A further look of the genetic origin and singularity of the Torbiscal Iberian pig line

  • Carmen Rodríguez-Valdovinos INIA, Dpto. Mejora Genética Animal, Ctra. de la Coruña km 7, 28040 Madrid
  • Juan García-Casco INIA, Dpto. Mejora Genética Animal, Ctra. de la Coruña km 7, 28040 Madrid
  • Fabián García-Ruiz INIA, Dpto. Mejora Genética Animal, Ctra. de la Coruña km 7, 28040 Madrid
  • Yolanda Núñez-Moreno INIA, Dpto. Mejora Genética Animal, Ctra. de la Coruña km 7, 28040 Madrid
  • Luis Silió-López INIA, Dpto. Mejora Genética Animal, Ctra. de la Coruña km 7, 28040 Madrid
Keywords: pedigree analysis, piglet weight, diallel-cross, Fst index, genetic diversity, genetic differentiation

Abstract

Although the Torbiscal line of Iberian pigs has been largely studied, some aspects of its history are not well known. In this paper, we used pedigree-based methods on a complete genealogy of 4,077 entries in order to get a comprehensive analysis of its four founder strains and to evaluate the expected genetic contribution of each ancestral strain to the successive generations of the composite Torbiscal line. Between-strain differences and specific heterotic effects on piglet weight at 50 days of age were estimated from records of 9,052 piglets born in 1,571 litters of a complete diallel cross among the four strains. Moreover, we assessed the genetic singularity of the current Torbiscal pigs by other three studies, based on whole genome SNP genotypes, focused on the measure of its genetic diversity and differentiation with respect to other domestic and wild pig populations. The STRUCTURE algorithm detected two uppermost levels of the whole population structure, corresponding to European and Asian ancestries. These results confirmed the exclusive European origin of the Torbiscal and other Iberian pigs and the admixed origin of the Duroc breed. Finally, the comparison of Torbiscal with a representative pool of Iberian pigs showed a maximum genetic differentiation in regions of chromosomes three and seven, including some genes related to the regulation of muscle development.

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Author Biography

Juan García-Casco, INIA, Dpto. Mejora Genética Animal, Ctra. de la Coruña km 7, 28040 Madrid

Centro de I+D en Cerdo Ibérico - Zafra

Investigador OPIs

References

Akey JM, Ruhe AI, Akey DT, Wong AK, Connelly CF, Madeoy J, Nicholas TJ, Neff MW, 2010. Tracking footprints of artificial selection in the dog genome. Proc Natl Acad Sci USA 107: 1160-1165. https://doi.org/10.1073/pnas.0909918107

Alves E, Óvilo C, Rodríguez MC, Silió L, 2003. Mitochondrial DNA sequence variation and phylogenetic relationships among Iberian pigs and other domestic and pig populations. Anim Genet 34: 319-324. https://doi.org/10.1046/j.1365-2052.2003.01010.x

Alves E, Fernández AI, Barragán C, Óvilo C, Rodríguez C, Silió L, 2006. Inference of hidden population substructure of the Iberian pig breed using multilocus microsatellite data. Span J Agric Res 4: 37-46. https://doi.org/10.5424/sjar/2006041-176

Alves E, Fernández AI, Fernández-Rodríguez A, Pérez D, Benítez R, Óvilo C, Rodríguez MC, Silió L, 2009. Identification of mitochondrial markers for genetic traceability of European wild boar and Iberian and Duroc pigs. Animal 3: 1216-1223. https://doi.org/10.1017/S1751731109004819

Ayuso M, Óvilo C, Rodríguez-Bertos A, Rey AI, Daza A, Fenández A, González-Bulnes A, López-Bote CJ, Isabel B, 2015. Dietary vitamin A restriction affects adipocyte differentiation and fatty acid composition of intramuscular fat in Iberian pigs, Meat Sci 108: 9-16. https://doi.org/10.1016/j.meatsci.2015.04.017

