Genetic relationships of the Yucatan black hairless pig with Iberian breeds using single nucleotide polymorfisms
DOI:
https://doi.org/10.11606/issn.1678-4456.bjvras.2023.195697Keywords:
Genetic diversity, Yucatan black hairless pig, Inbreeding, Single nucleotide polymorphismAbstract
To conduct ex-situ creole pig conservation programs, it is essential to determine which breeding animals will be used, preferentially those with a more significant Iberian genetic component to preserve their origin. This study used a Yucatan
black hairless pigs (YBHP) subpopulation to estimate its genetic diversity and population structure. One hundred four adult pigs were selected for the absence of hair, black skin (without spots), black hoof, and straight snout. The porcine-GGP-50K
chip was used for SNP genotyping in YBHP, and information on Iberian and Yucatán hairless pigs from the United States (USYU) was taken from databases. All analysis was performed using PLINK v1.9 and v2.1 software. Inbreeding and fixation
index values were lower in YBHP, with high observed heterozygosity and allogamy index values, which agree with those obtained in the populations of Canarias and Chato Murciano. According to the clusters generated by the “Genome-Wide
Identity by State” analysis, four groups were identified, one of which included pigs from Guadyerbas, USYU, and YBHP. Between populations, YBHP was closely related to the hairless pigs from Guadyerbas, USYU, and Canarias. Principal
component analysis showed the same result. According to the results obtained from the runs of homozygosity investigation, aimed to get pools consensus of regions of overlapping, 119 SNPs associated with genes and biological processes were
identified. The BMP7 and NSUN2 genes were associated with epithelial cell differentiation, morphogenesis, and epithelial development. For nutrient metabolism: energy, the HADHA, PPARA, ADD1/SREBF1, and FAT1genes were identified.
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References
Alonso I, Ibáñez-Escriche N, Noguera J, Casellas J, Martín de Hijas-Villalba M, Gracia-Santana M, Varona L. Genomic differentiation among varieties of Iberian pig. Span J Agric Res. 2020;18(1):e0401. http://dx.doi.org/10.5424/sjar/2020181-15411.
Ángel-Hernández A, García MCA, Valencia PM, Gutiérrez CAJ, García MAM, Gómez SJA, Morales-Flores S. Estudio de cerdos criollos mexicanos para instalación del Centro de Conservación en la Universiad de Guanajuato, México. Actas Iberoam Conserv Anim. 2018;12:77-84.
Ángel-Hernández A, García-Munguía CA, García-Munguía AM, Ortiz-Ortiz JR, Sierra-Vásquez AC, Morales-Flores S. Sistema de producción del cerdo pelón mexicano en la Península de Yucatán. Nova Sci. 2020;12(24):1-22. https://doi.org/10.21640/ns.v12i24.2234.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25(1):25-9. http://dx.doi.org/10.1038/75556. PMid:10802651.
Blanco S, Kurowski A, Nichols J, Watt FM, Benitah SA, Frye M. The RNA–Methyltransferase Misu (NSun2) poises epidermal stem cells to differentiate. PLoS Genet. 2011;7(12):e1002403. http://dx.doi.org/10.1371/journal.pgen.1002403. PMid:22144916.
Burgos-Paz W, Souza CA, Megens HJ, Ramayo-Caldas Y, Melo M, Lemus-Flores C, Caal E, Soto HW, Martínez R, Álvarez LA, Aguirre L, Iñiguez V, Revidatti MA, Martínez- López OR, Llambi S, Esteve-Codina A, Rodríguez MC, Crooijmans RPMA, Paiva SR, Schook LB, Groenen M A M, Pérez-Enciso M. Porcine colonization of the Americas: a 60k SNP story. Heredity. 2013;110(4):321-30. http://dx.doi.org/10.1038/hdy.2012.109. PMid:23250008.
Casellas J, Ibáñez-Escriche N, Varona L, Rosas JP, Noguera JL. Inbreeding depression load for litter size in Entrepelado and Retinto Iberian pig varieties. J Anim Sci. 2019;97(5):1979- 86. http://dx.doi.org/10.1093/jas/skz084. PMid:30869129.
