Exploring the genetic of three Hairless Pig breed populations in Mexico
Keywords:
genetic diversity, landscape genetics, native breeds, genetic resources
Abstract
The objective of this research was to carry out a molecular genetic characterization of three Hairless Pig (HP) breed populations located in México in the states of Nayarit, Oaxaca and Yucatán to identify variations, selection effects and population genetic relationships. From blood samples, a total of 163 animals from three populations of HP were successfully genotyped. Genotyped SNP data was employed to compute genetic diversity, population structure and landscape genetic analysis. The parameters of minor allele frequency (MAF), observed heterozygosity (Ho) and Wright’s fixation index (FIS) pointed out that the population of Nayarit is the one with the greatest genetic diversity (MAF: 0.362, Ho: 0.336, FIS: 0.061). Principal Component Analysis (PCA) and a Neighbor-joining phylogenetic tree analysis showed diversification among the three HP populations and pointed out a closer genetic relationship between the HP populations and the Iberian pig breed. The Admixture analysis showed as well common ancestry shared from commercial and Iberian breeds in the HP populations in different gradients. For the analysis of the relationships between geographic and genetic distances, Mantel test was computed and the results described a distribution pattern of the geographical locations along the genetic distances similar to the clustering pattern of the PCA and Neighbor-joining phylogenetic tree analysis. The results obtained manage to present the HP poor conservation state and the need to stablish a genetic conservation program meaning an effort to prevent the loss of a significant cultural, natural and genetic resource.
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References
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Burgos-Paz, W., Souza, C. A., Megens, H. J., Ramayo-Caldas, Y., Melo, M., Lemus-Flores, C., Caal, E., Soto, H.W., Martínez, R., Álvarez, L. A., Aguirre, L., Iñaguez, V., Revidatti, M. A., Martínez-Lopéz, O.R., Llambi, S., Esteve-Codina, A., Rodríguez, M.C., Crooijmans, R. P. M. A., Paiva, S. R., Schook L.B.. Groenen M.A. & Pérez-Enciso, M. (2013). Porcine colonization of the Americas: a 60k SNP story. Heredity, 110, 321–330. https://doi.org/10.1038/hdy.2012.109.
Cesconeto, R. J., Joost, S., McManus, C. M., Paiva, S. R., Cobuci, J. A., & Braccini, J. (2017). Landscape genomic approach to detect selection signatures in locally adapted Brazilian swine genetic groups. Ecology and Evolution, 7(22), 9544-9556. https://doi.org/10.1002/ece3.3323.
Chang, C. C., Chow, C. C., Tellier, L. C., Vattikuti, S., Purcell, S. M., & Lee, J. J. (2015). Second-generation PLINK: Rising to the challenge of larger and richer datasets. GigaScience, 4(1), 7. https://doi.org/10.1186/s13742-015-0047-8.
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DeWoody, J. A., Harder, A. M., Mathur, S., & Willoughby, J. R. (2021). The long‐standing significance of genetic diversity in conservation. Molecular Ecology, 30(17), 4147-4154. https://doi.org/10.1111/mec.16051.
Govindarajan, R., Duraiyan, J., Kaliyappan, K., & Palanisamy, M. (2012). Microarray and its applications. Journal of Pharmacy and Bioallied Sciences, 4(6), 310-312. https://doi.org/10.4103/0975-7406.100283.
Hancock, J.F. (2022). Spanish Conquest and Colonization of the Americas. In: World Agriculture Before and After 1492. Springer, Cham. https://doi.org/10.1007/978-3-031-15523-9_5.
Hernández, A., García Munguía, C. A., García Munguía, A. M., Ortíz Ortíz, J. R., Sierra Vásquez, Á. C., & Morales Flores, S. (2020). Sistema de producción del Cerdo Pelón Mexicano en la Península de Yucatán. Nova Scientia, 12(24). https://doi.org/10.21640/ns.v12i24.2234.
