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Seeds of local breeds of pigs are stored in the National Cryobank (CBN) in the form of pellets (59 boars) or straws (78 boars). They are intended to be used for conservation programs. A genomic characterization of the CBN collections on the one hand and of recent animals (240 animals) on the other hand is carried out by genotyping (70K chip). The Basque, Gascon, Cul Noir Limousin, Bayeux Pig, Western White Pig and Nustrale breeds are thus studied over three periods: average birth years 1986 (pellets), 1998 (flakes) and 2014 (recent animals). Multidimensional analysis of the genotyping data shows a grouping of animals by breed. Some traceability errors of the oldest seeds (pellets) are detected. The average genomic similarity between animals of the same breed is lowest in the Nustrale breed and highest in the Basque breed. In recent animal samples, the absence of certain alleles found in the DNA of older seeds underlines the interest of CBN. The evolution over time of the halothane status of local breeds differs according to regular or irregular genotyping practices. Finally, the genomic inbreeding (FROH) of animals, defined as the proportion of genome in homozygous chromosome segments, is estimated. The Bayeux breed, considered as the most inbred on the basis of pedigrees, is in a more favourable situation than the Basque and Cul Noir Limousin breeds at the genomic level. FROH values above 0.22 seem to be associated with more frequent breeding failures with CBN seeds.
In this study, the genome of the six local French pig breeds was characterized from a sampling of recent animals and CBN stored seeds. Recommendations for the use of CBN material could be made to take into account the genomic inbreeding and halothane genotype of the animals that produced the seeds, as well as the few traceability errors of the oldest CBN doses. While boars with the lowest FROH are the most interesting in terms of genetic variability, more inbred CBN boars may carry original alleles. Nevertheless, the use of seeds with high genomic inbreeding may require the development of specific insemination methods to compensate for the possible lack of fertilizing power. This dataset will also be used to develop molecular tools for breed assignment. Further studies of genetic diversity may also be carried out.
This work was carried out within the framework of the Caraloporc project funded in 2015 by the CRB-Anim project, an infrastructure of the Investissements d'Avenir program. Part of the genotyping data comes from the H2020 TREASURE program (GA n°634476). The text reflects only the opinion of the authors.