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

Boccardo, Antonio; Marelli, S.P.; Pravettoni, D.; Bagnato, A.; Busca, Giuseppe; Strillacci, M.G.

doi:10.3390/ani10030498

Cited by 9 publications

(11 citation statements)

References 41 publications

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“…Pedigree analyses based on extensive data revealed average litter size and life expectancy for the Leonberger dogs included in our study that are in agreement with previously reported results [ 52 ]. Long ROH segments (~ 10 Mb) occur as a result of recent inbreeding, whereas short ROH (< 2 Mb) indicate genomic regions that are identical by descent from older ancestors [ 12 ]. In the Leonberger dogs studied here, the 1- to 2-Mb segments account for approximately 25% of the detected ROH and those that are longer than 8 Mb account for about 20% (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Polymorphic microsatellite marker genotype data have been used to evaluate the genetic diversity in dogs (e.g. [7,8]), and more recently, genomewide single nucleotide polymorphism (SNP) genotype data have been used in several breeds [9][10][11][12][13]. Based on SNP data, runs of homozygosity (ROH) can be characterized, which enable quantification of the extent of inbreeding in diploid individuals, especially in the case of incomplete, unreliable, or missing pedigree information [14].…”

Section: Introductionmentioning

confidence: 99%

“…In general, studies are based on SNP genotyping data of variable marker density and generally for less than 100 selected individuals per breed; e.g. Boccardo et al [12] analysed only 34 individuals of the German shorthaired pointer breed to estimate a genomic inbreeding coefficient F_ROH of 0.17, whereas a mean inbreeding coefficient of only 0.023 was found based on genealogical information, showing the latter was incomplete.…”

Section: Introductionmentioning

confidence: 99%

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Genomic diversity and population structure of the Leonberger dog breed

et al. 2020

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Background Leonberger is a giant dog breed formed in the 1850s in Germany. Its post-World War II popularity has resulted in a current global population of ~ 30,000 dogs. The breed has predispositions to neurodegenerative disorders and cancer, which is likely due in large part to limited genetic diversity. However, to date there is no scientific literature on the overall demography and genomic architecture of this breed. Results We assessed extensive pedigree records, SNP array genotype data, and whole-genome sequences (WGS) on 142,072, 1203 and 39 Leonberger dogs, respectively. Pedigree analyses identified 22 founder animals and revealed an apparent popular sire effect. The average pedigree-based inbreeding coefficient of 0.29 and average kinship of 0.31 show a dramatic loss of genetic diversity. The observed average life span decreased over time from 9.4 years in 1989 to 7.7 years in 2004. A global health survey confirmed a high prevalence of cancer and neurological disorders. Analysis of SNP-based runs of homozygosity (ROH) identified 125,653 ROH with an average length of 5.88 Mb, and confirmed an average inbreeding coefficient of 0.28. Genome-wide filtering of the WGS data revealed 28 non-protein-changing variants that were present in all Leonberger individuals and a list of 22 potentially pathogenic variants for neurological disorders of which 50% occurred only in Leonbergers and 50% occurred rarely in other breeds. Furthermore, one of the two mtDNA haplogroups detected was present in one dog only. Conclusions The increasing size of the Leonberger population has been accompanied by a considerable loss of genetic diversity after the bottleneck that occurred in the 1940s due to the intensive use of popular sires resulting in high levels of inbreeding. This might explain the high prevalence of certain disorders; however, genomic data provide no evidence for fixed coding variants that explain these predispositions. The list of candidate causative variants for polyneuropathy needs to be further evaluated. Preserving the current genetic diversity is possible by increasing the number of individuals for breeding while restricting the number of litters per sire/dam. In addition, outcrossing would help optimize long-term genetic diversity and contribute to the sustainability and health of the population.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genomic diversity and population structure of the Leonberger dog breed

et al. 2020

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“…The first of these is the epha6 gene which was found to be associated with temperament in Guzerat (Bos indicus), a Brazilian breed of domestic cattle [63]. The second one of these is the fmn1 gen which appears to be associated with energy and trainability in dogs (Canis familiaris) [64]. Another one was the dyrk1ab gene, where knockout studies in zebrafish found it to be associated with traits related to social deficiencies relevant to autism [65].…”

Section: Discussionmentioning

confidence: 99%

Genomic Signatures of Domestication Selection in the Australasian Snapper (Chrysophrys auratus)

