Keep Garfagnina alive. An integrated study on patterns of homozygosity, genomic inbreeding, admixture and breed traceability of the Italian Garfagnina goat breed.
The objective of this study was to investigate the genomic background of the Garfagnina (GRF) goat breed that faces the risk of extinction. In total, 48 goats genotyped with the Illumina CaprineSNP50 BeadChip were analyzed together with 214 goats belonging to 9 Italian breeds (~25 goats/breed) from the AdaptMap project [Argentata (ARG), Bionda dellAdamello (BIO), Ciociara Grigia (CCG), Di Teramo (DIT), Garganica (GAR), Girgentana (GGT), Orobica (ORO), Valdostana (VAL) and Valpassiria (VSS)]. We estimated i) runs of homozygosity (ROH), ii) admixture ancestries and iii) traceability success via discriminant analysis on principal components (DAPC) based on cross-validation. For GRF, an excess of frequent ROH (more than 45% in the GRF samples analyzed) was detected on CHR 12 at, roughly 50.25-50.94Mbp (ARS1 assembly), spanned between the CENPJ (centromere protein) and IL17D (interleukin 17D) genes. The same area was also present in DIT, while the broader region (~49.25-51.94Mbp) was shared among the ARG, CCG, and GGT. Admixture analysis depicted the uniqueness of the GRF breed, with a small part of common ancestry shared with BIO, VSS, ARG and CCG breeds. The DAPC model resulted in a 100% assignment success. We hope this work will contribute to the efforts of preventing the GRF from extinction and to add value to all the socio-agro-economic factors related with the farming of the GRF breed.