Estimation of population differentiation using pedigree and molecular data in Black Slavonian pig

Kristina Gvozdanović, Dubravko Škorput, Ivona Djurkin Kušec, Krešimir Salajpal, Goran Kušec

Abstract


Submitted 2020-07-17 | Accepted 2020-08-24 | Available 2020-12-01

https://doi.org/10.15414/afz.2020.23.mi-fpap.241-249

The aim of the study was to investigate the genetic differentiation of the Black Slavonian pig population. Two parallel analyses were performed using genealogical records and molecular data. Pedigree information of 6,099 pigs of the Black Slavonian breed was used to evaluate genetic variability and population structure. Additionally, 70 pigs were genotyped using 23 microsatellite markers. Genealogical data showed shrinkage in genetic diversity parameters with effective population size of 23.58 and inbreeding of 3.26%. Expected and observed heterozygosity were 0.685 and 0.625, respectively, and the average number of alleles per locus was 7.826. Bayesian clustering algorithm method and obtained dendrograms based on pedigree information and molecular data revealed the existence of four genetic clusters within the Black Slavonian pig. Wright’s FIS, FST and FIT from pedigree records were 0.017, 0.006, and 0.024, respectively, and did not prove significant population differentiation based on the geographical location of herds, despite the natural mating system. Obtained results indicate that despite the increased number of animals in the population, genetic diversity of Black Slavonian pig is low and conservation programme should focus on strategies aimed at avoiding further loss of genetic variability. Simultaneous use of genealogical and molecular data can be useful in conservation management of Black Slavonian pig breed.

Keywords: autochthonous pig breed, microsatellite, genealogical data, genetic structuring

References

Barros, E. A., Brasil, L. H. de A., Tejero, J. P., Delgado-Bermejo, J. V. & Ribeiro, M. N. (2017). Population structure and genetic variability of the Segureña sheep breed through pedigree analysis and inbreeding effects on growth traits. Small Ruminant Research, 149, 128-133.

Belkhir, K. (2004). GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. http://www. genetix. univ-montp2. fr/genetix/genetix. htm.

Boichard, D., Maignel, L. & Verrier, E. (1997). The value of using probabilities of gene origin to measure genetic variability in a population. Genetics Selection Evolution, 29, 5.

Caballero, A. & Toro, M. A. (2000). Interrelations between effective population size and other pedigree tools for the management of conserved populations. Genetics Research, 75, 331-343.

Casellas, J., Ibanez-escriche, N., Varona, L., Rosas, J. P. & Noguera, J. L. (2019). Inbreeding depression load for litter size in Entrepelado and Retinto Iberian pig varieties. Journal of Animal Science, 97(5), 1979–1986.

Cortés, O., Martinez, A. M., Cañon, J., Sevane, N., Gama, L. T., Ginja, C., Landi, V., Zaragoza, P., Carolino, N., Vicente, A., Sponenberg, P. & Delgado, J. V. for the BioPig Consortium. (2016). Conservation priorities of Iberoamerican pig breeds and their ancestors based on microsatellite information. Heredity, 117(1), 14-24.

Commission on Genetic Resources for Food and Agriculture Food and Agriculture Organization. (2011). Molecular genetic characterization of animal genetic resources. FAO.

Croatian Agency for Agriculture and Food. (2020). Annual Report 2019: Pig breeding, Osijek, Croatia.

Crovetti, A., Sirtori, F., Pugliese, C., Franci, O. & Bozzi, R. (2013). Pedigree analysis of Cinta Senese and Mora Romagnola breeds. Acta Agriculturae Slovenica, Suppl. 4, 41-44.

D’Alessandro, E., Giosa, D., Sapienza, I., Giuffrè, L., Cigliano, R. A., Romeo, O. & Zumbo, A. (2019). Whole genome SNPs discovery in Nero Siciliano pig. Genetics and Molecular Biology, 42(3), 594-602.

Diniz-Filho, J. A. F., Melo, D. B., de Oliveira, G., Collevatti, R. G., Soares, T. N., Nabout, J. C., Lima, J., Dobrovolski, R., Chaves, L. J., Naves, R. V., Loyola, R. D. & Telles M. P. de C. (2012). Planning for optimal conservation of geographical genetic variability within species. Conservation Genetics, 13(4), 1085-1093.

Druml, T., Salajpal, K., Dikic, M., Urosevic, M., Grilz-Seger, G., & Baumung, R. (2012). Genetic diversity, population structure and subdivision of local Balkan pig breeds in Austria, Croatia, Serbia and Bosnia-Herzegovina and its practical value in conservation programs. Genetics Selection Evolution, 44(1), 5.

Earl, D. A. & vonHoldt, B. M. (2012). STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources, 4(2), 359-361.

Evanno, S., Regnaut, S. & Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Molecular Ecology, 14, 2611–2620.

FAO (2000). Secondary guidelines for development of national farm animal genetic resources management plans: Management of small populations at risk. Rome: Food and Agriculture Organization.

Francis, R. M. (2017). Pophelper: an R package and web app to analyse and visualize population structure. Molecular Ecology Resources, 17(1), 27-32.

Goyache, F., Gutiérrez, J. P., Fernández, I., Gomez, E., Alvarez, I., Díez, J. & Royo, L. J. (2003). Using pedigree information to monitor genetic variability of endangered populations: the Xalda sheep breed of Asturias as an example. Journal of Animal Breeding and Genetics, 120, 95-105.

Gutiérrez, J. P. & Goyache, F. (2005). A note on ENDOG: a computer program for analysing pedigree information. Journal of Animal Breeding and Genetics, 122, 172-176.