Kawęcka, A., Gurgul, A., & Miksza-Cybulska, A. (2016). The Use of SNP Microarrays for Biodiversity Studies of Sheep – A Review. Annals of Animal Science, 16(4), 975-987. https://doi.org/10.1515/aoas-2016-0017.
Lemus-Flores, C., Alonso-Morales, R., Toledo-Alvarado, H., Sansor-Nah, R., Burgos-Paz, W., & Dzib-Cauich, D. (2020). Diversidad genética y estructura poblacional del cerdo negro lampiño de Yucatán usando chip SNP50. Abanico veterinario, 10, 1-12. https://doi.org/10.21929/abavet2020.10.
Lemus-Flores, C., Bugarín Prado, J. O., Valdivia Bernal, R., Segura Correa, J. C., & Sansor-Nah, R. (2023). Genetic relationships of the Yucatan black hairless pig with Iberian breeds using single nucleotide polymorfisms. Brazilian Journal of Veterinary Research and Animal Science, 60, e195697. https://doi.org/10.11606/issn.1678-4456.bjvras.2023.195697.
Lemus-Flores, C., Ulloa-Arvizu, R., Ramos-Kuri, M., Estrada, F. J., & Alonso, R. A. (2001). Genetic analysis of Mexican hairless pig populations. Journal of Animal Science, 79(12), 3021-3026. https://doi.org/10.2527/2001.79123021.
Li, S.-J., Yang S.-H., Zhao S.-H., Fan B., Yu M., Wang H.-S., Li M.-H., Liu B., Xiong T.-A. and Li K. (2004). Genetic diversity analyses of 10 indigenous Chinese pig populations based on 20 microsatellites. Journal of Animal Science, 82(2), 368–374. https://doi.org/10.2527/2004.822368.
Meuwissen, T. H. E., Sonesson, A. K., Gebregiwergis, G., & Woolliams, J. A. (2020). Management of Genetic Diversity in the Era of Genomics. Frontiers in Genetics, 11, 880. https://doi.org/10.3389/fgene.2020.00880.
Monteiro, A. N. T. R., Wilfart, A., Utzeri, V. J., Batorek Lukač, N., Tomažin, U., Costa, L. N., Čandek-Potokar, M., Fontanesi, L., & Garcia-Launay, F. (2019). Environmental impacts of pig production systems using European local breeds: The contribution of carbon sequestration and emissions from grazing. Journal of Cleaner Production, 237, 117843. https://doi.org/10.1016/j.jclepro.2019.117843.
Muñoz, M., Bozzi, R., García-Casco, J., Núñez, Y., Ribani, A., Franci, O., García, F., Škrlep, M., Schiavo, G., Bovo, S., Utzeri, V. J., Charneca, R., Martins, J. M., Quintanilla, R., Tibau, J., Margeta, V., Djurkin-Kušec, I., Mercat, M. J., Riquet, Estellé, J., Zimmer, C., Razmaite, V., Araujo, J. P., Radović, Č., Savić, R., Karolyi, D., Gallo, M., Čandek-Potokar, M., Fernández, A. I., Fontanesi, L. & Óvilo C. (2019). Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip. Scientific Reports, 9(1), 13546. https://doi.org/10.1038/s41598-019-49830-6.
Peakall, R., & Smouse, P.E. (2012). GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics, 28, 2537-2539. https://doi:10.1093/bioinformatics/bts460.
Perrier, X. & Jacquemoud-Collet, J.P. 2006. DARwin Software. http://darwin.cirad.fr/darwin.
Pimentel, F., McManus, C., Soares, K., Rodrigues-Caetano, A., Assis de Faria, D., Rezende-Paiva, S., Ianella, P. (2023). Landscape Genetics for Brazilian Equines. Journal of Equine Veterinary Science. 126, 104251. ISSN 0737-0806. https://doi.org/10.1016/j.jevs.2023.104251.
