Diversidade genética e estrutura populacional do porco preto sem pêlos de Yucatan usando o chip SNP50K
Palavras-chave:
diversidade genéticaResumo
A estrutura populacional e a diversidade genética de 104 porcos pretos sem pêlos de Yucatan (NLY) e oito da raça Duroc foram caracterizadas usando um chip SNP50K. A estrutura populacional foi obtida, uma análise de componentes principais (PCA), menor frequência de alelos (MAF), heterozigosidade observada (Ho), consanguinidade (F), índice de fixação de indivíduos nas subpopulações (Fis), índice de alogamia (t) e análise de associação para identificar diferentes SNPs entre populações. De acordo com a análise de mistura, a população do NLY é dividida em três subpopulações. O componente genético de Duroc nas subpopulações de NLY é baixo de 0,0036 a 0,0353, mostrando uma subpopulação com maior diversidade genética, com menores valores de F, Fis e maiores Ho e t. Os SNPs foram identificados (p <1,21E-50 a p <6,4E-20), associados a genes e processos biológicos. Genes EHF, DST, PDE8A, FOXA1 e VCL relacionados à diferenciação celular epitelial, morfogênese e desenvolvimento epitelial. Outros 30 SNPs
relacionados ao metabolismo de nutrientes, 23 SNPs no transporte de nutrientes, 11 SNPs na imunidade, 10 SNPs no músculo, esqueleto e embrião e sete SNPs nas sinapses e receptores. O NLY está distante de Duroc, com estrutura populacional e diversidade genética diferentes, com genes diferentes envolvendo processos biológicos importantes.
Referências
ALEXANDER DH, Novembre J, Lange K. 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Research. 19:1655–1664. https://doi.org/10.1101/gr.094052.109
ASHBURNER M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Sherlock G. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature genetics. 25(1):25–29. https://doi.org/10.1038/75556
BENÍTEZ OW, Sánchez DM. 2001. Los cerdos criollos en América Latina. En: FAO (ed.) Los cerdos locales en los sistemas tradicionales de producción. Estudio FAO Producción y Sanidad Animal. Pp.13-35. http://www.fao.org/3/a-y2292s.pdf
BURGOS-PAZ W, Souza CA, Megens HJ, Ramayo-Caldas Y, Melo M, Lemus-Flores C, Caal E, Soto HW, Martínez R, Álvarez LA. 2013. Porcine colonization of the Americas: a 60k SNP story. Heredity. 110:321–330. https://www.nature.com/articles/hdy2012109
CHANG CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. 2015. Second generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. 4:7. https://academic.oup.com/gigascience/article/4/1/s13742-015-0047-8/2707533
DAD-IS. 2020. Sistema de Información sobre la Diversidad de los Animales Domésticos (DAD-IS@fao.org). FAOIn: http://www.fao.org/dad-is/browse-by-country-and-species/es/
ESTEVE Codina A, Paudel Y, Ferretti L, Raineiri E. 2013. Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs. BMC Genomics. 14:148- https://doi.org/10.1186/1471-2164-14-148
FAO. Food and Agriculture Organization. 2019. Domestic Animal Diversity Information System (DADIS). Retrieved March 31, 2020, from http://www.fao.org/dad-is/regional-national-nodes/efabis/en/
GROENEN M, Archibald A, Uenishi H, Tuggle C, Takeuchi Y, Rothschild M. 2012. Pig genomes provide insight into porcine demography and evolution. Nature. 491: 393–398. https://www.ensembl.org/Sus_scrofa/Info/Index
KANG L, Liu Y, Jin Y, Li M, Song J, Zhang Y, Zhang Y and Yang Y. 2020 Mutations of MACF1, Encoding Microtubule-Actin Crosslinking-Factor 1, Cause Spectraplakinopathy. Frontiers in Neurology. 10:1335. https://doi.org/10.3389/fneur.2019.01335
KWON DJ, Lee YS, Shin D, Won KH, Song KD. 2019. Genome analysis of Yucatan miniature pigs to assess their potential as biomedical model animals. Asian-Australas J Anim Sci. 32(2):290‐296. doi:10.5713/ajas.18.0170
LEMUS C, Alonso ML. 2005. El cerdo Pelón Mexicano y otros cerdos criollos. 1ª Edición. Editorial Universitaria. Universidad Autónoma de Nayarit. México. Pp. 251. https://www.amazon.com.mx/cerdo-pel%C3%B3n-mexicano-cerdos-criollos-ebook/dp/B0153G544M