Gvozdanović, K., Margeta, V., Margeta, P., Djurkin Kušec, I., Galović, D., Dovč, P. & Kušec, G. (2019). Genetic diversity of autochthonous pig breeds analyzed by microsatellite markers and mitochondrial DNA D-loop sequence polymorphism. Animal Biotechnology, 30(3), 242-251.

Gvozdanović, K., Djurkin Kušec, I., Margeta, P., Salajpal, K., Džijan, S., Bošnjak, Z. & Kušec, G. (2020). Multiallelic marker system for traceability of Black Slavonian pig meat. Food Control, 109, 106917.

International Society for Animal Genetics (ISAG)/Food and Agricultural Organization (FAO) (2011). Molecular genetic characterization of animal genetic resources. Rome: FAO Animal Production and Health Guidelines.

Jombart, T. (2008). adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics, 24, 1403–1405.

Jombart, T., Devillard, S. & Balloux, F. (2010). Discriminant analysis of principal components: A new method for the analysis of genetically structured populations. BMC Genetics, 11(1), 94.

Kramarenko, S. S., Lugovoy, S. I., Kharzinova, V. R., Lykhach, V. Y., Kramarenko, A. S. & Lykhach, A. V. (2018). Genetic diversity of Ukrainian local pig breeds based on microsatellite markers. Regulatory Mechanisms in Biosystems, 9(2), 177-182.

Lacy, R. C. (1987). Loss of genetic diversity from managed populations: interacting effects of drift, mutation, immigration, selection, and population subdivision. Conservation Biology, 1, 143-158.

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.

Lukić, B., Smetko, A., Mahnet, Ž., Klišanić, V., Špehar, M., Raguž, N. & Kušec, G. (2015). Population genetic structure of autochthonous Black Slavonian Pig. Poljoprivreda, 21(1), 28-32.

Ma, L., Ya-Jie J. & Zhang, D. X. (2015). Statistical measures of genetic differentiation of populations: Rationales, history and current states. Current Zoology, 61(5): 886–897.

Margeta, P., Margeta, V. & Budimir, K. (2013). How black is really Black Slavonian pig? Acta Agriculturae Slovenica, Suppl. 4, 25-28.

Margeta, P., Margeta, V., Gvozdanović, K., Galović, D., Djurkin Kušec, I. & Kušec, G. (2016). Microsatellite multiplex method for potential use in Black Slavonian pig breeding. Acta Agriculturae Slovenica, 5, 66-70.

Margeta, P., Gvozdanovic, K., Djurkin Kušec, I., Radišić, Ž., Kusec, G. & Margeta, V. (2018). Genetic analysis of Croatian autochthonous pig breeds based on microsatellite markers. Archivos de Zootecnia, 1, 13-16.

Mariani, E., Summer, A., Ablondi, M. & Sabbioni, A. (2020). Genetic variability and management in Nero di Parma swine breed to preserve local diversity. Animals, 10(3), 538.

Meuwissen, T. H. E. & Luo, Z. (1992). Computing inbreeding coefficients in large populations. Genetics Selection Evolution, 24, 305.

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, J., 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.

Nei, M. (1973). Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences, 70(12), 3321-3323.

Nei, M., Tajima, F. & Tateno, Y. (1983). Accuracy of estimated phylogenetic trees from molecular data. Journal of Molecular Evolution, 19(2), 153-170.

Nei, M., (1987). Molecular Evolutionary Genetics. Columbia University Press, New York, 512 pp.

Pritchard, J. K., Stephens, M. & Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155, 945–959.

Posta, J., Szabó, P. & Komlósi, I. (2016). Pedigree analysis of Mangalica pig breeds. Annals of Animal Science, 16(3), 701-709.

R Development Core Team. (2018). A language and environment for statistical computing. R Foundation for Statistical Computing. Retrieved May 5, 2020 from http://www.R-project.org/.

Sargolzaei, M., Iwaisaki, H. & Colleau, J. J. (2006). CFC: a tool for monitoring genetic diversity. Proc. 8th World Congr. Genet. Appl. Livest. Prod., CD-ROM Communication, (27-28), 13-18.

Scali, M., Vignani, R., Bigliazzi, J., Paolucci, E., Bernini, A., Spiga, O., Niccolai, N. & Cresti, M. (2012). Genetic differentiation between Cinta

Senese and commercial pig breeds using microsatellite. Electronic Journal of Biotechnology, 15(2), 1-11.

Silió, L., Barragán, C., Fernández, A.I., García‐Casco, J. & Rodríguez, M. C. (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. Animal Breeding and Genetics, 133(2),145-154.

Toomey, A. H., Knight, A. T. & Barlow, J. (2017). Navigating the space between research and implementation in conservation. Conservation Letters, 10(5), 619-625.

Wang, J. (2014). Marker-based estimates of relatedness and inbreeding coefficients: an assessment of current methods. Journal of Evolutionary Biology, 27, 518–530.

Wright, S. (1931). Evolution in mendelian populations. Genetics, 16, 97-159.

Wright, S. (1978). Evolution and the genetics of populations: Vol. 4. Variability within and among natural populations. University of Chicago Press: Chicago. USA.

Yang, B., Cui, L., Perez-Enciso, M., Traspov, A., Crooijmans, R. P. M. A., Zinovieva, N., Schook, L. B., 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, M. A. M., Huang, L. & Megens, H.-J. (2017). Genome-wide SNP data unveils the globalization of domesticated pigs. Genetics Selection Evolution, 49(1), 71.

Zhang, J., Jiao, T. & Zhao, S. (2016). Genetic diversity in the mitochondrial DNA D-loop region of global swine (Sus scrofa) populations. Biochemical and Biophysical Research Communications, 473(4), 814-820.

 


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