R Core Team. (2021). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org. Rosado-Aguilar, J.,A., Rodríguez-Vivas, R.,I., Bolio-González, M.,E., Gutiérrez-Ruiz, E., Aguilar Caballero, A. J., Ortega-Pacheco, A., Torres-Acosta, J.F.J., Gutiérrez-Blanco, E. (2022). El cerdo pelón mexicano: alternativa alimenticia y principales zoonosis parasitarias. Bioagrociencias, 15(1), 47-55. https://doi:10.56369/BAC.4144.
Šalamon, D., Margeta, P., Klišanić, V., Menčik, S., Karolyi, D., Mahnet, Ž., Škorput, D., Luković, Z., & Salajpal, K. (2019). Genetic diversity of the Banija spotted pig breed using microsatellite markers. Journal of Central European Agriculture, 20(1), 36-42. https://doi.org/10.5513/JCEA01/20.1.2467.
Sierra, A.C., Poot, T.B., Díaz, Z.I. Cordero A.H., & Delgado J.V. (2005). El Cerdo Pelón Mexicano, una raza en peligro. Archivos de Zootecnia, 54, 165-170. http://hdl.handle.net/10396/2822.
Sierra-Vásquez, Á. C., Ortiz-Ortiz, J. R., Bojórquez-Cat, J. C., Canul-Solís, M. A., Tamayo-Canul, J. R., Rodríguez-Pérez, J. C., Sanginés-García, J. R., Magaña-Magaña, M. A., & Montes-Pérez, R. C. (2016). Conservación y uso sustentable del cerdo pelón en Yucatán. Quehacer Científico en Chiapas, 11(1), 13-28. https://www.dgip.unach.mx/index.php/difusion-y-divulgacion-del-conocimiento/16-revista-quehacer-cientifico-en-chiapas.
Yang, B., Cui, L., Perez-Enciso, M., Traspov, A., Crooijmans, R., Zinovieva, N., Schook, L., Archibald, A., Gatphayak, K., Knorr, P., Triantafyllidis, A., Alexandri, P. Semiadi, G., Hanette, O., Dias, D., Dovc, P., Uimari, P., lacolina, L., Scandura, M, Martien, Groenen A. M., Lusheng Hua & Jan Megens, H. (2017). Genome-wide SNP data unveils the globalization of domesticated pigs. Genetics Selection Evolution, 49:71-85. https://doi.org/10.1186/s12711-017-0345-y.
Zhong, Z., Wang, Z., Xie, X., Tian, S., Wang, F., Wang, Q., Ni, S., Pan, Y., & Xiao, Q. (2023). Evaluation of the Genetic Diversity, Population Structure and Selection Signatures of Three Native Chinese Pig Populations. Animals, 13(12), 2010. https://doi.org/10.3390/ani13122010.
Zorc, M., Škorput, D., Gvozdanović, K., Margeta, P., Karolyi, D., Luković, Z., Salajpal, K., Savić, R., Muñoz, M., Bovo, S., Djurkin Kušec, I., Radović, Č., Kušec, G., Čandek Potokar, M., & Dovč, P. (2022). Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia. Genetics Selection Evolution, 54, 30. https://doi.org/10.1186/s12711-022-00718-6.
Published
2024-07-01
How to Cite
Lemus, G., Rodríguez, J., Burgos, W., Lemus, C., & Carmona, C. (2024). Exploring the genetic of three Hairless Pig breed populations in Mexico. Revista De La Facultad De Agronomía De La Universidad Del Zulia, 41(3), e244122. Retrieved from https://produccioncientificaluz.org/index.php/agronomia/article/view/42411
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Section
Animal Production
Copyright (c) 2024 Gilberto Lemus Avalos, Javier Germán Rodríguez Carpena, William Orlando Burgos Paz, Clemente Lemus Flores, Carlos Alfredo Carmona Gasca
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
