scholarly journals Rank-invariant estimation of inbreeding coefficients

Heredity ◽  
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.

Inbreeding effects on some reproductive traits in Markhoz goats

2018 ◽  
Vol 58 (12) ◽  
pp. 2178 ◽  
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.

scholarly journals Genetic inbreeding depression load for morphological traits and defects in the Pura Raza Española horse

2020 ◽  
Vol 52 (1) ◽  
Author(s):  
Julia Poyato-Bonilla ◽  
Davinia I. Perdomo-González ◽  
María J. Sánchez-Guerrero ◽  
Luis Varona ◽  
Antonio Molina ◽  
...  
Keyword(s):  
Inbreeding Depression ◽  
Morphological Traits ◽  
Reference Population ◽  
Inbreeding Coefficient ◽  
Inbreeding Coefficients ◽  
Population Average ◽  
Recent Approach ◽  
Morphological Defects ◽  
And Performance ◽  
Genetic Value

Abstract Background Inbreeding is caused by mating between related individuals and is associated with reduced fitness and performance (inbreeding depression). Several studies have detected heterogeneity in inbreeding depression among founder individuals. Recently, a procedure was developed to predict hidden inbreeding depression load that is associated with founders using the Mendelian sampling of non-founders. The objectives of this study were to: (1) analyse the population structure and general inbreeding, and (2) test this recent approach for predicting hidden inbreeding depression load for four morphological traits and two morphology defects in the Pura Raza Española (PRE) horse breed. Results The regression coefficients that were calculated between trait performances and inbreeding coefficients demonstrated the existence of inbreeding depression. In total, 58,772,533 partial inbreeding coefficients (Fij) were estimated for the whole PRE population (328,706 horses). We selected the descendants of horses with a Fij ≥ 6.25% that contributed to at least four offspring and for which morphological traits were measured for the subsequent analysis of inbreeding depression load (639 horses). A pedigree was generated with the last five generations (5026 animals) used as the reference population (average inbreeding coefficient of 8.39% and average relatedness coefficient of 10.76%). Heritability estimates ranged from 0.08 (cresty neck) to 0.80 (height at withers), whereas inbreeding depression load ratios ranged from 0.01 (knock knee) to 0.40 (length of shoulder), for an inbreeding coefficient of 10%. Most of the correlations between additive and inbreeding depression load genetic values and correlations between inbreeding depression load genetic values for the different traits were positive or near 0. Conclusions Although the average inbreeding depression loads presented negative values, a certain percentage of the animals showed neutral or even positive values. Thus, high levels of inbreeding do not always lead to a decrease in mean phenotypic value or an increase in morphological defects. Hence, individual inbreeding depression loads could be used as a tool to select the most appropriate breeding animals. The possibility of selecting horses that have a high genetic value and are more resistant to the deleterious effects of inbreeding should help improve selection outcomes.

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

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.

scholarly journals Population Structure Analysis of the Border Collie Dog Breed in Hungary

Animals ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 250 ◽  
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.

scholarly journals Assessment of Inbreeding Depression and Inbreeding Trend of Production Traits in Iraqi Holstein Cows

2019 ◽  
pp. 1-9
Author(s):  
Farzad Moradpour ◽  
Hana Hamidi
Keyword(s):  
Inbreeding Depression ◽  
Milk Fat ◽  
Fixed Effects ◽  
Continuous Variable ◽  
Inbreeding Coefficient ◽  
Holstein Cows ◽  
Production Traits ◽  
Inbreeding Coefficients ◽  
Identical By Descent ◽  
Related Individuals

Inbreeding is defined as the probability that two alleles at any locus are identical by descent and occur when related individuals are mated to each other. A total of 123427, 115810 and 88361 records of 412-d yields of milk, fat and protein of Iraqi Holstein cows were collected from 1995 to 2010 in 838 herds used to estimation the inbreeding depression and inbreeding trend. Pedigree records of Iraqi Holstein cow were used to assessment inbreeding coefficients and these coefficients ranged from 0 to 42%. Animal model was used to estimation inbreeding depression on traits. Fixed effects included in statistical model were herd – year, age at calving and inbreeding coefficient as continuous and discrete variable. When considering inbreeding as continuous variable in model, the inbreeding depression for 412-d yields of milk, fat and protein were -28.19, -0.98 and -0.88 kg per 1% increase in inbreeding in Iraqi Holsteins, respectively. In this group of animal that inbreeding coefficient was between 0 < F ≤ 5.34 inbreeding was not caused reduction in production traits. However, in group of animal that inbreeding coefficient was greater than 5.34, and inbreeding depression in production traits was observed. The result of this study confirms of inbreeding depression in Iraqi Holstein cows.

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

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.

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

2016 ◽  
Vol 58 ◽  
pp. 63-71 ◽  
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.

scholarly journals Population structure of Czech cold-blooded breeds of horses

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

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

2009 ◽  
Vol 52 (1) ◽  
pp. 51-64 ◽  
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.

scholarly journals The projection of a test genome onto a reference population and applications to humans and archaic hominins

2014 ◽  
Author(s):  
Melinda A Yang ◽  
Kelley Harris ◽  
Montgomery Slatkin
Keyword(s):  
Numerical Analysis ◽  
Population Size ◽  
Demographic History ◽  
Reference Population ◽  
Average Weight ◽  
1000 Genomes Project ◽  
1000 Genomes ◽  
Test Genome ◽  
History Of ◽  
Past Population

We introduce a method for comparing a test genome with numerous genomes from a reference population. Sites in the test genome are given a weight w that depends on the allele frequency x in the reference population. The projection of the test genome onto the reference population is the average weight for each x, w(x). The weight is assigned in such a way that if the test genome is a random sample from the reference population, w(x)=1. Using analytic theory, numerical analysis, and simulations, we show how the projection depends on the time of population splitting, the history of admixture and changes in past population size. The projection is sensitive to small amounts of past admixture, the direction of admixture and admixture from a population not sampled (a ghost population). We compute the projection of several human and two archaic genomes onto three reference populations from the 1000 Genomes project, Europeans (CEU), Han Chinese (CHB) and Yoruba (YRI) and discuss the consistency of our analysis with previously published results for European and Yoruba demographic history. Including higher amounts of admixture between Europeans and Yoruba soon after their separation and low amounts of admixture more recently can resolve discrepancies between the projections and demographic inferences from some previous studies.

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