The German Shorthair Pointer Dog Breed (Canis lupus familiaris): Genomic Inbreeding and Variability.

Antonio Boccardo,Davide Pravettoni,Alessandro Bagnato,Stefano Paolo Marelli,Giuseppe Achille Busca,Maria Giuseppina Strillacci

doi:10.3390/ani10030498

Antonio Boccardo, Davide Pravettoni + Show 4 more

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https://doi.org/10.3390/ani10030498

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Abstract

Simple SummaryIn order to protect domestic animals’ biodiversity, a deep knowledge of the genomic makeup is required. The authors describe the genomic architecture of the German Short Hair Pointer breed and analyze the inbreeding levels under a genomic and a genealogic perspective. Twenty-four dogs from Italy were genotyped and analyzed jointly with 10 dogs from USA, whose genotypes were available from a published research. The authors investigated the genomic structural variation of the breed using runs of homozygosity—the direct measurement of the proportion of homozygous DNA, i.e., genomic inbreeding. Some traits clearly revealed the selection objectives addressed in the breed. The results describe a low inbred population with quite good levels of genetic variability.The German Shorthaired Pointer (GSHP) is a breed worldwide known for its hunting versatility. Dogs of this breed are appreciated as valuable companions, effective trackers, field trailers and obedience athletes. The aim of the present work is to describe the genomic architecture of the GSHP breed and to analyze inbreeding levels under a genomic and a genealogic perspective. A total of 34 samples were collected (24 Italian, 10 USA), and the genomic and pedigree coefficients of inbreeding have been calculated. A total of 3183 runs of homozygosity (ROH) across all 34 dogs have been identified. The minimum and maximum number of Single Nucleotide Polymorphisms (SNPs) defining all ROH are 40 and 3060. The mean number of ROH for the sample was 93.6. ROH were found on all chromosomes. A total of 854 SNPs (TOP_SNPs) defined 11 ROH island regions (TOP_ROH), in which some gene already associated with behavioral and morphological canine traits was annotated. The proportion of averaged observed homozygotes estimated on total number of SNPs was 0.70. The genomic inbreeding coefficient based on ROH was 0.17. The mean inbreeding based on genealogical information resulted 0.023. The results describe a low inbred population with quite a good level of genetic variability.

Highlights

Dog selection is based on the breed standards that usually define the selection objectives for morphological traits and the behavioral predisposition of each breed [1]
The aim of this study is to describe the genomic architecture of German Shorthaired Pointer (GSHP) breed and to analyze the inbreeding levels of the breed under a genomic and a genealogic perspective, to supply effective data helpful for the design of breeding plans and conservation projects
The Principal component analysis (PCA) supported the results of the ADMIXTURE: as shown in Figure 1B, all individuals belong to a unique cluster

Summary

Introduction

Dog selection is based on the breed standards that usually define the selection objectives for morphological traits and the behavioral predisposition of each breed [1]. Physical and physiological characteristics are determined by the genetic composition of the breeds which may have been affected by population bottlenecks due to specific directional selection practices. In this occurrence, a reduced number of ancestors, jointly to the large use of popular sires (e.g., the top winning male of the year) may result in an increase in homozygosity at population level [3,5,6].

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