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(7):1-16. http://dx.doi.org/10.1186/s13742-015-0047-8. PMid:25722852.
Chi L, Delgado-Olguín P. Expression of NOL1/NOP2/sun domain (Nsun) RNA methyltransferase family genes in early mouse embryogenesis. Gene Expr Patterns. 2013;13(8):319-27. http://dx.doi.org/10.1016/j.gep.2013.06.003. PMid:23816522.
Esteve-Codina A, Kofler R, Himmelbauer H, Ferretti L, Vivancos AP, Groenen MAM, Folch JM, Rodríguez MC, Pérez-Enciso M. Partial short-read sequencing of a highly inbred Iberian pig and genomics interference thereof. Heredity. 2011;107(3):256-64. http://dx.doi.org/10.1038/hdy.2011.13. PMid:21407255.
Esteve-Codina A, Paudel Y, Ferretti L, Raineri E, Megens HJ, Silió L, Rodríguez MC, Groenen MA, Ramos-Onsins SE, Pérez-Enciso M. Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs. BMC Genomics. 2013;14(1):148. http://dx.doi.org/10.1186/1471-2164-14-148. PMid:23497037.
Fabuel EC, Barragán C, Silio L, Rodríguez MC, Toro MA. Analysis of genetic diversity and conservation priorities in Iberian pigs based on microsatellite markers. Heredity. 2004;93(1):104-13. http://dx.doi.org/10.1038/sj.hdy.6800488. PMid:15150539.
Faria DA, Wilson C, Paiva S, Blackburn HD. Assessing Sus scrofa diversity among continental United States, and Pacific islands populations using molecular markers from a gene banks collection. Sci Rep. 2019;9(1):3173. http://dx.doi.org/10.1038/s41598-019-39309-9. PMid:30816173.
Food and Agriculture Organization – FAO. Domestic animal diversity information system (DAD-IS) [Internet]. Rome: FAO; 2019 [cited 2022 Nov 10]. Available from: http://www.fao.org/dad-is/regionalnational-nodes/efabis/en/.
GeneCards. The human gene database. GeneCards version 5.13 [Internet]. Rehovot: Weizmann Institute of Science; 2022 [cited 2022 Nov 10]. Available from: https://www.genecards.org/cgi-bin/carddisp.p.
Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ, Li S, Larkin DM, Kim H, Frantz LA, Caccamo M, Ahn H, Aken BL, Anselmo A, Anthon C, Auvil L, Badaoui B, Beattie CW, Bendixen C, Berman D, Blecha F, Blomberg J, Bolund L, Bosse M, Botti S, Bujie Z, Bystrom M, Capitanu B, Carvalho-Silva D, Chardon P, Chen C, Cheng R, Choi SH, Chow W, Clark RC, Clee C, Crooijmans RP, Dawson HD, Dehais P, De Sapio F, Dibbits B, Drou N, Du ZQ, Eversole K, Fadista J, Fairley S, Faraut T, Faulkner GJ, Fowler KE, Fredholm M, Fritz E, Gilbert JG, Giuffra E, Gorodkin J, Griffin DK, Harrow JL, Hayward A, Howe K, Hu ZL, Humphray SJ, Hunt T, Hornshøj H, Jeon JT, Jern P, Jones M, Jurka J, Kanamori H, Kapetanovic R, Kim J, Kim JH, Kim KW, Kim TH, Larson G, Lee K, Lee KT, Leggett R, Lewin HA, Li Y, Liu W, Loveland JE, Lu Y, Lunney JK, Ma J, Madsen O, Mann K, Matthews L, McLaren S, Morozumi T, Murtaugh MP, Narayan J, Nguyen DT, Ni P, Oh SJ, Onteru S, Panitz F, Park EW, Park HS, Pascal G, Paudel Y, Perez-Enciso M, Ramirez-Gonzalez R, Reecy JM, Rodriguez-Zas S, Rohrer GA, Rund L, Sang Y, Schachtschneider K, Schraiber JG, Schwartz J, Scobie L, Scott C, Searle S, Servin B, Southey BR, Sperber G, Stadler P, Sweedler JV, Tafer H, Thomsen B, Wali R, Wang J, Wang J, White S, Xu X, Yerle M, Zhang G, Zhang J, Zhang J, Zhao S, Rogers J, Churcher C, Schook LB. Pig genomes provide insight into porcine demography and evolution. Nature. 2012;491(7424):393-8. http://dx.doi.org/10.1038/nature11622. PMid:23151582.