Béjar F, Rodríguez MC, Toro MA, 1993.Estimation of genetic trends for weaning weight and teat number in Iberian pigs using mixed model methodology. Livest Prod Sci 33: 239-251. https://doi.org/10.1016/0301-6226(93)90005-3

Benítez R, Núñez Y, Fernández A, Isabel B, Fernández AI, Rodríguez C, Barragán C, Martín- Palomino P, López-Bote C, Silió L, Óvilo C, 2015. Effects of dietary fat saturation on fatty acid saturation and gene transcription in different tissues of Iberian pigs. Meat Sci 102: 59-68. https://doi.org/10.1016/j.meatsci.2014.12.005

Benítez R, Fernández A, Isabel B, Núñez Y, De Mercado E, Gómez-Izquierdo E, García-Casco J, López-Bote C, Óvilo C, 2018. Modulatory effects of breed, feeding status, and diet on adipogenic, lipogenic, and lipolytic gene expression in growing Iberian and Duroc pigs. Inter J Molec Sci 19: 22. https://doi.org/10.3390/ijms19010022

Benito J, Vázquez C, Menaya C, Ferrera JL, García-Casco JM, Silio L, Rodrigañez J, Rodríguez MC, 2000. Evaluation of the productive parameters in different strains of iberian pigs. Opt Mediterr 41: 113-121.

Boichard D Maignel L, Verrier E, 1997. The value of using probabilities of gene origin to measure genetic variability in a population. Genet Sel Evol 29: 5-23. https://doi.org/10.1186/1297-9686-29-1-5

Burgos-Paz W, Souza CA, Megens HJ, Ramayo-Caldas Y, Melo M, Lemús-Flores C, Caal E, Soto HW, Martínez R, Álvarez LA et al., 2013. Porcine colonization of the Americas: a 60k SNP story. Heredity 110: 321-330. https://doi.org/10.1038/hdy.2012.109

Caballero A, 1995. On the effective size of populations with separate sexes with particular reference to sex-linked genes. Genetics 139: 1007-1011.

Caballero A, Toro M, 2000. Interrelations between effective population size and other pedigree tools for the management of conserved populations. Genet Res 75: 331–343. https://doi.org/10.1017/S0016672399004449

Caballero A, Toro M, 2002. Analysis of genetic diversity for the management of conserved subdivided populations. Conserv Genet 3: 289-299. https://doi.org/10.1023/A:1019956205473

Carrapiso AI, García C, 2008. Effect of the Iberian pig line on dry-cured ham characteristics. Meat Sci 80: 529-534. https://doi.org/10.1016/j.meatsci.2008.02.004

Cervantes I, Pastor JM, Gutiérrez JP, Goyache F, Molina A, 2011. Computing effective population size from molecular data: The case of three rare Spanish ruminant populations. Livest Sci 138: 202-206. https://doi.org/10.1016/j.livsci.2010.12.027

Daza A, Menoyo D, Olivares A, Cordero G, López-Bote CJ, 2007 Effect of Iberian pig feeding system on tissue fatty-acid composition and backfat rheological properties. J Anim Feed Sci 16: 408-419. https://doi.org/10.22358/jafs/66797/2007

Dickerson GE, 1969. Experimental approaches in utilizing breed resources. Anim Breed Abstr 37: 191-202.

Dobao MT, Rodrigañez J, Silió L, 1983. Seasonal influence on fecundity and litter performance characteristics in Iberian pigs. Livest Prod Sci 10: 601-610. https://doi.org/10.1016/0301-6226(83)90052-0

Dobao MT, Rodrigañez J, Silió L, 1984. Choice of companions in social play in piglets. App Anim Behav Aci 13: 359-366.

