Inbreeding effects on some reproductive traits in Markhoz goats

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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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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Genome-Wide Association Study for Reproductive Traits in a Duroc Pig Population

Animals ◽

10.3390/ani9100732 ◽

2019 ◽

Vol 9 (10) ◽

pp. 732 ◽

Cited By ~ 1

Author(s):

Zhang ◽

Chen ◽

Ye ◽

He ◽

Huang ◽

...

Keyword(s):

Association Study ◽

Candidate Genes ◽

Litter Size ◽

Production Efficiency ◽

Genome Wide Association Study ◽

Reproductive Traits ◽

Genome Wide Association ◽

Litter Weight ◽

Genome Wide ◽

A Genome

In the pig industry, reproductive traits constantly influence the production efficiency. To identify markers and candidate genes underlying porcine reproductive traits, a genome-wide association study (GWAS) was performed in a Duroc pig population. In total, 1067 pigs were genotyped using single-nucleotide polymorphism (SNP) chips, and four reproductive traits, including litter size at birth (LSB), litter weight at birth (LWB), litter size at weaning (LSW), and litter weight at weaning (LWW), were examined. The results showed that 20 potential SNPs reached the level of suggestive significance and were associated with these traits of interest. Several important candidate genes, including TXN2, KCNA1, ENSSSCG00000003546, ZDHHC18, MAP2K6, BICC1, FAM135B, EPHB2, SEMA4D, ST3GAL1, KCTD3, FAM110A, TMEM132D, TBX3, and FAM110A, were identified and might compose the underlying genetic architecture of porcine reproductive traits. These findings help to understand the genetic basis of porcine reproductive traits and provide important information for molecular breeding in pigs.

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MASS SELECTION IN A PIG POPULATION. 2. THE EFFECTS OF INBREEDING WITHIN THE SELECTED POPULATIONS

Canadian Journal of Animal Science ◽

10.4141/cjas77-081 ◽

1977 ◽

Vol 57 (4) ◽

pp. 627-634 ◽

Cited By ~ 4

Author(s):

HITOSHI MIKAMI ◽

H. T. FREDEEN ◽

A. P. SATHER

Keyword(s):

Litter Size ◽

Reproductive Performance ◽

Degrees Of Freedom ◽

Regression Coefficients ◽

Longissimus Dorsi ◽

Mass Selection ◽

Cross Sectional ◽

Litter Weight ◽

Daily Gain ◽

Size At Birth

The regression of reproductive performance of dams and post-natal performance of progeny on inbreeding was examined for a population of replicated lines subjected to mass selection over a period of nine generations. Inbreeding advanced by 2.0–2.3% per generation. Regression coefficients per 1% increase in inbreeding, based on 817 degrees of freedom for first parity sows, were −.56 ±.23 kg for dam weight at first parturition (12 mo), −.48 ±.19 kg for dam weight change from parturition to weaning, −.013 ±.034 for litter size at birth, −.103 ±.033 for litter size at weaning and −1.36 ±.36 kg for litter weight at weaning. Regressions for post-natal traits, estimated for progeny produced by second parity dams during the final three generations (638 df) were 10.3 ± 4.0 g for birth weight, 16.8 ± 32.7 g for weaned weight, −4.53 ± 1.22 g for post-weaning daily gain, −.34 ±.16 mm for backfat,.10 ±.04 cm2 for cross-sectional area of the longissimus dorsi, and.09 ±.04% for estimated yield of trimmed retail product from the carcass.

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The effects of inbreeding on the components of litter size in mice

Genetics Research ◽

10.1017/s0016672300010776 ◽

1967 ◽

Vol 10 (1) ◽

pp. 73-80 ◽

Cited By ~ 23

Author(s):

J. C. McCarthy

Keyword(s):

