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

Abstract

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 identified 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 flow 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 identified 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.

Turopolje Pig: Between Conservation and Sustainability

“…Low genetic diversity of the Turopolje pig was also found in the study by Schiavo et al [26]. Zorc et al [2] used genomic data in the most recent study and showed that the genetic diversity of the Turopolje pig breed was very low compared to five other local breeds: the Black Slavonian pig, the Banija spotted pig, the Krškopolje pig, the Moravka pig, and the Serbian swallow-bellied Mangalitza population. Numerous studies have confirmed that low genetic diversity resulting from a high increase in inbreeding in the population can have harmful effects on reproductive traits.…”

“…The production performance of the Turopolje pigs is also low, with low fertility and modest fattening performances, but with excellent meat quality traits [1]. Due to its long genesis, isolated breeding area, and specific low-input rearing technique, the Turopolje pig has preserved its genetic uniqueness, as confirmed by Zorc et al [2]. Moreover, the Turopolje pig in Croatia is differentiated from other pig breeds from the broader geographical area.…”

Genome-Wide Detection for Runs of Homozygosity in Baoshan Pigs Using Whole Genome Resequencing

“…Although F PED was lower than F ROH , it was not as accurate as F ROH because of the incomplete genealogy and the default inbreeding coefficient of 0 for the starting generation, which underestimated the true inbreeding level [42]. The F ROH of the six native pig breeds from Croatia, Serbia, and Slovenia were closer to the true level of inbreeding than the F PED , with the highest inbreeding coefficients among the six breeds for the Turopolje pig, with F ROH and F PED values of 0.508 and 0.038, respectively [43]. In fact, the absence of genealogical records resulted in inbreeding phenomena that originally occurred in distant generations not being considered, and the originally longer chain of genealogical pathways was artificially shortened; thus, the accuracy of inbreeding coefficient estimates was not as accurate as inbreeding coefficients calculated based on the ROH of genes [44].…”

Runs of Homozygosity Detection and Selection Signature Analysis for Local Goat Breeds in Yunnan, China

“…ROH islands, first identified by Nothnagel et al [ 17 ], provide insights into exploring genomic regions with significant inbreeding in populations [ 18 ]. The ROH islands were observed in various livestock species, including cattle [ 19 ], pigs [ 20 ], horses [ 21 ], sheep [ 22 ], and goats [ 23 ]. However, there has been limited research on the identification of ROH in local goat breeds from Yunnan province, China.…”