Esteve-Codina A, Paudel Y, Ferretti L, Raineri E, Jan Megens H, Silió L, Rodríguez MC, Groenen M, Ramos-Onsins S, Pérez-Enciso M, 2013. Dissecting structural and nucleotide genomewide variation in inbred Iberian pigs. BMC Genomics 14: 148. https://doi.org/10.1186/1471-2164-14-148

Evanno S, Regnaut S, Goudet J, 2005. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Mol Ecol 14: 2611-2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x

Fabuel E, Barragán C, Silió L, Rodríguez MC, Toro MA, 2004. Analysis of genetic diversity and conservation priorities in Iberian pigs based on microsatellite markers. Heredity 93: 104-113. https://doi.org/10.1038/sj.hdy.6800488

Fernández A, Rodríguez MC, Rodrigáñez J, Silió L, Toro MA, 2002a. Use of Bayesian analysis of growth functions to estimate crossbreeding parameters in Iberian pigs. Livest Prod Sci 73: 213-223. https://doi.org/10.1016/S0301-6226(01)00249-4

Fernández A, Rodrigáñez J, Toro MA, Rodríguez C, Silió L, 2002b. Inbreeding effects on the parameters of the growth function in three strains of Iberian pigs. J Anim Sci 80: 2267-2275. https://doi.org/10.2527/2002.8092267x

Fernández A, Rodrigáñez J, Zuzuárregui J, Rodríguez MC, Silió L, 2008a. Genetic parameters for litter size and weight at different parities in Iberian pigs. Span J Agric Res 6 (Special issue): 98-106. https://doi.org/10.5424/sjar/200806S1-378

Fernández A, Alves E, Fernández A, De Pedro E, López-García MA, Óvilo C, Rodríguez MC, Silió L, 2008b. Mitochondrial genome polymorphisms associated with longissimus muscle composition in Iberian pigs. J Anim Sci 86: 1283-1290. https://doi.org/10.2527/jas.2007-0568

Forero, 1999. Estudio comparativo de cinco estirpes de cerdo ibérico. Diputación Provincial de Huelva, Spain. Servicio de Publicaciones, 254 pp.

García Casco JM, 1993. Aspectos genéticos de la mejora de caracteres de crecimiento en cerdos ibéricos. Doctoral thesis, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid.

García-Casco J, Fernandez A, Rodriguez MC, Silió L, 2012. Heterosis for litter size and growth in crosses of four strains of Iberian pig. Livest Sci 147:1-8. https://doi.org/10.1016/j.livsci.2012.03.005

Gómez-Raya L, Rodríguez MC, Barragán C, Silió L, 2015. Genomic inbreeding coefficients based on the distribution of the length of runs of homozygosity in a closed line of Iberian pigs. Genet Sel Evol 47: 81. https://doi.org/10.1186/s12711-015-0153-1

Hedrick PW, 2005. A standardized genetic differentiation measure. Evolution 59: 1633-1638. https://doi.org/10.1111/j.0014-3820.2005.tb01814.x

Hernández P, Zomeño L, Ariño B, Blasco A, 2004. Antioxidant, lipolytic and proteolytic enzyme activities in pork meat from different genotypes. Meat Sci 66: 525-529. https://doi.org/10.1016/S0309-1740(03)00155-4

Ibáñez-Escriche N, Varona L, Magallón E, Noguera J, 2014. Crossbreeding effects on pig growth and carcass traits from two Iberian strains. Animal 8: 1569-1576. https://doi.org/10.1017/S1751731114001712

Ibáñez-Escriche N, Magallón E, González E, Tejeda JF, Noguera J, 2016. Genetic parameter and crossbreeding effects of fat deposition and fatty acid profiles in Iberian pig lines. J Anim Sci 94: 28-37. https://doi.org/10.2527/jas.2015-9433

James JW, 1972. Computation of genetic contributions from pedigrees. Theor Appl Genet 42: 272-273. https://doi.org/10.1007/BF00277555

