Inbreeding in Pembroke Welsh Corgi Population in Poland

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

Roczniki Naukowe Polskiego Towarzystwa Zootechnicznego ◽

10.5604/01.3001.0013.5082 ◽

2018 ◽

Vol 14 (3) ◽

pp. 9-18

Author(s):

Elżbieta Bednarek ◽

Anna Sławińska ◽

Sławomir Mroczkowski

Keyword(s):

Trend Analysis ◽

Inbreeding Coefficient ◽

Polish Population ◽

Inbreeding Coefficients ◽

The Mean ◽

Dog Breed ◽

Related Individuals ◽

Inbreeding Level ◽

The Individual

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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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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PEDIGREE ANALYSIS OF 222 ALMOND GENOTYPES REVEALS TWO WORLD MAINSTREAM BREEDING LINES BASED ON ONLY THREE DIFFERENT CULTIVARS

10.1101/2020.06.16.154021 ◽

2020 ◽

Author(s):

Felipe Pérez de los Cobos ◽

Pedro J. Martínez-García ◽

Agustí Romero ◽

Xavier Miarnau ◽

Iban Eduardo ◽

...

Keyword(s):

Genetic Variability ◽

Critical Role ◽

Inbreeding Coefficient ◽

Genetic Contribution ◽

Breeding Programs ◽

Breeding Lines ◽

Inbreeding Coefficients ◽

Geographical Regions ◽

The Usa ◽

The Mean

ABSTRACTLoss of genetic variability is a steadily increasing challenge in tree breeding programs due to the repeated use of a reduced number of founder genotypes. High-quality pedigree data of 222 almond [Prunus dulcis (Miller) D.A. Webb, syn. P. amygdalus (L) Batsch] cultivars and breeding selections were used to study global genetic variability in modern breeding programs from Argentina, Australia, France, Greece, Israel, Italy, Russia, Spain and the USA. Inbreeding coefficients, pairwise relatedness and genetic contribution were calculated for these genotypes. The results reveal two mainstream breeding lines based on three cultivars from two different geographical regions: ‘Tuono’-‘Cristomorto’ (local landraces from Puglia, Italy) and ‘Nonpareil’ (chance seedling selected in California, USA, from French original stock). Direct descendants from ‘Tuono’ or ‘Cristomorto’ number 75 (sharing 30 descendants), while ‘Nonpareil’ has 72 direct descendants. The mean inbreeding coefficient of the analyzed genotypes was 0.036, with 13 genotypes presenting a high inbreeding coefficient, over 0.250. Breeding programs from the USA, France and Spain showed inbreeding coefficients of 0.067, 0.050 and 0.034, respectively. According to their genetic contribution, modern cultivars from Israel, France, the USA, Spain and Australia, trace back to six, five, four, four and two main founding genotypes respectively. Among the group of 65 genotypes carrying the Sf allele for self-compatibility, the mean relatedness coefficient was 0.133, with ‘Tuono’ as the main founding genotype (23.75% of total genetic contribution). Increasing as well as preserving current genetic variability is required in almond breeding programs worldwide to assure genetic gain and continuing breeding progress. Breeding objectives, apart from high and efficient productivity, should include disease resistance and adaptation to climate change. Ultimately, any new commercial almond cultivar has to be economically viable and breeders play a critical role in achieving this goal.

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Distributional characterizations and testing for differences of relatedness and inbreeding of a subpopulation of American Hereford bulls

Translational Animal Science ◽

10.1093/tas/txab008 ◽

2021 ◽

Vol 5 (1) ◽

Author(s):

M A Simmons ◽

P K Riggs ◽

S Sanders ◽

A D Herring ◽

J O Sanders ◽

...

Keyword(s):

