Analysis of the inbreeding level in the Polish population of the Alpine Dachsbracke dog breed in the years 2000-2016

The aim of the study was to analyse the level of inbreeding in the Alpine Dachsbracke dog breed. The research was conducted using pedigrees of 405 individuals of this breed (195 male and 210 female), born in the years 2000-2016. The inbreeding coefficients (Fx) were estimated based on four-generation pedigrees. The individual inbreeding coefficients ranged from 0% to 25%. The average inbreeding coefficient for the population was 2.25% and did not differ between sexes (P>0.05). For 49.4% of individuals, the mean Fx value was 4.55%. The Fx values between years of birth were highly significant (P<0.0001). The trend analysis showed no significant changes in Fx during the period analysed. The mean inbreeding coefficient in the Polish population of Alpine Dachsbracke dogs was not high, but attention should be paid to the inbreeding coefficients of certain individuals, and mating of closely related individuals should be avoided.

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Inbreeding in Pembroke Welsh Corgi Population in Poland

Annals of Animal Science ◽

10.1515/aoas-2015-0027 ◽

2015 ◽

Vol 15 (4) ◽

pp. 861-866 ◽

Cited By ~ 2

Author(s):

Wiesław Piotr Świderek ◽

Katarzyna Fiszdon ◽

Natalia Kacprzak

Keyword(s):

Inbreeding Coefficient ◽

Polish Population ◽

Kennel Club ◽

Inbreeding Coefficients ◽

The Mean

Abstract The objective of this study was to determine changes in the coefficients of inbreeding for a comparatively new Polish population of Pembroke Welsh Corgis. Calculations were based on 780 pedigrees of dogs born between 1979 and 2010 and registered with the Polish Kennel Club. The mean inbreeding coefficients for animals born during those years varied from 0.4% to 8.93%. The lowest individual inbreeding coefficient was 0.06%, whereas the highest reached 25.1%.

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

Animals ◽

10.3390/ani10030498 ◽

2020 ◽

Vol 10 (3) ◽

pp. 498 ◽

Cited By ~ 1

Author(s):

Antonio Boccardo ◽

Stefano Paolo Marelli ◽

Davide Pravettoni ◽

Alessandro Bagnato ◽

Giuseppe Achille Busca ◽

...

Keyword(s):

Canis Lupus ◽

Inbreeding Coefficient ◽

Nucleotide Polymorphisms ◽

Canis Lupus Familiaris ◽

Runs Of Homozygosity ◽

Single Nucleotide ◽

The Mean ◽

Dog Breed ◽

Genomic Inbreeding ◽

Genealogical Information

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.

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Inbreeding effects on some reproductive traits in Markhoz goats

Animal Production Science ◽

10.1071/an17043 ◽

2018 ◽

Vol 58 (12) ◽

pp. 2178 ◽

Cited By ~ 3

Author(s):

P. Mahmoudi ◽

A. Rashidi ◽

M. Razmkabir

Keyword(s):

Litter Size ◽

Inbreeding Depression ◽

Reproductive Traits ◽

Information Criterion ◽

Inbreeding Coefficient ◽

Regression Coefficients ◽

Litter Weight ◽

Inbreeding Coefficients ◽

Poisson Models ◽

The Individual

The objective of this study was to estimate the inbreeding coefficient and its effects on reproductive traits in Markhoz goats. The pedigree file included 5351 kids produced by 234 bucks and 1470 does. Average inbreeding coefficient for the whole population was 2.68%, and the minimum and maximum inbreeding coefficients were 0.05% and 31.25%, respectively. Average coefficient of inbreeding for inbred population was 5.17% and the number of inbred animals in the population was 2777. For investigating effects of inbreeding coefficient on reproductive traits, 3443 records were available for litter size at birth (LSB), litter size at weaning (LSW), total litter weight at birth (TLWB) and mean of litter weight at birth (MLWB). Furthermore, available records for total litter weight at weaning (TLWW) and mean of litter weight at weaning (MLWW) were 2918. Inbreeding depression was estimated as the linear regression of performance on the individual inbreeding coefficient of kids and dams using the most appropriate animal model based on Akaike’s information criterion. Furthermore, inbreeding depressions for LSB and LSW were estimated using threshold and Poisson models. Regression coefficients of LSB, LSW, TLWB, TLWW, MLWB and MLWW on inbreeding coefficient of kids were –0.035, –0.019, –0.077 kg, –0.782 kg, –0.009 kg and –0.332 kg, respectively. Furthermore, regression coefficients of LSB, LSW, TLWB, TLWW, MLWB and MLWW on inbreeding coefficient of dams were 0.064, –0.013, 0.241 kg, 0.638 kg, 0.028 kg and –1.783 kg, respectively. The obtained results from this study showed that inbreeding depression is controlled by an appropriate mating system policy.