James JW, McBride G, 1958. The spread of genes by natural and artificial selection in a closed poultry flock. J Genet 56: 55-62. https://doi.org/10.1007/BF02984720

Lacy RC, Alaks G, Walsh A, 1996. Hierarchical analysis of inbreeding depression in Peromyscus polionotus. Evolution 50: 2187-2200. https://doi.org/10.1111/j.1558-5646.1996.tb03609.x

Larson G, Albarella U, Dobney K, Rowley-Conwy P, Schibler J, Tresset A, Vigné JD, Edwards CJ, Schlumbaum A, Dinu A et al., 2007. Proc Nat Acad Sci 104: 15276-15281. https://doi.org/10.1073/pnas.0703411104

Legarra A, Varona L, López de Maturana E, 2011. TM Threshold Model. http://snp.toulouse.inra. fr/~alegarra/manualtm.pdf; [last accessed March 2013].

López-Bote CJ, Toldrá F, Daza A, Ferrer JM, Menoyo D, Silió L, Rodríguez MC, 2008. Effect of exercise on skeletal muscle proteolytic enzyme activity and meat quality characteristics in Iberian pigs. Meat Sci 79: 71-76. https://doi.org/10.1016/j.meatsci.2007.08.002

Muñoz G, Óvilo C, Sánchez A, Rodríguez MC, 2004. Mapping of the porcine estrogen receptor β gene (ESR- β) and association study with litter size in Iberian pigs. Anim Genet 35: 242-244. https://doi.org/10.1111/j.1365-2052.2004.01141.x

Muñoz M, Rodríguez MC, García-Cortés LA, Gonzalez A, García-Casco JM, Silió L, 2017. Direct and maternal additive effects are not the main determinants of Iberian piglet perinatal mortality. J Anim Breed Genet 134: 512-519. https://doi.org/10.1111/jbg.12298

Muriel E, Ruíz J, Ventanas J, Petrón MJ, Antequera T, 2004. Meat quality characteristics in different lines of Iberian pigs. Meat Sci 67: 299-307. https://doi.org/10.1016/j.meatsci.2003.11.002

Nei M, 1973. Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci 70 (12): 3321-3323. https://doi.org/10.1073/pnas.70.12.3321

Odriozola M, 1976. Investigación sobre los datos acumulados en dos piaras experimentales. IRYDA, Madrid.

Óvilo C, Benítez R, Fernández A, Núñez Y, Ayuso M, Fernández AI, Rodríguez C, Isabel B, Rey AI, López-Bote C, Silió L, 2014a. Longissimus dorsi transcriptome analysis of purebred and crossbred Iberian pigs differing in muscle characteristics. BMC Genomics 15: 413. https://doi.org/10.1186/1471-2164-15-413

Óvilo C, Benítez R, Fernández A, Isabel B, Núñez Y, Fernández AI, Rodríguez C, Daza A, Silió L, López-Bote C, 2014b. Dietary energy source largely affects tissue fatty acid composition but has minor influence on gene transcription in Iberian pigs. J Anim Sci 92: 939-954. https://doi.org/10.2527/jas.2013-6988

Pérez-Enciso M, Gianola D, 1992. Estimates of genetic parameters for litter size in six strains of Iberian pigs. Livest Prod Sci 32: 283-293. https://doi.org/10.1016/S0301-6226(12)80007-8

Piórkowska K, Żukowski K, Ropka-Molik K, Tyra M., 2018. Detection of genetic variants between different Polish Landrace and Puławska pigs by means of RNA-seq analysis. Anim Genet 49 (3): 215-225. https://doi.org/10.1111/age.12654

Pritchard JK, Stephens M, Donnelly T, 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945-959.