LEMUS-FLORES C, Ulloa-Arvizu R, Ramos-Kuri M, Estrada FJ, Alonso RA. 2001. Genetic analysis of Mexican hairless pig populations. Journal Animal Science. 79:3021–3026. https://doi.org/10.2527/2001.79123021x
OGATA N. 2019. 1519, Hernán Cortés y el Cerdo en México. Diversidad Biológica y Cultural Trópico Americano. Centro de Investigaciones Tropicales (CITRO), Universidad Veracruzana. Disponible: http://etnoecologia.uv.mx/diversidad_biocultural/cerdo-pelon-mexicano/
MONTENEGRO M, Llambí S, Castro G, Barlocco N, Vadell A, Landi V, Delgado JV, Martínez A. 2015. Genetic characterization of Uruguayan Pampa Rocha pigs with microsatellite markers. Genetics and Molecular Biology. 38(1):48-54. https://doi.org/10.1590/S1415-475738120140146
NITURAD C E, Lev D, Vera M, Crzewska A, Schubert J, Lerman-Sagie T, Kroes H, Oegema R, Traverso M, Specchio N, Lassota M, Chelly J, Bennett-Back O, Carmi N, Koffler-Brill T, Lacomino M, Trivisano M, Capovilla G, Striano P, Nawara M, Rzonca S, Fischer U, Bienek M, Jensen C, Hu H, Thiele H, Altmüller J, Krause R, May P, Becker F, Balling R, Biskup S, Haas SA, Nürnberg P, Van Gassen
KLI, Lerche H, Zara F, Maljevic S, Leshinsky-Silver E. 2017. GABRA3 variants are associated with epileptic seizures, encephalopathy and dysmorphic features. Brain. 140(11):2879–2894. https://doi.org/10.1093/brain/awx236 https://academic.oup.com/brain/article/140/11/2879/4372140
NOM-051-ZOO-1995. Norma Oficial Mexicana NOM-051-ZOO-1995. Trato humanitario en la movilización de animales. Pp 23. http://publico.senasica.gob.mx/?doc=531
NOM-062-ZOO-1999. NORMA Oficial Mexicana NOM-062-ZOO-1999. Especificaciones técnicas para la producción, cuidado y uso de los animales de laboratorio. Pp 58. http://publico.senasica.gob.mx/?doc=743
PARDAL-FERNÁNDEZ J M, Carrascosa-Romero M C, Álvarez S, Medina-Monzón M C, Caamaño M B, de Cabo C. 2018. A new severe mutation in the SLC5A7 gene related to congenital myasthenic syndrome type 20. Neuromuscular Disorders. 28(10):881‐884. https://doi.org/10.1016/j.nmd.2018.06.020
PURCELL S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D. 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. American Journal Human Genetics. 81(3):559–575. https://doi.org/10.1086/519795. https://www.cell.com/ajhg/fulltext/S0002-9297(07)61352-4
RAMÍREZ O, Burgos-Paz W, Casas E, Ballester M, Bianco E, Olalde I, Santpere G, Novella V, Gut M, Lalueza C, Saña M, Pérez-Enciso M. 2015. Genome data from a sixteenth century pig illuminate modern breed relationships. Heredity. 114:175–184. https://www.nature.com/articles/hdy201481
SCARPA R, Drucker AG, Anderson S, Ferraes-Ehuan N, Gómez V, Risopatrón CR, Rubio-Leonel O. 2003. Valuing genetic resources in peasant economies: the case of ‘hairless’ creole pigs in Yucatan. Ecological Economics. 45:427–443. https://doi.org/10.1016/S0921-8009(03)00095-8
SPSS. Statistical Package for the Social Sciences. 2011. IBM® SPSS® Statistics v20 for Windows: advanced statistic release. SPSS, Chicago. USA. ftp://public.dhe.ibm.com/software/analytics/spss/documentation/statistics/20.0/es/client/Manuals/IBM_SPSS_Statistics_Base.pdf
SU Y, Long Y, Liao X, Ai H, Zhang Z, Yang B, Xiao S, Tang J, Xin W, Huang L, Ren J, Ding N. 2014. Detection of genomic signatures for pig hairlessness using high-density SNP data. Frontiers of Agricultural Science and Engineering. 1(4):307–313. https://doi.org/10.15302/J-FASE-2014039
WEIR BS, Cockerham CC. 1984. Estimating F-statistics for the analysis of population structure. Evolution. 38:1358–1370. https://doi.org/10.2307/2408641
XIU-KAI C, Jing W, Xian-Yong L, Chu-Zhao L, Chun-Lei Z, Xing-Lei Q, Hong C. 2013. Genetic variants in BMP8B gene are associated with growth traits in Chinese native cattle. Gene. 532(1):115-120. https://doi.org/10.1016/j.gene.2013.09.059
YANG B, Cui L, Perez-Enciso M., Traspov A, Crooijmans R, Zinovieva N, Schook L, Archibald A. 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
YING Y, Liu X M, Marble A, Lawson K A, Zhao G Q. 2000. Requirement of Bmp8 for the Generation of Primordial Germ Cells in the Mouse. Molecular Endocrinology. 14(7):1053-1063. https://doi.org/10.1210/mend.14.7.0479