Litter Size ◽

Inbreeding Depression ◽

First Generation ◽

Inbreeding Coefficient ◽

Ovulation Rate ◽

Corpora Lutea ◽

Base Population ◽

Pregnant Females ◽

Sib Mating ◽

Size At Birth

Twenty-four lines were bred from a base population of outbred Q mice by continued full-sib mating. Inbreeding depression in litter size at birth was observed. This decline in litter size was analysed in terms of ovulation rate, the incidence of preimplantation mortality and the incidence of postimplantation mortality. Pregnant females were dissected at 17½ days' gestation and the numbers of corpora lutea, or eggs, and of live and dead embryos were counted. Matings were arranged so that separate estimates of the effects of inbreeding in the mother and in the litter on the components of litter size could be obtained.In the first generation of inbreeding when the inbreeding coefficient of the litter was raised from 0 to 25% decline in litter size was attributable to an increased incidence of preimplantation mortality.In the second and fourth generations decline in litter size was attributable to (1) a reduction in the number of eggs ovulated by the inbred mothers, (2) an increased incidence of preimplantation mortality which resulted from inbreeding in the mother. No evidence of significant effects on mortality of inbreeding in the litter was obtained in the later generation of inbreeding.These findings are discussed in the context of previous work on the effects of inbreeding and crossing on litter size and its components in mice and pigs.

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Estimating inbreeding depression for growth and reproductive traits using pedigree and genomic methods in Argentinean Brangus cattle

Journal of Animal Science ◽

10.1093/jas/skab289 ◽

2021 ◽

Author(s):

Natalia S Forneris ◽

Carolina A Garcia-Baccino ◽

Rodolfo J C Cantet ◽

Zulma G Vitezica

Keyword(s):

Inbreeding Depression ◽

Mixed Model ◽

Growth Traits ◽

Reproductive Traits ◽

Single Step ◽

Multiple Trait ◽

Model Framework ◽

Data Set ◽

Inbreeding Coefficients ◽

Genomic Inbreeding

Abstract Inbreeding depression reduces mean phenotypic value of important traits in livestock populations. The goal of this work was to estimate the level of inbreeding and inbreeding depression for growth and reproductive traits in Argentinean Brangus cattle, in order to obtain a diagnosis and monitor breed management. Data comprised 359,257 (from which 1,990 were genotyped for 40,678 SNP) animals with phenotypic records for at least one of three growth traits: birth weight (BW), weaning weight (WW) and finishing weight (FW). For scrotal circumference (SC), 52,399 phenotypic records (of which 256 had genotype) were available. There were 530,938 animals in pedigree. Three methods to estimate inbreeding coefficients were used. Pedigree-based inbreeding coefficients were estimated accounting for missing parents. Inbreeding coefficients combining genotyped and nongenotyped animal information were also computed from matrix H of the single-step approach. Genomic inbreeding coefficients were estimated using homozygous segments obtained from a Hidden Markov model (HMM) approach. Inbreeding depression was estimated from the regression of the phenotype on inbreeding coefficients in a multiple-trait mixed model framework, either for the whole data set or the data set of genotyped animals. All traits were unfavorably affected by inbreeding depression. A 10% increase in pedigree-based or combined inbreeding would result in a reduction of 0.34 - 0.39 kg in BW, of 2.77 - 3.28 kg in WW and 0.23 cm in SC. For FW a 10% increase in pedigree-based, genomic or combined inbreeding would result in a decrease of 8.05 - 11.57 kg. Genomic inbreeding based on the HMM was able to capture inbreeding depression, even in such a compressed genotyped data set.

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Assessing Genetic Diversity and Estimating the Inbreeding Effect on Economic Traits of Inner Mongolia White Cashmere Goats Through Pedigree Analysis

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.665872 ◽

2021 ◽

Vol 8 ◽

Author(s):

Zhiying Wang ◽

Bohan Zhou ◽

Tao Zhang ◽

Xiaochun Yan ◽

Yongsheng Yu ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Inbreeding Depression ◽