Jiang Y, Jiang Y, Zhang H, Mei M, Song H, Ma X, Jiang L, Yu Z, Zhang Q, Ding X. A mutation in MAP2 is associated with prenatal hair follicle density. FASEB J. 2019;33(12):14479-90. http://dx.doi.org/10.1096/fj.201901187R. PMid:31751154.
Lemus-Flores C, Alonso-Morales R, Toledo-Alvarado H, Sansor-Nah R, Burgos-Paz W, Dzib-Cauich D. Genetic diversity and population structure of Yucatan black hairless pig using SNP50K chip. Abanico Veterinario. 2020;10:1-12.
Lemus-Flores C, Ulloa-Arvizu R, Ramos-Kuri M, Estrada FJ, Alonso RA. Genetic analysis of Mexican hairless pig populations. J Anim Sci. 2001;79(12):3021-6. http://dx.doi.org/10.2527/2001.79123021x. PMid:11811455.
Li CL, Pan YC, Me H.Polymorphism of the H-FABP, MC4R and ADD1 genes in the Meishan and four other pig populations in China. S Afr J Anim Sci. 2006;36(1):1-6. http://dx.doi.org/10.4314/sajas.v36i1.3976.
Miklas JW, Clark E, Levy S, Detraux D, Leonard A, Beussman K, Showalter MR, Smith AT, Hofsteen P, Yang X, Macadangdang J, Manninen T, Raftery D, Madan A, Suomalainen A, Kim DH, Murry CE, Fiehn O, Sniadecki NJ, Wang Y, Ruohola-Baker H. TFPa/HADHA is required for fatty acid beta-oxidation and cardiolipin re-modeling in human cardiomyocytes. Nat Commun. 2019;10(1):4671. http://dx.doi.org/10.1038/s41467-019-12482-1. PMid:31604922.
Minitab. Minitab 15 Statistical Software [computer software]. State College, PA: Minitab, Inc.; 2007 [cited 2022 Mar 14]. Available from: www.minitab.com.
Muñoz M, Bozzi R, García-Casco J, Núñez Y, Ribani A, Franci O, García F, Škrlep M, Schiavo G, Bovo S, Utzeri VJ, Charneca R, Martins JM, Quintanilla R, Tibau J, Margeta V, Djurkin-Kušec I, Mercat MJ, Riquet J, Estellé J, Zimmer C, Razmaite V, Araujo JP, Radović Č, Savić R, Karolyi D, Gallo M, Čandek-Potokar M, Fernández AI, Fontanesi L, Óvilo C. Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip. Sci Rep. 2019;9(1):13546. http://dx.doi.org/10.1038/s41598-019-49830-6. PMid:31537860.
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81(3):559-75. http://dx.doi.org/10.1086/519795. PMid:17701901.
Ramírez O, Burgos-Paz W, Casas E, Ballester M, Bianco E, Olalde I, Santpere G, Novella V, Gut M, Lalueza-Fox C, Saña M, Pérez-Enciso M. Genome data from a sixteenth century pig illuminate modern breed relationships. Heredity. 2015;114(2):175-84. http://dx.doi.org/10.1038/hdy.2014.81. PMid:25204303.
Ramos-Canché ME, Magaña-Magaña MA, Aguilar-Urquizo E, Pech-Zapata A, Piñeiro-Vázquez AT, Toledo-López VM, Sanginés-García JR. Óptimos económicos en la cría del cerdo pelón mexicano: propuesta de integración para cadena productiva. Ecosist Recur Agropecu. 2020;7(1):e2302. https://doi.org/10.19136/era.a7nl.2302.
