Abstract
The study aimed to characterize genetic diversity, genetic clusters, and phylogenetic relationships of 15 Vietnamese indigenous pig breeds across the country for supporting the decision making of the conservation strategies. For this purpose, 638 samples from the breeds together with two wild pig breeds and an exotic breed were genotyped with 19 microsatellite markers recommended from FAO/ISAG for diversity studies. The higher genetic diversity was observed for indigenous breeds (mean He = 0.67) and wild breeds (mean He = 0.74); the indigenous CoAluoi breed compared the out-breed Landrace (He = 0.59). Fifteen percent of the genetic variation came from differences among breeds. The unrooted neighbor-joining dendrogram obtained from Nei’s genetic distances showed three nodes with 100% supported bootstrap values. The first node included the three indigenous breeds (Hung, LungPu, and MuongKhuong), the second node included the indigenous BaXuyen and the exotic Landrace, and the third node included the two wild Thailand and Vietnam pig breeds. The discriminant analysis of principal component (DAPC) of 18 studied breeds resulted in 12 genetic clusters. Unlike the other indigenous breeds, the BaXuyen was in the same genetic cluster with the exotic Landrace—which agreed with the 100% bootstrap value of their node—so the BaXuyen should not be conserved. The five indigenous pig breeds—Huong, VanPa, Soc, ChuProng, and CoAluoi—were assigned to their own clusters, which agreed with the low supported bootstrap values of their nodes. These five breeds should be in the high conservation priority. Finally, the 9 indigenous pig breeds (MuongKhuong, LungPu, Hung, TapNa, MongCai, HaLang, Lung, Meo, and Ban breeds) formed four genetic admixture structures. These results suggest the conservation strategies should be built based on from five to nine pig groups thus reducing the cost of conservation whereas still remaining the genetic diversity of the studied breeds.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Barker J. (1994) A global protocol for determining genetic distances among domestic livestock breeds. In: Proceedings of the 5th World Congress on Genetics Applied to Livestock Production, Guelph and Ontario, Canada, pp. 501–8.
Berthouly C., Do Ngoc D., Thevenon S., Bouchel D., Van TN., Danes C., Grosbois V., Thanh HH., Chi CV. & MAILLARD J.C. (2009) How does farmer connectivity influence livestock genetic structure? A case-study in a Vietnamese goat population. Molecular Ecology 18, 3980–91.
Berthouly-Salazar C., Thévenon S., Van T.N., Nguyen B.T., Pham L.D., Chi C.V., Maillard J.C.J.E. & evolution (2012) Uncontrolled admixture and loss of genetic diversity in a local Vietnamese pig breed. 2, 962-75.
Cunningham E.P. (1993) Animal genetic resources — the perspective for developing countries. BSAP Occasional Publication 16, 33–5.
Fan B., Wang Z.G., Li Y.J., Zhao X.L., Liu B., Zhao S.H., Yu M., Li M.H., Chen S.L. & Xiong T.A. (2002) Genetic variation analysis within and among Chinese indigenous swine populations using microsatellite markers. Animal Genetics 33, 422–7.
FAO (2009) The State of Food and Agriculture – Livestock in the Balance. Rome. Available online at: http://www.fao.org/docrep/012/i0680e/i0680e.pdf). Accessed Jun 2017.
Goudet J. (1995) STAT (Version 1.2): A Computer Program to Calculate F-Statistics.. Heredity 86, 485–6.
Groenen M.A., Archibald A.L., Uenishi H., Tuggle C.K., Takeuchi Y., Rothschild M.F., Rogel-Gaillard C., Park C., Milan D. & Megens H.-J. (2012) Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491, 393.
Groeneveld L., Lenstra J., Eding H., Toro M., Scherf B., Pilling D., Negrini R., Finlay E., Jianlin H. & Groeneveld E.J.A.G. (2010) Genetic diversity in farm animals–a review. 41, 6–31.
Hongo H., Naotaka I., Takuma W., Nobuo S., Tomoko A., Dang V.B, Nguyen T.T., & Nguyen H.N. (2002) Variation in mitochondrial DNA of Vietnamese pigs: relationships with Asian domestic pigs and Ryukyu wild boars. Zoological Science 19, 1329–1335.
Ibeagha-Awemu E.M., Peters S.O., Bemji M.N., Adeleke M.A. & Do D.N. (2019) Leveraging available resources and stakeholder involvement for improved productivity of African livestock in the era of genomic breeding. Frontier in Genetics 10.
Ishihara S., Arakawa A., Taniguchi M., Luu Q., Pham D., Nguyen B., Mikawa S. & Kikuchi K. (2018) Genetic relationships among Vietnamese local pigs investigated using genome-wide SNP markers. Animal genetics 49, 86–9.
Jombart T. (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24, 1403–5.
Kim T.H., Kim K.S., Choi B.H., Yoon D.H., Jang G.W., Lee K.T., Chung H.Y., Lee H.Y., Park H.S. & Lee J.W. (2005) Genetic structure of pig breeds from Korea and China using microsatellite loci analysis. J Anim Sci 83, 2255–63.
Kreft S., Eckstein D., Junghans L., Kerestan C. & Hagen U. Global climate risk index 2014.
Laval G., Iannuccelli N., Legault C., Milan D., Groenen M.A., Giuffra E., Andersson L., Nissen P.H., Jorgensen C.B., Beeckmann P., Geldermann H., Foulley J.L., Chevalet C. & Ollivier L. (2000) Genetic diversity of eleven European pig breeds. Genet Sel Evol 32, 187–203.