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Pedigree analysis of 220 almond genotypes reveals two world mainstream breeding lines based on only three different cultivars

Horticulture Research ◽

10.1038/s41438-020-00444-4 ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Felipe Pérez de los Cobos ◽

Pedro J. Martínez-García ◽

Agustí Romero ◽

Xavier Miarnau ◽

Iban Eduardo ◽

...

Keyword(s):

Genetic Variability ◽

Tree Breeding ◽

Inbreeding Coefficient ◽

Genetic Contribution ◽

Pedigree Data ◽

Breeding Programs ◽

Breeding Lines ◽

Inbreeding Coefficients ◽

The Usa ◽

The Mean

AbstractLoss of genetic variability is an increasing challenge in tree breeding programs due to the repeated use of a reduced number of founder genotypes. However, in almond, little is known about the genetic variability in current breeding stocks, although several cases of inbreeding depression have been reported. To gain insights into the genetic structure in modern breeding programs worldwide, marker-verified pedigree data of 220 almond cultivars and breeding selections were analyzed. Inbreeding coefficients, pairwise relatedness, and genetic contribution were calculated for these genotypes. The results reveal two mainstream breeding lines based on three cultivars: “Tuono”, “Cristomorto”, and “Nonpareil”. Descendants from “Tuono” or “Cristomorto” number 76 (sharing 34 descendants), while “Nonpareil” has 71 descendants. The mean inbreeding coefficient of the analyzed genotypes was 0.041, with 14 genotypes presenting a high inbreeding coefficient, over 0.250. Breeding programs from France, the USA, and Spain showed inbreeding coefficients of 0.075, 0.070, and 0.037, respectively. According to their genetic contribution, modern cultivars from Israel, France, the USA, Spain, and Australia trace back to a maximum of six main founding genotypes. Among the group of 65 genotypes carrying the Sf allele for self-compatibility, the mean relatedness coefficient was 0.125, with “Tuono” as the main founding genotype (24.7% of total genetic contribution). The results broaden our understanding about the tendencies followed in almond breeding over the last 50 years and will have a large impact into breeding decision-making process worldwide. Increasing current genetic variability is required in almond breeding programs to assure genetic gain and continuing breeding progress.

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EFFECTS OF INBREEDING ON FLOWER YIELD IN GERBERA

HortScience ◽

10.21273/hortsci.27.6.586b ◽

1992 ◽

Vol 27 (6) ◽

pp. 586b-586

Author(s):

Hongzhan Huang ◽

James Harding ◽

Thomas Byrne

Keyword(s):

Finite Number ◽

Population Size ◽

Inbreeding Depression ◽

Negative Correlation ◽

Significant Negative Correlation ◽

Gerbera Hybrida ◽

Inbreeding Coefficients ◽

Flower Yield ◽

The Mean ◽

Inbreeding Level

Inbreeding depression is found in most flower crops. Limited population size can cause inbreeding even in outcrossed populations. The Davis population of Gerbera hybrida has been selected for increasing flower yield for 15 generations. The mean yield per plant of the population has been increased from 14.2 to 28.0 flowers per winter six-month period. In each generation 23 to 80 selected parents have been crossed at random. Inbreeding coefficients were estimated from the pedigrees of each of the 6199 plants in the 16 generations. The inbreeding level in this population was found to increase in each generation and currently is 16.5%. Mean yield and inbreeding per family have a statistically significant negative correlation in generations 13 to 16. The results indicate that inbreeding is increasing in this randomly outcrossed population because of its finite number of parents, and that yield is reduced by 3.9 flowers per six-month due to inbreeding.

