Garfagnina goats with Illumina CaprineSNP50 BeadChip

The objective of this study was to investigate the genetic diversity of
the Garfagnina (GRF) goat, a breed that currently risks extinction. For
this purpose, 48 goats were genotyped with the Illumina CaprineSNP50
BeadChip and analyzed together with 214 goats belonging to 9 other Italian
breeds (~25 goats/breed) from the AdaptMap project [Argentata (ARG),
Bionda dell’Adamello (BIO), Ciociara Grigia (CCG), Di Teramo (DIT),
Garganica (GAR), Girgentana (GGT), Orobica (ORO), Valdostana (VAL) and
Valpassiria (VSS)]. Comparative analyses were conducted on i) runs of
homozygosity (ROH), ii) admixture ancestries and iii) the accuracy of
breed traceability via discriminant analysis on principal components
(DAPC) based on cross-validation. For GRF, an excess of ROH (more than 45%
in GRF samples) was detected on CHR 12 at, roughly 50.25-50.94Mbp (ARS1
assembly), which spans the CENPJ (centromere protein) and IL17D
(interleukin 17D) genes. The same area of excess ROH was also present in
DIT, while a broader region (~49.25-51.94Mbp) was shared among the ARG,
CCG, and GGT. Admixture analysis revealed a small region of common
ancestry from GRFshared by BIO, VSS, ARG and CCG breeds. The DAPC model
yielded 100% assignment success for GRF. Overall, our results support the
identification of GRF as a distinct native Italian goat breed. This work
can contribute to planning conservation programmes to save GRF from
extinction and will improve the understanding of the socio-agro-economic
factors related with the farming of GRF.