Hostname: page-component-586b7cd67f-t8hqh Total loading time: 0 Render date: 2024-11-28T00:54:38.601Z Has data issue: false hasContentIssue false
  • English
  • Français

The footprint of recent and strong demographic decline in the genomes of Mangalitza pigs

Published online by Cambridge University Press:  04 April 2019

V. A. Bâlteanu ,
T. F. Cardoso ,
M. Amills Open the ORCID record for M. Amills [Opens in a new window] ,
I. Egerszegi Open the ORCID record for I. Egerszegi [Opens in a new window] ,
I. Anton ,
A. Beja-Pereira  and
A. Zsolnai Open the ORCID record for A. Zsolnai [Opens in a new window]
V. A. Bâlteanu
Affiliation:
Institute of Life Sciences, University of Agricultural Sciences and Veterinary Medicine, Calea Mănăştur 3-5, 400372 Cluj-Napoca, Romania
T. F. Cardoso
Affiliation:
Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain CAPES Foundation, Ministry of Education of Brazil, 7004020 Brasilia D. F., Brazil
M. Amills
Affiliation:
Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
I. Egerszegi
Affiliation:
Szent István University, Páter Károly u. 1., 2100 Gödöllő, Hungary
I. Anton
Affiliation:
NAIK-Research Institute for Animal Breeding, Nutrition and Food Science, Gesztenyes u. 1., 2053 Herceghalom, Hungary
A. Beja-Pereira
Affiliation:
Centro de Investigacao em Biodiversidade e Recursos Geneticos, Universidade do Porto (CIBIO-UP), Rua Padre Armando Quintas 7, 4485-661 Vairao, Portugal
A. Zsolnai*
Affiliation:
NAIK-Research Institute for Animal Breeding, Nutrition and Food Science, Gesztenyes u. 1., 2053 Herceghalom, Hungary
*
†E-mail: [email protected]
Get access

Abstract

The Mangalitza pig breed has suffered strong population reductions due to competition with more productive cosmopolitan breeds. In the current work, we aimed to investigate the effects of this sustained demographic recession on the genomic diversity of Mangalitza pigs. By using the Porcine Single Nucleotid Polymorphism BeadChip, we have characterized the genome-wide diversity of 350 individuals including 45 Red Mangalitza (number of samples; n=20 from Hungary and n=25 from Romania), 37 Blond Mangalitza, 26 Swallow-belly Mangalitza, 48 Blond Mangalitza × Duroc crossbreds, 5 Bazna swine, 143 pigs from the Hampshire, Duroc, Landrace, Large White and Pietrain breeds and 46 wild boars from Romania (n=18) and Hungary (n=28). Performance of a multidimensional scaling plot showed that Landrace, Large White and Pietrain pigs clustered independently from Mangalitza pigs and Romanian and Hungarian wild boars. The number and total length of ROH (runs of homozygosity), as well as FROH coefficients (proportion of the autosomal genome covered ROH) did not show major differences between Mangalitza pigs and other wild and domestic pig populations. However, Romanian and Hungarian Red Mangalitza pigs displayed an increased frequency of very long ROH (>30 Mb) when compared with other porcine breeds. These results indicate that Red Mangalitza pigs underwent recent and strong inbreeding probably as a consequence of severe reductions in census size.

Keywords

polymorphismspopulationstructureadmixturehomozygosity
Type
Research Article
Information
animal , Volume 13 , Issue 11 , November 2019 , pp. 2440 - 2446
Copyright
© The Animal Consortium 2019 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Footnotes

