Selection Signatures in Italian Livestock Guardian and Herding Shepherd Dogs

Abstract

Livestock guardian (LGD) and herding shepherd (HSD) dogs have distinct morphological and behavioural characteristics, long selected by farmers and breeders, to accomplish different tasks. This study aimed to find the genomic regions that best differentiate and characterise Italian LGD and HSD. Genomic data of 158 dogs of four LGD and five HSD breeds, obtained with the 170K canine SNPchip, were collected. The two groups were compared using FST and XP-EHH analyses, identifying regions containing 29 genes. Moreover, 16 islands of runs of homozygosity were found in LGD, and 15 in HSD; 4 of them were partially shared. Among the genes found that better differentiated HSD and LGD, several were associated with dog domestication and behavioural aspects; particularly, MSRB3 and LLPH were linked to herding behaviour in previous studies. Others, DYSK, MAP2K5, and RYR, were related to body size and muscle development. Prick ears prevailed in sampled HSD, and drop ears in LGD; this explains the identification of WIF1 and MSRB3 genes. Unexpectedly, a number of genes were also associated with eye development and functionality. These results shed further light on the differences that human selection introduced in dogs aimed at different duties, even in a limited geographic area such as Italy.

The Shepherd and the Hunter: A Genomic Comparison of Italian Dog Breeds

“…This study investigated the genomic differences in Italian hunting and shepherd dog breeds. Population structure analyses, including multidimensional scaling, genomic distances, and admixture analyses, showed a clear distinction between the two groups but also between gun dogs and hounds on one side and livestock guardian and herding shepherd dogs on the other, as previously reported [40].…”

“…Data analysed in this study were acquired through the genotyping of 274 dogs belonging to 15 different Italian dog breeds using the CanineHD BeadChip (Illumina, San Diego, CA, USA) [10,12,17,39,40]. The "Hunting dogs" group (HD) included 12 Bracco italiano (BRAC), 24 Cirneco dell'Etna (CIRN), 24 Lagotto Romagnolo (LAGO), 16 Segugio Italiano Pelo Forte (SIPF), 16 Segugio Italiano Pelo Raso (SIPR), and 24 Spinone Italiano (SPIN); the "Shepherd dogs" group (SD) consisted of 19 Pastore Apuano (APUA), 15 Bergamasco shepherd dogs (BERG), 15 Pastore d'Oropa (DORO), 30 Fonni's dogs (FONN), 23 Lupino del Gigante (LUGI), 12 Mannara dogs (MANN), 20 Maremma and the Abruzzi sheepdogs (MARM), 10 Pastore della Lessinia e del Lagorai (PALA), and 14 Pastore della Sila (SILA).…”

Genomic Analysis of the Endangered Fonni’s Dog Breed: A Comparison of Genomic and Phenotypic Evaluation Scores

“…DNA was extracted using DNeasy Blood and Tissue Kit (QIAGEN ® , Hilden, Germany) following the manufacturer's instructions and then genotyped via outsourcing with Canine 230K SNP BeadChips (Illumina ® , San Diego, CA, USA). This dataset was merged with publicly available SNP chip data [10][11][12] of 7 Fonni's dogs and 379 dogs from 24 Italian and foreign breeds that could be historically or phenotypically related to Fonni's dogs and have been indicated by Sardinian veterinarians as the most diffuse in Sardinia, especially for hunting activities: Pastore Apuano (APUA, n = 19), Bergamasco Shepherd (BERG, n = 15), Bracco Italiano (BRAC, n = 12), Cane Corso (CCIT, A quality control was performed on the genomic data using PLINK 1.9 [13]: only dogs with missingness per individual < 0.1 and SNPs with missingness per marker < 0.05 and minor allele frequency > 0.01 were retained. Related dogs were excluded.…”