Beta Distribution ◽

Genetic Parameters ◽

Inbreeding Coefficient ◽

Bootstrap Sampling ◽

Inbreeding Coefficients ◽

Beta Distributions ◽

Relationship Coefficient ◽

The Mean ◽

Population Genetic Parameters ◽

The Relationship

Abstract Beta distributions are characterized by two determining parameters and a parameter space from 0 to 1, and may be useful for examining population genetic parameters such as the relationship or inbreeding coefficients. Often subpopulations exist within breeds that are congregated around particular lineages of cattle or ancestors that breeders value. These subpopulations are more related to each other than to the majority of other animals; they may have higher inbreeding as well. Value may be added to these subpopulations because of their relatedness with important or renowned ancestors. The objectives of this work were to compare the relatedness and inbreeding of a group of 26 modern bulls from a subpopulation of the American Hereford breed relative to 1) 30 males with the most descendants present in the pedigree, 2) 15 renowned American Hereford bulls considered important individuals in the breed’s history, and 3) 19 prominent subpopulation male ancestors. Conformance of the mean relationship coefficients of the bulls with the three groups and the mean inbreeding coefficient with all pedigree animals to beta distributions was assessed by 1) visually determining the parameters of the beta distributions based on the entire pedigree, 2) testing the mean relationship coefficient or inbreeding coefficient of the group of subpopulation bulls for its positional inclusion in those distributions, and 3) bootstrap sampling methodology. The mean relationship coefficients of the 26 Trask bulls with the 30 bulls with the most descendants, the 15 renowned ancestors, and the 19 Trask male ancestors were 0.15, 0.132, and 0.208, respectively. Testing of these means in beta distributions indicated that the group of 26 Trask bulls were no more related to the three groups of bulls than all of the animals in the pedigree (0.06 < P < 0.25). Bootstrap sampling indicated that the 26 bulls were more related to the three groups of male ancestors than the remainder of the animals in the pedigree (P < 0.0001). The mean inbreeding coefficient of the 26 bulls (0.13) did not differ from the overall inbreeding coefficient (0.056) when tested using a beta distribution; however, bootstrap sampling indicated otherwise (P < 0.0001). Results may indicate the inadequacy of visually parameterizing a beta distribution. Quantification of pedigree relatedness of a group of animals to key ancestors, especially with no DNA available, may add value to that group and individuals.

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Effect of inbreeding and individual increase in inbreeding on growth in Nilagiri and Sandyno breeds of sheep

Animal Genetic Resources/Ressources génétiques animales/Recursos genéticos animales ◽

10.1017/s2078633615000338 ◽

2016 ◽

Vol 58 ◽

pp. 63-71 ◽

Cited By ~ 1

Author(s):

R. Venkataramanan ◽

A. Subramanian ◽

S.N. Sivaselvam ◽

T. Sivakumar ◽

C. Sreekumar ◽

...

Keyword(s):

Growth Traits ◽

Inbreeding Coefficient ◽

Pedigree Information ◽

Research Station ◽

Sheep Breeding ◽

Inbreeding Coefficients ◽

Equivalent Number ◽

Breeding Research ◽

Percent Increase ◽

Two Populations

SummaryIndividual increase in inbreeding coefficients (ΔFi) has been recommended as an alternate measure of inbreeding. It can account for the differences in pedigree knowledge of individual animals and avoids overestimation due to increased number of known generations. The effect of inbreeding (F) and equivalent inbreeding (EF) calculated fromΔFi, on growth traits were studied in Nilagiri and Sandyno flocks of sheep. The study was based on data maintained at the Sheep Breeding Research Station, Sandynallah. The pedigree information and equivalent number of generations were less in Sandyno compared with Nilagiri sheep. The average F and EF for the Nilagiri population were 2.17 and 2.44, respectively and the corresponding values for Sandyno sheep were 0.83 and 0.84, respectively. The trend of inbreeding over years in both the populations indicated that EF was higher during earlier generations when pedigree information was shallow. Among the significant effects of inbreeding, the depression in growth per 1 percent increase in inbreeding ranged from 0.04 kg in weaning weight to 0.10 kg in yearling weight. In general, more traits were affected by inbreeding in Nilagiri sheep, in which greater regression of growth traits was noticed with F compared with EF. Higher values of EF than F in earlier generations in both the populations indicate that EF avoided the potential overestimation of inbreeding coefficient during recent generations. In the Sandyno population, the magnitude of depression noticed among growth traits with significant effects of inbreeding was higher. The differences in response to F and EF noticed in the two populations and possible causes for the trait wise differences in response to F and EF are appropriately discussed.

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Population structure of Czech cold-blooded breeds of horses

Archives Animal Breeding ◽

10.5194/aab-54-1-2011 ◽

2011 ◽

Vol 54 (1) ◽

pp. 1-9

Author(s):

L. Vostrý ◽

Z. Čapková ◽

J. Přibyl ◽

B. Hofmanová ◽

H. Vostrá Vydrová ◽

...

Keyword(s):

Population Structure ◽

Genetic Variability ◽

Population Size ◽

Effective Population Size ◽

Inbreeding Coefficient ◽

Effective Population ◽

The Czech Republic ◽

Generation Interval ◽

Average Value ◽

Inbreeding Coefficients

Abstract. In order to estimate effective population size, generation interval and the development of inbreeding coefficients (Fx) in three original breeds of cold-blooded horses kept in the Czech Republic: Silesian Noriker (SN), Noriker (N) and Czech-Moravian Belgian horse (CMB) all animals of the particular breeds born from 1990 to 2007 were analysed. The average values of generation interval between parents and their offspring were: 8.53 in SN, 8.88 in N and 8.56 in CMB. Average values of effective population size were estimated to be: 86.3 in SN, 162.3 in N and 104.4 in CMB. The average values of inbreeding coefficient were 3.13 % in SN stallions and 3.39 % in SN mares, in the N breed 1.76 % and 1.26 % and in the CMB breed 3.84 % and 3.26 % respectively. Overall averages of Fx were: 3.23 %, 1.51 % and 3.55 % for the breeds SN, N and CMB. The average value of inbreeding coefficient Fx increased by 1.22 % in SN, by 0.35 % in N and by 1.01 % in CMB, respectively. This may lead to a reduction in genetic variability. Reduction in genetic variability could be either controlled in cooperation with corresponding populations of cold-blooded breeds in other European countries or controlled by number of sires used in population

