Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia

Zorc, Minja (author), Škorput, Dubravko (author), Gvozdanović, Kristina (author), Margeta, Polona (author), Karolyi, Danijel (author), Luković, Zoran (author), Salajpal, Krešimir (author), Savić, Radomir (author), Muñoz, Maria (author), Bovo, Samuele (author), Djurkin Kušec, Ivona (author), Radović, Čedomir (author), Kušec, Goran (author), Čandek-Potokar, Marjeta (author), Dovč, Peter (author)

Background: The importance of local breeds as genetic reservoirs of valuable genetic variation is well established. Pig breeding in Central and South-Eastern Europe has a long tradition that led to the formation of several local pig breeds. In the present study, genetic diversity parameters were analysed in six autochthonous pig breeds from Slovenia, Croatia and Serbia (Banija spotted, Black Slavonian, Turopolje pig, Swallow-bellied Mangalitsa, Moravka and Krskopolje pig). Animals from each of these breeds were genotyped using microsatellites and single nucleotide polymorphisms (SNPs). The results obtained with these two marker systems and those based on pedigree data were compared. In addition, we estimated inbreeding levels based on the distribution of runs of homozygosity (ROH) and identifed genomic regions under selection pressure using ROH islands and the integrated haplotype score (iHS). Results: The lowest heterozygosity values calculated from microsatellite and SNP data were observed in the Turopolje pig. The observed heterozygosity was higher than the expected heterozygosity in the Black Slavonian, Moravka and Turopolje pig. Both types of markers allowed us to distinguish clusters of individuals belonging to each breed.The analysis of admixture between breeds revealed potential gene fow between the Mangalitsa and Moravka, and between the Mangalitsa and Black Slavonian, but no introgression events were detected in the Banija spotted and Turopolje pig. The distribution of ROH across the genome was not uniform. Analysis of the ROH islands identifed genomic regions with an extremely high frequency of shared ROH within the Swallow-bellied Mangalitsa, which harboured genes associated with cholesterol biosynthesis, fatty acid metabolism and daily weight gain. The iHS approach to detect signatures of selection revealed candidate regions containing genes with potential roles in reproduction traits and disease resistance. Conclusions: Based on the estimation of population parameters obtained from three data sets, we showed the existence of relationships among the six pig breeds analysed here. Analysis of the distribution of ROH allowed us to estimate the level of inbreeding and the extent of homozygous regions in these breeds. The iHS analysis revealed genomic regions potentially associated with phenotypic traits and allowed the detection of genomic regions under selection pressure.

• Language: English
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: BF - Biotechnical Faculty
• Publication status: Published
• Publication version: Version of Record
• Year: 2022
• Number of pages: 23 str.
• Numbering: Vol. 54, iss. 1, art. 30
• PID: 20.500.12556/RUL-137347
• UDC: 636.4
• ISSN on article: 1297-9686
• DOI: 10.1186/s12711-022-00718-6
• COBISS.SI-ID: 106306307
• Publication date in RUL: 13.06.2022

Record is a part of a journal

• Title: Genetics selection evolution
• Shortened title: Genet. sel. evol.
• Publisher: Springer Nature
• ISSN: 1297-9686
• COBISS.SI-ID: 3183636

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.
• Licensing start date: 28.04.2022

Secondary language

• Language: Slovenian
• Keywords: prašičereja, prašiči, avtohtone pasme, populacije, genetska pestrost, Hrvaška, Srbija, Slovenija