Genomic Characterization of the Istrian Shorthaired Hound

Abstract

Istrian shorthaired hound is an old indigenous Croatian dog breed with historical traces of its origin, which date back to the 14th century. Due to its intelligence and great hunting abilities, it is considered an excellent hunting dog. Despite its ancient origin, there is no data on genetic diversity, population structure, and degree of inbreeding that could be used for advanced management and conservation of this breed. Our study aimed to provide a high-resolution population structure of the Istrian shorthaired hound using a 220K HD SNP array, to compare the obtained data with the genealogical records and to place the breed in a broader context of world dog populations. Relatively high population size and low inbreeding coefficient estimated from genealogical data indicate a preserved genetic diversity in this breed. The principle component analysis, the NeighborNet network, and TreeMix were used to determine the genetic relationship between the Istrian shorthaired hound and other breeds. The Istrian shorthaired hound was found to be genetically related to Italian hunting dogs sharing the same branch with the Segugio Italiano a Pelo Raso and Segugio Italiano a Pelo Forte. The ADMIXTURE analysis indicated that the Istrian shorthaired hound could be involved in the development of some other hunting dog breeds. The estimated effective population size (Ne) based on SNP data was similar to Ne calculated from genealogical data indicating the absence of bottlenecks and well-balanced use of breeding animals. The low genomic inbreeding coefficient, together with the higher number of short runs of homozygosity, observed in the Istrian shorthaired hound, confirms the ancient origin of the breed based on historical documents. The analysis of selective sweeps identified genomic regions with the strongest selection signals in the vicinity of the genes associated with cognitive performance and behavior. Genome analysis proved to be a useful tool for estimating population parameters and can be implemented in the conservation plan for this indigenous breed.

Keywords: Istrian shorthaired hound; SNP array; genealogical data; genetic diversity; population structure.

Figure 1

Historical traces of the breed’s origin [2].

Figure 2

Istrian shorthaired hound [2].

Figure 3

Average sum of ROH for the Istrian shorthaired hound, Grey wolf, and other 31 representative dog breeds. Blue: short (0.5 Mb ≤ ROH < 2.5 Mb), green: medium (2.5 Mb ≤ ROH < 5 Mb), and red: long (ROH > 5 Mb) ROH per breed.

Figure 4

PCA-scatter plot of 151 dog breeds and two wolf populations.

Figure 5

Zoom-in of the Mediterranean breeds cluster (Figure 4), highlighting a subset of 665 dogs which belong to 31 breeds related to the Istrian shorthaired hound (ISH).

Figure 6

NeighborNet network computed from pairwise Nei distances between Istrian shorthaired hound, 31 other dog breeds, and Grey wolf.

Figure 7

Population structure of Istrian shorthaired hound, 31 other dog breeds, and Grey wolf. Bayesian clustering performed with ADMIXTURE assuming K = 2 to K = 40. Each cluster is presented with a different color, and each individual is shown as a vertical bar representing the proportion of membership to a certain population.

Figure 8

Graph inferred by TreeMix for the Istrian shorthaired hound, 14 dog breeds, and Grey wolf as root, allowing eight migration events. Migration arrows are colored according to their weight. Horizontal branch lengths are proportional to the amount of genetic drift that occurred on the branch.

Figure 9

Manhattan plot of the distribution of ROH islands in 48 Istrian shorthaired hound genomes. The y-axis shows the number of overlapping ROH shared among individuals for each SNP. ROH islands, genomic regions where 70% or more samples shared ROH, were identified on chromosomes 10, 14, 22, 28, and 30.

Figure 10

Manhattan plot of genomic selection regions detected using iHS. The strongest signals were detected on chromosomes 15, 14, 4, 31, and 1.