a

V. A. Bâlteanu and T. F. Cardoso share the first authorship.

References

Alexander, DH and Lange, K 2011. Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinformatics 12, 246.CrossRefGoogle ScholarPubMed
Alexander, DH, Novembre, J and Lange, K 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Research 19, 1655–1664.CrossRefGoogle ScholarPubMed
Barbato, M, Orozco-terWengel, P, Tapio, M and Bruford, MW 2015. SNeP: a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data. Frontiers in Genetics 6, 109.CrossRefGoogle ScholarPubMed
Botstein, D, White, RL, Skolnick, M and Davis, RW 1980. Construction of genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics 32, 314–331.Google ScholarPubMed
Charlesworth, D and Willis, JH 2009. The genetics of inbreeding depression. Nature Reviews Genetics 10, 783–796.CrossRefGoogle ScholarPubMed
Chen, S, Gomes, R, Costa, V, Santos, P, Charneca, R, Zhang, Y, Liu, X, Wang, S, Bento, P, Nunes, J-L, Buzgó, J, Varga, G, Anton, I, Zsolnai, A and Beja-Pereira, A 2013. How immunogenetically different are domestic pigs from wild boars: a perspective from single-nucleotide polymorphisms of 19 immunity-related candidate genes. Immunogenetics 65, 737–748.CrossRefGoogle Scholar
Ciobanu, DC, Day, AE, Nagy, A, Wales, R, Rothschild, MF and Plastow, GS 2001. Genetic variation in two conserved local Romanian pig breeds using type 1 DNA markers. Genetics Selection Evolution 33, 417–432.CrossRefGoogle ScholarPubMed
Dent, EA and VonHoldt, BM 2011. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4, 359–361.Google Scholar
Draganescu, C, Ghita, E and Nagi, AI 2008. Note on the genetic history of the Romanian Saddleback (Bazna) pig breed conservation nucleus 1. Archiva Zootechnica 11, 65–69.Google Scholar
Egerszegi, I, Rátky, J, Solti, L and Brüssow, K-P 2003. Mangalica – an indigenous swine breed from Hungary (Review). Archives Animal Breeding 46, 245–256.CrossRefGoogle Scholar
Evanno, G, Regnaut, S and Goudet, J 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14, 2611–2620.CrossRefGoogle ScholarPubMed
Food and Agriculture Organization of the United Nations 2015. The second report on the state of the world’s animal genetic resources for food and agriculture. In FAO Commission on genetic resources for food and agriculture assessments (ed. Scherf BD and Pilling D). pp. 40–125. Food and Agriculture Organization of the United Nations, Rome. Retrieved on 15 February 2019 from http://www.fao.org/3/a-i4787e.pdf.Google Scholar
Giuffra, E, Kijas, JM, Amarger, V, Carlborg, O, Jeon, JT and Andersson, L 2000. The origin of the domestic pig: independent domestication and subsequent introgression. Genetics 154, 1785–1791.Google ScholarPubMed
Goedbloed, DJ, Megens, HJ, Van Hooft, P, Herrero-Medrano, JM, Lutz, W, Alexandri, P, Crooijmans, RPMA, Groenen, M, Van Wieren, SE, Ydenberg, RC and Prins, HHT 2013. Genome-wide single nucleotide polymorphism analysis reveals recent genetic introgression from domestic pigs into Northwest European wild boar populations. Molecular Ecology 22, 856–866.CrossRefGoogle ScholarPubMed
Hankó, B 1940. Ancient domestic animals of Hungary (Ősi magyar háziállataink). Tiszántúli Mg-i Kamara, Debrecen, Hungary.Google Scholar
Iacolina, L, Pertoldi, C, Amills, M, Kusza, S, Megens, HJ, Bâlteanu, VA, Bakan, J, Cubric-Curic, V, Oja, R, Saarma, U, Scandura, M, Šprem, N and Stronen, AV 2018. Hotspots of recent hybridization between pigs and wild boars in Europe. Scientific Reports 8, 17372.CrossRefGoogle Scholar
Kumar, S, Stecher, G and Tamura, K 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33, 1870–1874.CrossRefGoogle ScholarPubMed
Lencz, T, Lambert, C, DeRosse, P, Burdick, KE, Morgan, TV, Kane, JM, Kucherlapati, R, Malhotra, AK 2007. Runs of homozygosity reveal highly penetrant recessive loci in schizophrenia. Proceedings of the National Academy of Sciences of the United States of America 104, 19942–19947.CrossRefGoogle Scholar
Manunza, A, Amills, M, Noce, A, Cabrera, B, Zidi, A, Eghbalsaied, S, de Albornoz, EC, Portell, M, Mercadé, A, Sànchez, A and Balteanu, V 2016. Romanian wild boars and Mangalitza pigs have a European ancestry and harbour genetic signatures compatible with past population bottlenecks. Scientific Reports 6, 29913.CrossRefGoogle ScholarPubMed
Matiuti, M, Bogdan, AT, Crainiceanu, E and Matiuti, C 2010. Research regarding the hybrids resulted from the domestic pig and the wild boar. Scientific Papers: Animal Science and Biotechnologies 43, 188–191.Google Scholar
Pickrell, JK and Pritchard, JK 2012. Inference of population splits and mixtures from genome-wide allele frequency data. PLOS Genetics 8, e1002967.CrossRefGoogle ScholarPubMed
Purcell, S, Neale, B, Todd-Brown, K, Thomas, L, Ferreira, MAR, Bender, D, Maller, J, Sklar, P, de Bakker, PIW, Daly, MJ and Sham, PC 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics 81, 559–575.CrossRefGoogle ScholarPubMed
Raj, A, Stephens, M and Pritchard, JK 2014. fastSTRUCTURE: variational inference of population structure in large SNP data sets. Genetics 197, 573–589.CrossRefGoogle ScholarPubMed
Saura, M, Fernández, A, Varona, L, Fernández, AI, de Cara, M, Barragán, C and Villanueva, B 2015. Detecting inbreeding depression for reproductive traits in Iberian pigs using genome-wide data. Genetics Selection Evolution 47, 1.CrossRefGoogle ScholarPubMed
Silió, L, Rodríguez, MC, Fernández, A, Barragán, C, Benítez, R, Óvilo, C and Fernández, AI 2013. Measuring inbreeding and inbreeding depression on pig growth from pedigree or SNP-derived metrics. Journal of Animal Breeding and Genetics 130, 349–360.Google ScholarPubMed
Yang, B, Cui, L, Perez-Enciso, M, Traspov, A, Crooijmans, RPMA, Zinovieva, N, Schook, LB, 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 and Megens, H-J 2017. Genome-wide SNP data unveils the globalization of domesticated pigs. Genetics Selection Evolution 49, 71.CrossRefGoogle ScholarPubMed
Zsolnai, A, Szántó-Egész, R, Anton, I, Tóth, P, Micsinai, A and Rátky, J 2013. Mangalica fajták genetikai távolsága, elkülönítésük nukleotid polimorfizmust mutató DNS markerekkel [Genetic distance of Mangalica breeds, distinction by DNA markers showing nucleotide polymorphism]. Hungarian Veterinary Journal 135, 303–307.Google Scholar
Supplementary material: Image

Bâlteanu et al. supplementary material

Bâlteanu et al. supplementary material 1

Download Bâlteanu et al. supplementary material(Image)
Image 34.9 MB
Supplementary material: PDF

Bâlteanu et al. supplementary material

Bâlteanu et al. supplementary material 2

Download Bâlteanu et al. supplementary material(PDF)
PDF 675.9 KB