Baesjou

Wellenreuther

2021

Genes

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Domestication of teleost fish is a recent development, and in most cases started less than 50 years ago. Shedding light on the genomic changes in key economic traits during the domestication process can provide crucial insights into the evolutionary processes involved and help inform selective breeding programmes. Here we report on the recent domestication of a native marine teleost species in New Zealand, the Australasian snapper (Chrysophrys auratus). Specifically, we use genome-wide data from a three-generation pedigree of this species to uncover genetic signatures of domestication selection for growth. Genotyping-By-Sequencing (GBS) was used to generate genome-wide SNP data from a three-generation pedigree to calculate generation-wide averages of FST between every generation pair. The level of differentiation between generations was further investigated using ADMIXTURE analysis and Principal Component Analysis (PCA). After that, genome scans using Bayescan, LFMM and XP-EHH were applied to identify SNP variants under putative selection following selection for growth. Finally, genes near candidate SNP variants were annotated to gain functional insights. Analysis showed that between generations FST values slightly increased as generational time increased. The extent of these changes was small, and both ADMIXTURE analysis and PCA were unable to form clear clusters. Genome scans revealed a number of SNP outliers, indicative of selection, of which a small number overlapped across analyses methods and populations. Genes of interest within proximity of putative selective SNPs were related to biological functions, and revealed an association with growth, immunity, neural development and behaviour, and tumour repression. Even though few genes overlapped between outlier SNP methods, gene functionalities showed greater overlap between methods. While the genetic changes observed were small in most cases, a number of outlier SNPs could be identified, of which some were found by more than one method. Multiple outlier SNPs appeared to be predominately linked to gene functionalities that modulate growth and survival. Ultimately, the results help to shed light on the genomic changes occurring during the early stages of domestication selection in teleost fish species such as snapper, and will provide useful candidates for the ongoing selective breeding in the future of this and related species.

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“…Leroy et al [ 12 ] included the SHP (F = 0.035) and the Griffon Korthals (F = 0.056) in a genetic diversity study of 60 French dog populations. Italian SHPs had an F of 0.023 [ 23 ]. Because classical inbreeding coefficients do not take into account the degree of inbreeding in ancestors, ancestral inbreeding coefficients were developed some time ago [ 24 , 25 , 26 ].…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Trends of Ancestral and New Inbreeding in Deutsch Drahthaar Assessed by Pedigree Data

Michels

Distl

2022

Animals

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Loss of genetic diversity and high inbreeding rates confer an increased risk of congenital anomalies and diseases and thus impacting dog breeding. In this study, we analyzed recent and ancestral inbreeding as well as other measures of genetic variability in the Deutsch Drahthaar (DD) dog population. Analyses included pedigree data from 101,887 animals and a reference population with 65,927 dogs born between 2000 and 2020. The mean equivalent complete generations was 8.6 with 69% known ancestors in generation 8. The mean realized effective population size was 92 with an increasing trend from 83 to 108 over birth years. The numbers of founders, effective founders and effective ancestors, as well as founder genomes, were 814, 66, 38 and 16.15, respectively. Thirteen ancestors explained 50% of the genetic diversity. The mean coefficient of inbreeding and individual rate of inbreeding (ΔFi) were 0.042 and 0.00551, respectively, with a slightly decreasing trend in ΔFi. Exposure of ancestors to identical-by-descent alleles explored through ancestral coefficients of inbreeding showed a strong increasing trend. Comparisons between new and ancestral inbreeding coefficients according to Kalinowski et al. showed an average relative contribution of 62% of new inbreeding to individual inbreeding. Comparisons among average coancestry within the parental population and average inbreeding in the reference population were not indicative of genetic substructures. In conclusion, the creation of the DD dog breed about 120 years ago resulted in a popular breed with considerable genetic diversity without substructuring into lines or subpopulations. The trend of new inbreeding was declining, while ancestral inbreeding through ancestors who were autozygous at least once in previous generations was increasing.

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

Cited by 9 publications

References 41 publications

Genomic diversity and population structure of the Leonberger dog breed

Genomic diversity and population structure of the Leonberger dog breed

Genomic Signatures of Domestication Selection in the Australasian Snapper (Chrysophrys auratus)

Genetic Diversity and Trends of Ancestral and New Inbreeding in Deutsch Drahthaar Assessed by Pedigree Data

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