Rey A, Daza A, López-Carrasco, López-Bote C, 2006. Feeding Iberian pigs with acorns and grass in either free-range or confinement affects the carcass characteristics and fatty acids and tocopherols accumulation in Longissimus dorsi muscle and backfat. Meat Sci 73: 66-74. https://doi.org/10.1016/j.meatsci.2005.10.018

Rodríguez MC, Rodrigáñez J, Silió L, 1994. Genetic analysis of maternal ability in Iberian pigs. J Anim Breed Genet 111: 220-227. https://doi.org/10.1111/j.1439-0388.1994.tb00461.x

Rodrigáñez J, Toro MA, Rodríguez MC, Silió L, 1998. Effect of founder allele survival and inbreeding depression on litter size in a closed line of Large White pigs. Anim Sci 67: 573-582. https://doi.org/10.1017/S1357729800033014

Rodrigáñez J, Barragán C, Alves E, Gortázar C, Toro MA, Silió L, 2008. Genetic diversity and allelic richness in Spanish wild and domestic pig populations estimated from microsatellite markers. Span J Agric Res 6 (Special issue): 107-115. https://doi.org/10.5424/sjar/200806S1-379

Silió L, Rodríguez MC, Toro MA, Rodrigáñez J, 1994. Maternal and individual genetic effects on piglet weight. Proc 5th World Congress Genetics Applied Livestock Production, Guelph, Ontario, (Canada), August 7-12.

Silió L, Rodríguez MC, Fernández A, Barragán C, Benítez R, Óvilo C, Fernández AI, 2013. Measuring inbreeding and inbreeding depression on pig growth from pedigree and SNP-derived metrics. J Anim Breed Genet 130: 349-360. https://doi.org/10.1111/jbg.12031

Silió L, Barragán C, Fernández AI, García-Casco J, Rodríguez MC, 2016. Assessing effective population size, coancestry and inbreeding effects on litter size using the pedigree and SNP data in closed lines of the Iberian pig breed. J Anim Breed Genet 133: 145-154. https://doi.org/10.1111/jbg.12168

Toro MA, Silió L, Rodrigáñez J, Dobao MT, 1988. Inbreeding and family index selection for prolificacy in pigs. Anim Prod 46: 79-85. https://doi.org/10.1017/S0003356100003135

Toro MA, Rodrigáñez J, Silió L, Rodríguez MC, 2000. Genealogical analysis of a closed herd of black hairless Iberian pigs. Conserv Biol 14: 1843-1851. https://doi.org/10.1046/j.1523-1739.2000.99322.x

Toro MA, Barragán C, Rodrigáñez J, Rodríguez MC, Silió L, 2002. Estimation of coancestry in Iberian pigs using molecular markers. Conserv Genet 3: 309-320. https://doi.org/10.1023/A:1019921131171

Toro MA, Fernández A, García-Cortés LA, Rodrigáñez J, Silió L, 2006. Sex ratio variation in Iberian pigs. Genetics 173: 911-917. https://doi.org/10.1534/genetics.106.055939

Vaughan HW, 1950. Breeds of live stock in America. Long's College Book Co., Columbus, OH, USA.

Woolliams JA, Mäntysaari EA, 1995. Genetic contributions of Finnish Ayrshire bulls over four generations. Anim Sci 61: 177-187. https://doi.org/10.1017/S1357729800013709

Yang B, Cui L, Pérez-Enciso M, Traspov A, Crooijmans RPMA, Zinovieva N, Schook L, Archibald A, Gatphayak K, Knorr C et al., 2017. Genome-wide SNP data unveils the globalization of domesticated pigs. Genet Sel Evol 49: 71. https://doi.org/10.1186/s12711-017-0345-y

Published
2019-04-15
How to Cite
Rodríguez-Valdovinos, C., García-Casco, J., García-Ruiz, F., Núñez-Moreno, Y., & Silió-López, L. (2019). A further look of the genetic origin and singularity of the Torbiscal Iberian pig line. Spanish Journal of Agricultural Research, 17(1), e0402. https://doi.org/10.5424/sjar/2019171-13618
Section
Animal breeding, genetics and reproduction