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Pedigree structure of American bison (Bison bison) population

Czech Journal of Animal Science ◽

10.17221/120/2017-cjas ◽

2018 ◽

Vol 63 (No. 12) ◽

pp. 507-517 ◽

Cited By ~ 1

Author(s):

E. Skotarczak ◽

P. Ćwiertnia ◽

T. Szwaczkowski

Keyword(s):

Mean Value ◽

Bison Bison ◽

Pedigree Information ◽

Effective Population ◽

Pedigree Structure ◽

Breeding Programs ◽

Inbreeding Coefficients ◽

Animal Populations ◽

The Mean ◽

Inbreeding Level

An effective realization of breeding programs in zoos is strongly determined by completeness of animal pedigree information. The knowledge of pedigree structure allows to maintain optimal genetic variability of a given population. The aim of this study was to estimate the parameters describing the pedigree structure of American bison housed in zoos in the context of further management of the population. Finally, 4269 American bison were analysed (1883 males, 2217 females, and 169 with unknown sex). The registered animals were born between years 1874 and 2013. The following pedigree parameters were estimated: number of fully traced generations, number of complete generations equivalent, index of pedigree completeness, individual inbreeding coefficients, increase of inbreeding for each individual, effective population size, and genetic diversity. The maximum number of fully traced generations was 3 (the mean value is 0.693). The mean inbreeding coefficient for the population studied was 3.26%, whereas individual increase in inbreeding ranged from 0 to 25.12%. Although the pedigree parameters (including the inbreeding level) in the American bison obtained in the present study seem to be acceptable (from the perspective of other wild animal populations), they can be over/underestimated due to incomplete pedigree.

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Rank-invariant estimation of inbreeding coefficients

Heredity ◽

10.1038/s41437-021-00471-4 ◽

2021 ◽

Author(s):

Qian S. Zhang ◽

Jérôme Goudet ◽

Bruce S. Weir

Keyword(s):

Genetic Data ◽

Reference Population ◽

Inbreeding Coefficient ◽

Allele Sharing ◽

Ancestral Allele ◽

1000 Genomes ◽

Inbreeding Coefficients ◽

Identical By Descent ◽

Invariant Estimation ◽

The Individual

AbstractThe two alleles an individual carries at a locus are identical by descent (ibd) if they have descended from a single ancestral allele in a reference population, and the probability of such identity is the inbreeding coefficient of the individual. Inbreeding coefficients can be predicted from pedigrees with founders constituting the reference population, but estimation from genetic data is not possible without data from the reference population. Most inbreeding estimators that make explicit use of sample allele frequencies as estimates of allele probabilities in the reference population are confounded by average kinships with other individuals. This means that the ranking of those estimates depends on the scope of the study sample and we show the variation in rankings for common estimators applied to different subdivisions of 1000 Genomes data. Allele-sharing estimators of within-population inbreeding relative to average kinship in a study sample, however, do have invariant rankings across all studies including those individuals. They are unbiased with a large number of SNPs. We discuss how allele sharing estimates are the relevant quantities for a range of empirical applications.

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Inbreeding and Mortality Risk in a Captive Population of Mhorr Gazelle (Nanger dama mhorr)

Annals of Tropical Research ◽

10.32945/atr38113.2016 ◽

2016 ◽

pp. 159-167

Author(s):

Ana Marquiza Quilicot ◽

Roswitha Baumung

Keyword(s):

Mortality Risk ◽

Management Practices ◽

Reference Population ◽

Effective Number ◽

Inbreeding Coefficients ◽

In Captivity ◽

Weaning Age ◽

Efficient Breeding ◽

Inbreeding Level ◽

The Individual

This study aimed to evaluate the genetic variation and examine the association of inbreeding level on mortality risk (at days 7, 30 and 180 – weaning age) of Mhorr gazelle in captivity for the year 1969–2000 as recorded in the studbook record kept by Australasian Regional Association of Zoological Parks and Aquaria (ARAZPA). The effective number of founders, ancestors and founder genomes was found to be 3.42, 3, and 1.44 for the studied reference population. The reference population is composed of animals which are alive, with known parents and known sex. Animals that are less than 10 years old (based on birth dates up to 2008) with no remarks on its death are considered alive. The population may not have experienced a severe bottleneck, as the values on the effective number of founders and ancestors are almost equal. However, the effective number of founder genomes is low, which demonstrates gene loss due to genetic drift. The mean inbreeding coefficients of the individual, sire and dam were found to be 0.2971 ± 0.1043, 0.2300 ± 0.1141 0.2339 ± 0.1070, respectively. The maximum inbreeding level of the population is 0.5247 (52.47%). This means that parent–offspring or full-sib mating must have happened. The increase in inbreeding level of an individual was found to be significantly associated (p<0.10) with an increase in p mortality risk at day 180 or weaning age. Increasing inbreeding level of sires was found to be significantly associated with increasing risk in mortality at day 30, which indicates that inbred parents also can influence the survival of an offspring. Efficient breeding programs are as important for decreasing mortality in captive populations, as the provision of optimum zoo management practices.

