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. 2022 Dec 21;10(1):3.
doi: 10.3390/vetsci10010003.

Selection Signatures in Italian Livestock Guardian and Herding Shepherd Dogs

Arianna Bionda  1 , Matteo Cortellari  1 , Daniele Bigi  2 , Vincenzo Chiofalo  3   4 , Luigi Liotta  3 , Paola Crepaldi  1
Affiliations

Selection Signatures in Italian Livestock Guardian and Herding Shepherd Dogs

Arianna Bionda et al. Vet Sci. .

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.

Keywords: Italian shepherd dogs; SNPs; behavioural genes; selection signatures.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Multidimensional scaling plot representing the first and second principal components. Herding shepherd dogs are represented with diamonds, whereas livestock guardians are represented with circles; each colour indicates a different breed.
Figure 2
Figure 2
Admixture analysis of all the enrolled individuals, considering a number of clusters (K) equal to two (A) and seven (B), which resulted in the best fitting model. Each colour represents a different cluster. Herding dog breeds: Pastore Apuano (APUA), Bergamasco shepherd dog (BERG), Pastore d’Oropa (DORO), Lupino del Gigante (LUGI), and Pastore della Lessinia e del Lagorai (PALA); livestock guardian breeds: Fonni’s dog (FONN), Mannara dog (MANN), Maremma and the Abruzzi sheepdog (MARM), and Pastore della Sila (SILA).
Figure 3
Figure 3
Manhattan plots of Wright’s fixation index (FST) (A) and single SNP cross-population extended haplotype homozygosity (XP-EHH) (B) analyses comparing livestock guardian and herding shepherd dog breeds. Top 1% FST absolute values ranged from 0.13 to 0.31, and top 1% log (XP-EHH) from 2.7 to 5.1, as indicated by the grey dashed lines.
See this image and copyright information in PMC

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