Saura M, Fernández A, Varona L, Fernández AI, de Cara MAR, Barragán C, Villanueva B. Detecting inbreeding depression for reproductive traits in Iberian pigs using genome-wide data. Genet Sel Evol. 2015;47(1):1-9. http://dx.doi.org/10.1186/s12711-014-0081-5. PMid:25595431.
Schiavo G, Bertolini F, Utzeri VJ, Ribani A, Geraci C, Santoro L, Óvilo C, Fernández AI, Gallo M, Fontanesi L. Taking advantage from phenotype variability in a local animal genetic resource: identification of genomic regions associated with the hairless phenotype in Casertana pigs. Anim Genet. 2018;49(4):321-5. http://dx.doi.org/10.1111/age.12665. PMid:29672877.
Secretaría de Agricultura, Ganadería y Desarrollo Rural (MX). Norma Oficial Mexicana NOM-051-ZOO-1995. Trato humanitario en la movilización de animales [Internet]. Diario Oficial de la Federación; México; 1998 Mar 23 [cited 2022 Mar 14]. Available from: http://publico.senasica.gob.mx/?doc=531.
Secretaría de Agricultura, Ganadería, Desarrollo Rural, Pesca y Alimentación (MX). Norma Oficial Mexicana NOM-062-ZOO-1999. Especificaciones técnicas para la producción, cuidado y uso de los animales de laboratorio [Internet]. Diario Oficial de la Federación; México; 2001 Aug 23 [cited 2022 Mar 14]. Available from: http://publico.senasica.gob.mx/?doc=743.
Sierra AC, Poot TB, Diaz ZI, Cordero AH, Delgado JV. El cerdo Pelón Mexicano, una raza en peligro. Arch Zootec [Internet]. 2005 [cited 2022 Mar 14];54(206-207):165-70. Available from: https://www.redalyc.org/pdf/495/49520708.pdf
Stachowiak M, Szydlowski M, Flisikowski K, Flisikowska T, Bartz M, Schnieke A, Switonski M. Polymorphism in 3′ untranslated region of the pig PPARA gene influences its transcript level and is associated with adipose tissue accumulation. J Anim Sci. 2014;92(6):2363-71. http://dx.doi.org/10.2527/jas.2013-7509.
Su Y, Long Y, Liao X, Ai H, Zhang Z, Yang B, Xiao S, Tang J, Xin W, Huang L, Ren J, Ding N. Detection of genomic signatures for pig hairlessness using high-density SNP data. Front Agric Sci Eng. 2014;1(4):307-13. http://dx.doi.org/10.15302/J-FASE-2014039.
Tang F, Yang X, Liu D, Zhang X, Huang X, He X, Shi J, Li Z, Wu Z. Co-expression of fat1 and fat2 in transgenic pigs promotes synthesis of polyunsaturated fatty acids. Transgenic Res. 2019;28(3-4):369-79. http://dx.doi.org/10.1007/s11248- 019-00127-4. PMid:31037571.
Toro MA, Rodrigañez J, Silio L, Rodríguez C. Genealogical analysis of a closed herd of Black Hairless Iberian pigs. Conserv Biol. 2000;14(6):1843-51. http://dx.doi.org/10.1111/j.1523-1739.2000.99322.x. PMid:35701909.
Weir BS, Cockerham CC. Estimating F-statistics for the analysis of population structure. Evolution. 1984;38(6):1358-70. PMid:28563791.
Yang B, Cui L, Perez-Enciso M, Traspov A, Crooijmans R, Zinovieva N, Schook L, 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 MAM, Huang L, Megens H-J. Genome-wide SNP data unveils the globalization of domesticated pigs. Genet Sel Evol. 2017;49(1):71-85. http://dx.doi.org/10.1186/s12711-017-0345-y. PMid:28934946.
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