Animal Bioscience

Asian Australasian Association of Animal Production Societies (아세아태평양축산학회)
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Genetic characteristics of Korean Jeju Black cattle with high density single nucleotide polymorphisms

  • Alam, M. Zahangir (Department of Biotechnology, Yeungnam University) ;
  • Lee, Yun-Mi (Department of Biotechnology, Yeungnam University) ;
  • Son, Hyo-Jung (Department of Biotechnology, Yeungnam University) ;
  • Hanna, Lauren H. (Department of Animal Sciences, North Dakota State University) ;
  • Riley, David G. (Department of Animal Sciences, Texas A&M University) ;
  • Mannen, Hideyuki (Graduate School of Agricultural Science, Kobe University) ;
  • Sasazaki, Shinji (Graduate School of Agricultural Science, Kobe University) ;
  • Park, Se Pill (Faculty of Biotechnology, Jeju National University) ;
  • Kim, Jong-Joo (Department of Biotechnology, Yeungnam University)
  • Received : 2019.11.15
  • Accepted : 2020.06.29
  • Published : 2021.05.01
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Abstract

Objective: Conservation and genetic improvement of cattle breeds require information about genetic diversity and population structure of the cattle. In this study, we investigated the genetic diversity and population structure of the three cattle breeds in the Korean peninsula. Methods: Jeju Black, Hanwoo, Holstein cattle in Korea, together with six foreign breeds were examined. Genetic diversity within the cattle breeds was analyzed with minor allele frequency (MAF), observed and expected heterozygosity (HO and HE), inbreeding coefficient (FIS) and past effective population size. Molecular variance and population structure between the nine breeds were analyzed using a model-based clustering method. Genetic distances between breeds were evaluated with Nei's genetic distance and Weir and Cockerham's FST. Results: Our results revealed that Jeju Black cattle had lowest level of heterozygosity (HE = 0.21) among the studied taurine breeds, and an average MAF of 0.16. The level of inbreeding was -0.076 for Jeju Black, while -0.018 to -0.118 for the other breeds. Principle component analysis and neighbor-joining tree showed a clear separation of Jeju Black cattle from other local (Hanwoo and Japanese cattle) and taurine/indicine cattle breeds in evolutionary process, and a distinct pattern of admixture of Jeju Black cattle having no clustering with other studied populations. The FST value between Jeju Black cattle and Hanwoo was 0.106, which was lowest across the pair of breeds ranging from 0.161 to 0.274, indicating some degree of genetic closeness of Jeju Black cattle with Hanwoo. The past effective population size of Jeju Black cattle was very small, i.e. 38 in 13 generation ago, whereas 209 for Hanwoo. Conclusion: This study indicates genetic uniqueness of Jeju Black cattle. However, a small effective population size of Jeju Black cattle indicates the requirement for an implementation of a sustainable breeding policy to increase the population for genetic improvement and future conservation.