Lemke U, Huyen L.T.T., Roessler R., Thuy L.T & Zárate A.V. (2005) Impact Of the Use of Exotic Compared to Local Pig Breeds on Socio-economic Development and Biodiversity in Vietnam. Tropentag 2005 Stuttgart-Hohenheim, October 11-13, 2005 (http://www.tropentag.de/2005/abstracts/full/251.pdf). Accessed Jun 2018.
Lemke U., Mergenthaler M., Roßler R., Huyen L., Herold P., Kaufmann B., Zarate A.V.J.P.N. & Information (2008) Pig production in Vietnam--A review. CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources 2008 Vol.3 No.023 pp.15 pp. ref.99
Li S.J., Yang S.L., Zhao S.H., Fan B., Yu M., Wang H.S., Li M.H., Liu B., Xiong T.A., Li K. (2004) Genetic diversity analyses of 10 indigenous Chinese pig populations based on 20 microsatellites. J. Anim. Sci., 82, 368–374
Martinez A.M., Delgado J.V., Rodero A., Vega-Pla J.L. (2000) Genetic structure of the Iberian pig breed using microsatellites. Anim. Genet., 31, 295–301
Paradis E., Claude J. & Strimmer K. (2004) APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289–90.
Park S., D, E (2001) Trypanotolerance in West African Cattle and the Population Genetic Effects of Selection [ Ph.D. thesis ] University of Dublin.
Pham K.T., Hoang N.D., Duc N.L., Hendriks W.H. & Verstegen M.W.A. (2010) Nutritional Constraints and Possibilities for Pig Production on Smallholders Farms in Central Vietnam. Asian-Australas J Anim Sci 23, 253–62.
Pham L.D., Do D.N., Binh N.T., Van Ba N., Thuy T.T.T., Hoan T.X., Cuong V.C. & Kadarmideen H.N. (2013) Assessment of genetic diversity and population structure of Vietnamese indigenous cattle populations by microsatellites. Livestock Science 155, 17–22.
Pham L., Do D.N., Nam L., Van Ba N., Minh L., Hoan T., Cuong V. & Kadarmideen H. (2014) Molecular genetic diversity and genetic structure of Vietnamese indigenous pig populations. Journal of animal breeding and genetics 131, 379–86.
Raymond M. & Rousset F. (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J. Heredity 86, 248–9.
Rege J.E.O. & Gibson J.P. (2003) Animal genetic resources and economic development: issues in relation to economic valuation. Ecological Economics 45, 319–30.
San Cristobal M, Chevalet C, Haley CS, Joosten R, Rattink AP, Harlizius B, Groenen MAM, Amigues Y, Boscher MY, Russell G, Law A, Davoli R, Russo V, Dèsautés C, Alderson L, Fimland E, Bagga M, Delgado JV, Vega-Pla JL, Martinez AM, Ramos AM, Glodek P, Meyer JN, Gandini G, Matassino D, Plastow GS, Siggens KW, Laval G, Archibald A, Milan D, Hammond K, Cardellino R. Genetic diversity within and between European pig breeds using microsatellite markers. Anim Genet. 2006;37:189–198. doi: https://doi.org/10.1111/j.1365-2052.2005.01385.x
Tạ T.B.D., Đặng H.B., Nguyễn V.T., Ngô T.K.C., Phạm V.S., Nguyễn H.C. & Nguyễn T.N.C.S. (2013) Một số giống lợn bản địa việt nam. In: Bản tốn và khai thác nguốn gen vật nuôi việt nam (Ed. by C.T. Phạm), pp. 52–93. National Institute of Animal Science, Hanoi [in Vietnamese].
Team R.C. (2013) R: A language and environment for statistical computing.
Thuy N., Melchinger-Wild E., Kuss A., Cuong N., Bartenschlager H. & Geldermann H. (2006) Comparison of Vietnamese and European pig breeds using microsatellites. Journal of animal science 84, 2601–8.
Wang J.Y., Guo J.F., Zhang Q., Hu H.M., Lin H.C., Wang C., Zhang Y. & Wu Y. (2011) Genetic Diversity of Chinese Indigenous Pig Breeds in Shandong Province Using Microsatellite Markers. Asian-Aust. J. Anim. Sci. 24, 28–36.
Weir B.S. & Cockerham C.C. (1984) Estimating F-statistics for the analysis of populations structure. Evolution 38, 1358–70.
Yang B., Cui L., Perez-Enciso M., Traspov A., Crooijmans R.P.M.A., Zinovieva N., Schook L.B., Archibald A., Gatphayak K., Knorr C., Triantafyllidis A., Alexandri P., Semiadi G., Hanotte O., Dias D., Dovč P., Uimari P., Iacolina L., Scandura M., Groenen M.A.M., Huang L. & Megens H.-J. (2017) Genome-wide SNP data unveils the globalization of domesticated pigs. Genetics Selection Evolution 49, 71.
Yusuf A.A. & Francisco H. (2009) Climate change vulnerability mapping for Southeast Asia. http://hdl.handle.net/10625/46380. Assessed May 2019.
Acknowledgments
The authors would like to thank local farmers for their help during sampling process.
Funding
This study was financed by the Vietnam National Program of Development of Biotechnology in Agriculture, Ministry of Agriculture and Rural Development.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflicts of interest.
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
ESM 1
(JPG 182 kb)
Rights and permissions
About this article
Cite this article
Van Ba, N., Nam, L.Q., Do, D.N. et al. An assessment of genetic diversity and population structures of fifteen Vietnamese indigenous pig breeds for supporting the decision making on conservation strategies. Trop Anim Health Prod 52, 1033–1041 (2020). https://doi.org/10.1007/s11250-019-02090-y
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11250-019-02090-y