Distribution of polymorphisms in major and candidate genes for productive and domestication-related traits in European local pig breeds

TREASURE is a multidisciplinary European project focused on the development of activities for the benefit of sustainable pork chains based on European local pigs. One of its main objectives is the genetic characterization of local pig breeds participating in the project, by using genetic and genomic tools. The most relevant genes and mutations associated with pig productive, meat quality, reproductive and disease resistance traits were prioritized and analysed in order to identify useful markers for authentication, traceability, conservation and breeding programmes. A panel of 32 SNPs were selected and a genotyping chip was designed and employed to genotype 48 animals from each one of 20 breeds included in the project (Schwäbisch Hällisches, Iberian, Black Majorcan, Basque, Gascon, Black Slavonian, Turopolje, Apulo Calabrese, Casertana, Cinta Senese, Mora Romagnola, Black Sicilian, Sarda, Lithuanian indigenous wattle, Old Lithuanian White, Alentejano, Bisaro, Mangalitsa, Moravka, Krskopolje). Twenty seven SNPs located in 24 genes were succesfully genotyped (MC1R, TYRP1, NR6A, PCK1, RYR1, IGF2, MC4R, PHKG1, SCD, GBP5, TAS2R39, TAS2R4, MUC4, ESR1, CYP2E1, LEP, CAST, MTTP, CYB5A, FTO, PPARGC1A, CAPN1, PPARD, CTSL). Results show very interesting findings, as lack or scarce segregation of markers in genes involved in coat color or productive and reproductive traits, such as MC1R, ESR1 or CTSL in all the analysed breeds, with useful implications for traceability. On the other hand, major gene alleles with contrasted effects on production and fatness (such as RYR1, IGF2, MC4R, LEP), meat quality (SCD, CAST, MTTP) or disease resistance (MUC4, GBP5) segregate in most breeds, in some cases with intermediate frequencies, opening selection possibilities. These results joint with ongoing genomic, transcriptomic and metagenomic assays, will provide essential information regarding genetic diversity, structure, selective signatures and population-specific biological processes responsible for specific production and quality traits. TREASURE project is funded under European Union’s Horizon 2020 research and innovation programme, grant no. 634476.