Signatures of selection in Mora Romagnola, a highly inbreed autochthonous pig breed

Mora Romagnola is an Italian autochthonous pig breed, characterised by a blackish coat with lighter shades on the abdomen and a distinctive dorsal line of thick, dense hair known as the ‘Sparta line’. Historically, pigs with similar phenotypic traits have been found in various areas of Northern Italy, but currently, they are only raised in the eastern part of the Emilia-Romagna region, originating the pig population of this breed. The Mora Romagnola breed experienced a significant population decline, putting it at risk of extinction, due to the introduction of cosmopolitan breeds. Its conservation program began in the 1990s. Products from Mora Romagnola pigs are part of a breed-specific branded value chain that provides a profitable economic gain to farmers, crucial for the sustainable conservation of this animal genetic resource. This study aimed to characterise the genomic features of Mora Romagnola and evaluate the level of inbreeding in the breed population. Approximately 250 Mora Romagnola pigs were genotyped for a total of 68516 SNPs using the GGP Porcine HD single nucleotide polymorphism array. Using this genomic data, several inbreeding parameters were calculated and runs of homozygosity (ROH) islands were identified. These analyses revealed a high level of inbreeding in this breed and suggested that the population had recently experienced a bottleneck. The inbreeding coefficient based on the deviation from observed versus expected heterozygosity, FHOM, had an average value of 0.18 ± 0.13, and reached a maximum of 0.64. The FROH coefficient resulted in values ranging from 0.036 to 0.632, with an average value of 0.292 ± 0.095. The average number of ROH per animal was 92.2 ± 20, with a minimum of 17 and a maximum of 130. Additionally, 12 genomic regions showed evidence of selective pressure, as indicated by the high frequency of homozygous regions in the population. These homozygosity hotspots were present in more that 75% of the analysed animals and the most relevant were located on SCC1 between 208.9Mbp and 277.2Mbp and on SCC15 between 104.7Mbp and 105.0Mbp, encompassing several QTLs related to production traits, such as weight gain or number of vertebrae. Integrating this genomic information into the Mora Romagnola herd book will help improve breed conservation programs for this autochthonous genetic resource. This study was carried out within the Agritech National Research Center (Spoke 1) and received funding from the European Union Next-GenerationEU under the National Recovery and Resilience Plan (NRRP), Mission 4, Component 2, Investment 1.4, Call D. D.3138 published on 12 / 16 / 2021 amended D.D. 3175 on 18 / 12 / 2021, CN00000022 – CUP J33C22001150008. O074