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Population Structure Analysis of the Border Collie Dog Breed in Hungary

Animals ◽

10.3390/ani9050250 ◽

2019 ◽

Vol 9 (5) ◽

pp. 250 ◽

Cited By ~ 5

Author(s):

Virág Ács ◽

Árpád Bokor ◽

István Nagy

Keyword(s):

Genetic Diversity ◽

Reference Population ◽

Inbreeding Coefficient ◽

Pedigree Data ◽

Effective Population ◽

Inbreeding Coefficients ◽

Population Structure Analysis ◽

Dog Breed ◽

Fixation Indices ◽

Mixed Line

Pedigree data of the Border Collie dog breed were collected in Hungary to examine genetic diversity within the breed and its different lines. The database was based on available herd books dating from the development of the breed (in the late 1800s) to the present day. The constructed pedigree file consisted of 13,339 individuals, of which 1566 dogs (born between 2010 and 2016) composed the alive reference population which was active from breeding perspective. The breed is subdivided by phenotype, showing a thicker coat, harmonic movement, a wide skull, and heavier bones for the show type, and a thinner or sometimes short coat and smaller body for the working line, while the mixed line is quite heterogeneous (a combination of the above). Thus, the reference population was dissected according to the existing lines. The number of founders was 894, but eight individuals were responsible for contributing 50% of the genetic variability. The reference population had a pedigree completeness of 99.6% up to 15 generations and an inbreeding coefficient of 9.86%. Due to the changing breed standards and the requirements of the potential buyers, the effective population size substantially decreased between 2010 and 2016. Generation intervals varied between 4.09 and 4.71 years, where the sire paths were longer due to the later initial age of breeding in males compared to females. Genetic differences among the existing lines calculated by fixation indices are not significant; nonetheless ancestral inbreeding coefficients are able to show contrasts.

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THE APPLICATION OF RAPD FINGERPRINTING TO ASSESS INBREEDING LEVELS IN THE CULTURED POPULATIONS OF GIANT FRESHWATER PRAWN, Macrobrachium rosenbergii

Indonesian Aquaculture Journal ◽

10.15578/iaj.5.1.2010.73-82 ◽

2010 ◽

Vol 5 (1) ◽

pp. 73

Author(s):

Imron Imron ◽

Dadan Sunandar ◽

Rommy Suprapto ◽

Nunuk Listyowati

Keyword(s):

Macrobrachium Rosenbergii ◽

Pedigree Analysis ◽

Inbreeding Coefficient ◽

Freshwater Prawn ◽

Giant Freshwater Prawn ◽

Rapd Fingerprinting ◽

Inbreeding Coefficients ◽

Technical Simplicity ◽

Inbreeding Level

Inbreeding has been one of central issues with regard to genetic quality of aquaculture species, including giant fresh water prawn (GFP). Conventional methods for the estimation of inbreeding level are available, such as pedigree analyses which requires a good pedigree record which, unfortunately, is rarely available. Likewise, microsatellite molecular markers commonly applied to obtain the coefficient inbreeding estimates are both laborious and expensive. Hence, an alternative method of inbreeding assessment which is relatively easy but reliable is in need. This study was aimed to explore the applicability of RAPD fingerprinting, which is known to be simple and affordable, to estimate inbreeding level of GFP population. Three GFP populations namely inbred, outbred, and farm populations with inbreeding level of 25%, 0%, and unknown, respectively, were genotyped using five polymorphic RAPD primers. The inbreeding levels mentioned within the first two populations were determined using pedigree analysis. RAPD banding patterns were then used to calculate band sharing index (BSI) and inbreeding coefficient (F). Assessment of the applicability of inbreeding level estimates obtained by RAPD markers was performed by comparing them to those estimated by pedigree analysis. Results show that RAPD fingerprinting was capable of delineating populations differing in their inbreeding coefficients. The pattern resulted from molecular inbreeding coefficient within the inbred and outbred groups, was congruent with that shown by pedigree analysis, while the farm population showed closeness to the inbred group. While the accuracy of the estimate needs to be verified further, this study suggests that RAPD fingerprinting is applicable to estimate population inbreeding level, particularly due to its technical simplicity and cost affordability.

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