Genomic inbreeding in European autochthonous pig breeds: analysis of runs of homozygosity

Conservation and management of autochthonous pig genetic resources are designed considering inbreeding. Inbreeding is traditionally calculated using pedigree information which is summarized in an inbreeding coefficient (FPED). However, FPED has several limits, some of them, are more important in local breeds in which many animals could have incomplete pedigree information, as mating events cannot be correctly registered in extensive production systems. The availability of commercial single nucleotide polymorphism (SNP) arrays in all main livestock species, including the pig, has opened new opportunities to estimate the inbreeding level directly using whole genome information. Runs of homozygosity (ROH) are chromosome regions that are homozygous at each polymorphic position. The ROH length and the genome proportion covered by ROH are good indicators of the age, origin and level of autozygosity and thus inbreeding. In this study we analysed ROH in a total of 1129 pigs from 20 European autochthonous pig breeds (Alentejana, Apulo-Calabrese, Basque, Bísara, Majorcan Black, Black Slavonian, Casertana, Cinta Senese, Gascon, Iberian, Krskopolje, Lithuanian indigenous wattle, Lithuanian White Old Type, Mora Romagnola, Moravka, Nero Siciliano, Sarda, Schwäbisch-Hällisches Schwein, Swallow-Bellied Mangalitsa and Turopolje; from nine different countries: Croatia, France, Germany, Italy, Lithuania, Portugal, Serbia, Slovenia, Spain) and three cosmopolitan breeds (Italian Large White, Italian Landrace and Italian Duroc). All animals were genotyped with the GGP Porcine HD Genomic Profiler v1 chip (68,528 SNPs). PLINK software was used to identify five size classes of ROH (1-2 Mbp, 2–4 Mbp, 4–8 Mbp, 8–16 Mbp and >16 Mbp). Then the genomic inbreeding coefficient, defined as the proportion of genome covered by all ROH and divided by the total length of autosomal genome (FROH), was calculated for each animal and averaged over all pigs analyzed for each breed (40-50 per breed). Alentejana pigs had the lowest averaged FROH (0.029 ± 0.018) whereas Apulo-Calabrese had the highest averaged FROH (0.103 ± 0.038). The highest FROH individual value was observed in a Black Slavonian pig (0.295). Apulo-Calabrese, Casertana and Sarda breeds had the highest number of ROH >16 Mbp, suggesting that their autozygosity was derived from recent ancestors whereas Italian Large White and Italian Landrace had a high frequency of short ROH, indicating a remote origin of common ancestors. This study contributed to understand the population genetic history of the investigated pig breeds and provided information that could be useful to manage these pig genetic resources.