adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics. 2008;24(11):1403–1405.
  • R Core Team R: a language and environment for statistical computing. R Foundation for Statistical Computing. 2021; https://www.R-project.org/ Last accessed on 20-03-2023.
  • Wang W, Gan J, Fang D, et al. Genome-wide SNP discovery and evaluation of genetic diversity among six Chinese indigenous cattle breeds in Sichuan. PLOS One. 2018;13(8):e0201534.
  • Devadasan MJ, Kumar DR, Vineeth MR, et al. Reduced representation approach for identification of genome-wide SNPs and their annotation for economically important traits in Indian Tharparkar cattle. 3 Biotech. 2020;10(7):309.
  • Senczuk G, Mastrangelo S, Ciani E, et al. The genetic heritage of Alpine local cattle breeds using genomic SNP data. Genet Sel Evol. 2020;52(1):1–12.
  • Kasarda R, Moravčíková N, Olšanská B, et al. The evaluation of genomic diversity and selection signals in the autochthonous Slovak Spotted cattle. Czech J Anim Sci. 2021;66(7):251–261.
  • Kim S, Cheong HS, Shin HD, et al. Genetic diversity and divergence among Korean cattle breeds assessed using a BovineHD single-nucleotide polymorphism chip. Asian-Australas J Anim Sci. 2018;31(11):1691–1699.
  • Iso‐Touru T, Tapio M, Vilkki J, et al. Genetic diversity and genomic signatures of selection among cattle breeds from Siberia, eastern and northern Europe. Anim Genet. 2016;47(6):647–657.
  • Bhuiyan MSA, Lee SH, Hossain SMJ, et al. Unraveling the genetic diversity and population structure of Bangladeshi indigenous cattle populations using 50K SNP markers. Animals. 2021;11(8):2381.
  • Özșensoy Y, Kurar E, Doğan M, et al. Genetic characterization of some native cattle breeds in Turkey by using STR markers. Res J Biol Sci. 2010;3(1):163–171.
  • Özşensoy Y, Kurar E, Doğan M, et al. Phylogenetic relationships of native Turkish cattle breeds using microsatellite markers. Turk J Vet Anim Sci. 2019;43(1):23–29.

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