Keywords

References

  1. Oldenbroek K,van der Waaij L. Textbook animal breeding: animal breeding and genetics for BSc students. Wageningen, Netherlands: Wageningen University and Research Centre; 2014.
  2. Struken EM, Lee SH, Jang GW, Porto-Neto LR, Gondro C. Towards breed formation by island model divergence in Korean cattle. BMC Evol Biol 2015;15:284. https://doi.org/10.1186/s12862-015-0563-2
  3. Kim JH, Oh JH, Song JH, et al. Molecular genetic analysis of ancient cattle bones excavated from archaeological sites in Jeju, Korea. Mol Cells 2005;20:325-30. https://doi.org/10.1016/j.molcel.2005.09.001
  4. Lee SH, Park BH, Sharma A, et al. Hanwoo cattle: origin, domestication, breeding strategies and genomic selection. J Anim Sci Technol 2014;56:2. https://doi.org/10.1186/2055-0391-56-2
  5. Sudrajad P, Seo DW, Choi TJ, et al. Genome-wide linkage disequilibrium and past effective population size in three Korean cattle breeds. Anim Genet 2017;48:85-9. https://doi.org/10.1111/age.12488
  6. Kim EY, Song DH, Park MJ, et al. Post-death cloning of endangered Jeju Black cattle (Korean native cattle): fertility and serum chemistry in a cloned bull and cow and their offspring. J Reprod Dev 2013;59:536-43. https://doi.org/10.1262/jrd.2013-047
  7. Zanella R, Peixoto JO, Cardoso FF, et al. Genetic diversity analysis of two commercial breeds of pigs using genomic and pedigree data. Genet Sel Evol 2016;48:24. https://doi.org/10.1186/s12711-016-0203-3
  8. Li Y, Kim JJ. Effective population size and signatures of selection using bovine 50K SNP chips in Korean native cattle (Hanwoo). Evol Bioinform 2015;11:143-53. https://doi.org/10.4137/EBO.S24359
  9. Tenesa A, Navarro P, Hayes BJ, et al. Recent human effective population size estimated from linkage disequilibrium. Genome Res 2007;17:520-6. https://doi.org/10.1101/gr.6023607
  10. Groeneveld LF, Lenstra JA, Eding H, et al. Genetic diversity in farm animals - a review. Anim Genet 2010;41:6-31. https://doi.org/10.1111/j.1365-2052.2010.02038.x
  11. Sharma A, Lim D, Chai HH, Choi BH, Cho Y. Demographic trends in Korean native cattle explained using bovine SNP50 beadchip. Genomics Inform 2016;14:230-3. https://doi.org/10.5808/GI.2016.14.4.230
  12. Ciani E, Cecchi F, Castellana E, et al. Poorer resolution of low-density SNP vs. STR markers in reconstructing genetic relationships among seven Italian sheep breeds. Large Anim Rev 2013;19:236-41.
  13. Fischer MC, Rellstab C, Leuzinger M, et al. Estimating genomic diversity and population differentiation - an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri. BMC Genomics 2017;18:69. https://doi.org/10.1186/s12864-016-3459-7
  14. Frkonja A, Gredler B, Schnyder U, Curik I, Solkner J. Prediction of breed composition in an admixed cattle population. Anim Genet 2012;43:696-703. https://doi.org/10.1111/j.1365-2052.2012.02345.x
  15. Purcell 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;81:559-75. https://doi.org/10.1086/519795
  16. Kijas JW, Townley D, Dalrymple BP, et al. A genome wide survey of SNP variation reveals the genetic structure of sheep breeds. PLoS One 2009;4:e4668. https://doi.org/10.1371/journal.pone.0004668
  17. Keenan K, McGinnity P, Cross TF, Crozier WW, Prodohl PA. diveRsity: An R package for the estimation and exploration of population genetics parameters and their associated errors. Methods Ecol Evol 2013;4:782-8. https://doi.org/10.1111/2041-210X.12067
  18. Excoffier L, Lischer HEL. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 2010;10:564-7. https://doi.org/10.1111/j.1755-0998.2010.02847.x
  19. Weir BS, Cockerham CC. Estimating F-statistics for the analysis of population structure. Evolution 1984;38:1358-70. https://doi.org/10.2307/2408641
  20. Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res 2009;19:1655-64. https://doi.org/10.1101/gr.094052.109
  21. Edea Z, Dadi H, Kim SW, et al. Genetic diversity, population structure and relationships in indigenous cattle populations of Ethiopia and Korean Hanwoo breeds using SNP markers. Front Genet 2013;4:35. https://doi.org/10.3389/fgene.2013.00035
  22. Nei M, Tajima F, Tateno Y. Accuracy of estimated phylogenetic trees from molecular data. J Mol Evol 1983;19:153-70. https://doi.org/10.1007/BF02300753
  23. Takezaki N, Nei M, Tamura K. POPTREE2: software for constructing population trees from allele frequency data and computing other population statistics with Windows interface. Mol Biol Evol 2010;27:747-52. https://doi.org/10.1093/molbev/msp312
  24. Lewontin RC. The interaction of selection and linkage. I. General considerations; heterotic models. Genetics 1964;49: 49-67. https://doi.org/10.1093/genetics/49.1.49
  25. Hill WG. Estimation of linkage disequilibrium in randomly mating populations. Heredity 1974;33:229-39. https://doi.org/10.1038/hdy.1974.89