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IDENTITY COEFFICIENTS IN FINITE POPULATIONS. I. EVOLUTION OF IDENTITY COEFFICIENTS IN A RANDOM MATING DIPLOID DIOECIOUS POPULATION

Genetics ◽

10.1093/genetics/86.3.697 ◽

1977 ◽

Vol 86 (3) ◽

pp. 697-713

Author(s):

C Chevalet ◽

M Gillois ◽

R F Nassar

Keyword(s):

Genetic Variability ◽

Population Size ◽

Effective Population Size ◽

Random Mating ◽

Matrix Multiplication ◽

Inbred Lines ◽

Inbreeding Coefficient ◽

Effective Population ◽

The Mean ◽

Over Time

ABSTRACT Properties of identity relation between genes are discussed, and a derivation of recurrent equations of identity coefficients in a random mating, diploid dioecious population is presented. Computations are run by repeated matrix multiplication. Results show that for effective population size (Ne) larger than 16 and no mutation, a given identity coefficient at any time t can be expressed approximately as a function of (1—f), (1—f)3 and (1—f)6, where f is the mean inbreeding coefficient at time t. Tables are presented, for small Ne values and extreme sex ratios, showing the pattern of change in the identity coefficients over time. The pattern of evolution of identity coefficients is also presented and discussed with respect to N eu, where u is the mutation rate. Applications of these results to the evolution of genetic variability within and between inbred lines are discussed.

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Effects of inbreeding on number of piglets born total, born alive and weaned in Austrian Large White and Landrace pigs

Archives Animal Breeding ◽

10.5194/aab-52-51-2009 ◽

2009 ◽

Vol 52 (1) ◽

pp. 51-64 ◽

Cited By ~ 2

Author(s):

A. Köck ◽

B. Fürst-Waltl ◽

R. Baumung

Keyword(s):

Inbreeding Depression ◽

Reproductive Performance ◽

Regression Models ◽

Inbreeding Coefficient ◽

Significant Positive Effect ◽

Weaned Piglets ◽

Large White ◽

Inbreeding Coefficients ◽

Negative Effect ◽

Positive Effect

Abstract. In this study records of 58 925 litters of Austrian Large White and 17 846 litters of Austrian Landrace pigs were analysed. Regression models were used to determine the effects of litter, dam and sire inbreeding on total number of born, born alive and weaned piglets in Large White and Landrace. In both populations, litter and dam inbreeding showed a negative effect on all traits. Sire inbreeding had no effect in Large White, whereas a significant positive effect was observed in Landrace. On average, inbred sires with an inbreeding coefficient of 10 % had 0.45 more piglets born total and 0.43 more piglets born alive in comparison to non-inbred sires. In a further analysis the total inbreeding coefficients of the animals were divided into two parts: »new« and »old« inbreeding. »New« inbreeding was defined as the period of the first five generations. It was shown that the observed inbreeding effects were not only caused by recent inbreeding. Reproductive performance was also affected by »old« inbreeding. Finally partial inbreeding coefficients of four important ancestors in each population were calculated to investigate if inbreeding effects are similar among these ancestors. The results revealed a varation of inbreeding effects among the four ancestors. Alleles contibuting to inbreeding depression were descendent from specific ancestors.

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Inbreeding coefficients of field populations ofKochia scopariausing chlorsulfuron resistance as a phenotypic marker

Weed Science ◽

10.1017/s0043174500091025 ◽

1998 ◽

Vol 46 (5) ◽

pp. 521-525 ◽

Cited By ~ 12

Author(s):

Mary J. Guttieri ◽

Charlotte V. Eberlein ◽

Edward J. Souza

Keyword(s):

Random Mating ◽

Inbreeding Coefficient ◽

Heterozygote Advantage ◽

Phenotypic Marker ◽

Inbreeding Coefficients ◽

Chlorsulfuron Resistance ◽

Recent Selection

Inbreeding coefficients were determined for nine southeastern Idaho kochia populations using chlorsulfuron resistance as a phenotypic marker. Inbreeding coefficients in six of the populations approximated 0, indicating that these field populations were random mating. One population had an inbreeding coefficient of 0.32, indicating partial selfing. No susceptible genotypes were identified in one population, which suggested recent selection and skewed the inbreeding coefficient. One population had an inbreeding coefficient of −0.19, suggesting either heterozygote advantage or some recent selection in the population. Our results suggest that kochia populations generally approximate random mating. Therefore, unlinked alleles will be independently assorted in field populations of kochia.

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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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