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Runs of homozygosity (ROH) are long stretches of genomic DNA which 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 work we investigated ROH in 20 European local 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 7 countries (Croatia, France, Germany, Italy, Lithuania, Portugal, Servia, Slovenia, Spain) and in 3 cosmopolitan breeds (Italian Large White, Italian Landrace and Italian Duroc). A total of 1129 pigs (45–50 per breed) were genotyped with the GGP Porcine HD Genomic Profiler v1 chip (68, 528 SNPs). PLINK software was used to analyze this data set. ROH were placed into 5 size classes (1–2 Mbp, 2–4 Mbp, 4–8 Mbp, 8–16 Mbp and >16 Mbp). 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 computed for each animal. 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 autozigosity 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. Several ROH islands were found along the genome and their distribution among breeds indicated the presence of common or breed specific selection sweeps. 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. This study has been funded by European Union’s H2020 RIA program (grant agreement No 634476). |