  26. Visser C, Lashmar SF, Van Marle-Koster E, Poli MA, Allain D. Genetic diversity and population structure in South African, French and Argentinian Angora goats from genome-wide SNP data. PLoS One 2016;11:e0154353. https://doi.org/10.1371/journal.pone.0154353
  27. VanLiere JM, Rosenberg NA. Mathematical properties of the r2 measure of linkage disequilibrium. Theor Popul Biol 2008;74:130-7. https://doi.org/10.1016/j.tpb.2008.05.006
  28. Lee SH, Clark S, van der Werf JHJ. Estimation of genomic prediction accuracy from reference populations with varying degrees of relationship. PLoS One 2017;12:e0189775. https://doi.org/10.1371/journal.pone.0189775
  29. Barbato M, Orozco-terWengel P, Tapio M, Bruford MW. SNeP: a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data. Front Genet 2015;6:109. https://doi.org/10.3389/fgene.2015.00109
  30. Corbin LJ, Liu AYH, Bishop SC, Woolliams JA. Estimation of historical effective population size using linkage disequilibria with marker data. J Anim Breed Genet 2012;129:257-70. https://doi.org/10.1111/j.1439-0388.2012.01003.x
  31. Sved JA. Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theor Popul Biol 1971;2:125-41. https://doi.org/10.1016/0040-5809(71)90011-6
  32. Vargas J, Landi V, Martinez A, et al. Molecular study of the Amazonian Macabea cattle history. PLoS One 2016;11: e0165398. https://doi.org/10.1371/journal.pone.0165398
  33. Browett S, McHugo G, Richardson IW, et al. Genomic characterisation of the indigenous Irish Kerry cattle breed. Front Genet 2018;9:51. https://doi.org/10.3389/fgene.2018.00051
  34. Meszaros G, Boison SA, Perez O'Brien AM, et al. Genomic analysis for managing small and endangered populations: a case study in Tyrol Grey cattle. Front Genet 2015;6:173. https://doi.org/10.3389/fgene.2015.00173
  35. Canas-Alvarez JJ, Gonzalez-Rodriguez A, Munilla S, et al. Genetic diversity and divergence among Spanish beef cattle breeds assessed by a bovine high-density SNP chip. J Anim Sci 2015;93:5164-74. https://doi.org/10.2527/jas.2015-9271
  36. Buzanskas ME, Ventura RV, Seleguim Chud TCS, et al. Study on the introgression of beef breeds in Canchim cattle using single nucleotide polymorphism markers. PLoS One 2017; 12:e0171660. https://doi.org/10.1371/journal.pone.0171660
  37. Ling X, Zhang W, Li J, et al. Genetic background analysis and breed evaluation of Yiling yellow cattle. J Integr Agric 2017;16:2246-56. https://doi.org/10.1016/S2095-3119(17)61679-4
  38. Edea Z, Bhuiyan MSA, Dessie T, Rothschild MF, Dadi H, Kim KS. Genome-wide genetic diversity, population structure and admixture analysis in African and Asian cattle breeds. Animal 2015;9:218-26. https://doi.org/10.1017/S1751731114002560
  39. Eusebi PG, Cortes O, Dunner S, Canon J. Genomic diversity and population structure of Mexican and Spanish bovine Lidia breed. Anim Genet 2017;48:682-5. https://doi.org/10.1111/age.12618
  40. Makina SO, Muchadeyi FC, van Marle-Koster E, MacNeil MD, Maiwashe A. Genetic diversity and population structure among six cattle breeds in South Africa using a whole genome SNP panel. Front Genet 2014;5:333. https://doi.org/10.3389/fgene.2014.00333
  41. Msalya G, Kim ES, Laisser ELK, et al. Determination of genetic structure and signatures of selection in three strains of Tanzania Shorthorn Zebu, Boran and Friesian cattle by genome-wide SNP analyses. PLoS One 2017;12:e0171088. https://doi.org/10.1371/journal.pone.0171088
  42. Karimi K, Strucken EM, Moghaddar N, Ferdosi MH, Esmailizadeh A, Gondro C. Local and global patterns of admixture and population structure in Iranian native cattle. BMC Genet 2016;17:108. https://doi.org/10.1186/s12863-016-0416-z
  43. Kelleher MM, Berry DP, Kearney JF, McParland S, Buckley F, Purfield DC. Inference of population structure of purebred dairy and beef cattle using high-density genotype data. Animal 2017;11:15-23. https://doi.org/10.1017/S1751731116001099
  44. Signer-Hasler H, Burren A, Neuditschko M, et al. Population structure and genomic inbreeding in nine Swiss dairy cattle populations. Genet Sel Evol 2017;49:83. https://doi.org/10.1186/s12711-017-0358-6
  45. Sharma A, Lee SH, Lim D, Chai HH, Choi BH, Cho Y. A genome-wide assessment of genetic diversity and population structure of Korean native cattle breeds. BMC Genet 2016;17: 139. https://doi.org/10.1186/s12863-016-0444-8
  46. Lin BZ, Sasazaki S, Mannen H. Genetic diversity and structure in Bos taurus and Bos indicus populations analyzed by SNP markers. Anim Sci J 2010;81:281-9. https://doi.org/10.1111/j.1740-0929.2010.00744.x
  47. Frankham R, Ballou JD, Briscoe DA. Introduction to conservation genetics. Cambridge, UK: Cambridge University Press; 2002.