Inner Mongolia ◽

Inbreeding Coefficient ◽

Production Performance ◽

Pedigree Information ◽

Economic Traits ◽

Inbreeding Coefficients ◽

Cashmere Goats

Objective: The purpose of this study was to discover the population structure and genetic diversity of Inner Mongolia White Cashmere goats (IMCGs) and demonstrate the effect of inbreeding on the live body weight (LBW), cashmere yield (CY), fiber length (FL), and fiber diameter (FD) of IMCGs.Materials and Methods: All data were collected from pedigree information and production performance records of IMCGs from 1983 to 2019. The population structure and genetic diversity were analyzed by Endog 4.8 software. Inbreeding coefficients were obtained by the pedigree package in R. Then, a linear regression model was used to analyze how inbreeding influences economic traits in IMCGs. Four levels of inbreeding coefficients (Fi) were classified in this study, including Fi = 0, 0< Fi ≤ 6.25, 6.25< Fi ≤ 12.5 and Fi≥12.5. Variance analysis was performed to determine whether inbreeding levels had a significant effect on economic traits in IMCGs.Results: The proportions of rams and dams in IMCGs for breeding were relatively small, with values of 0.8 and 20.5%, respectively. The proportion of inbred animals in the entire population was high, with values up to 68.6%; however, the average inbreeding coefficient and relatedness coefficient were 4.50 and 8.48%, respectively. To date, the population has experienced 12 generations. The average generation interval obtained in the present study was 4.11 ± 0.01 years. The ram-to-son pathway was lowest (3.97 years), and the ewe-to-daughter pathway was highest (4.24 years). It was discovered that the LBW, CY, and FL increased by 3.88 kg, 208.7 g, and 1.151 cm, respectively, with every 1% increase in the inbreeding coefficient, and the FD decreased by 0.819 μm with every 1% increase in the inbreeding coefficient. Additionally, multiple comparison analysis indicated that when the inbreeding coefficient was higher than 6.25%, the LBW showed an obvious decreasing trend. The threshold value of inbreeding depression in the CY is 12.5%. However, inbreeding depression has not been observed in the FL and FD.Conclusion: Pedigree completeness needs to be further strengthened. The degree of inbreeding in this flock should be properly controlled when designing breeding programs.

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

Genetics Selection Evolution ◽

10.1186/s12711-020-00582-2 ◽

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.

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The effects of inbreeding on carcass traits in the bacon pig

Animal Science ◽

10.1017/s0003356100033316 ◽

1959 ◽

Vol 1 (2) ◽

pp. 123-127 ◽

Cited By ~ 5

Author(s):

J. W. B. King ◽

R. C. Roberts

Keyword(s):

Litter Size ◽

Carcass Traits ◽

Selection Procedure ◽

Inbred Lines ◽

Inbreeding Coefficient ◽

Regression Coefficients ◽

Partial Regression ◽

Large White ◽

On Line ◽

Fat Thickness

Carcass measurements made on 1,463 Large White pigs from 88 inbred lines, at various degrees of inbreeding, have been analysed.Partial regression coefficients calculated within lines showed that each 10% increase in inbreeding coefficient significantly increased carcass weight by 0·46 lb., decreased mid-back fat thickness by 0·37 mm. and streak thickness by 0·36 mm.Partial regression coefficients calculated on all the material, or on line means showed, however, that the most highly inbred pigs tended to be shorter and fatter than average. Possible explanations of this finding are discussed and it is suggested that under the selection procedure adopted for litter size and weaning, weight favours the survival of these less desirable lines.

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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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Body weight, litter size, and energetics of reproduction in Clethrionomys gapperi and Microtus pennsylvanicus

Canadian Journal of Zoology ◽

10.1139/z81-113 ◽

1981 ◽

Vol 59 (5) ◽

pp. 785-789 ◽

Cited By ~ 24

Author(s):

Duncan G. L. Innes ◽

John S. Millar

Keyword(s):

Body Weight ◽

Litter Size ◽

Reproductive Effort ◽

Reproductive Traits ◽

Microtus Pennsylvanicus ◽

Clethrionomys Gapperi ◽

Field Vole ◽

Litter Weight ◽

Significant Difference ◽

Postpartum Weight

A forest vole, Clethrionomys gapperi, and a field vole, Microtus pennsylvanicus, were examined for differences in a number of reproductive traits, including the energy required to raise a litter. Average postpartum weight, litter weight, and neonate weight of C. gapperi were significantly less than those of M. pennsylvanicus. Although C. gapperi had a significantly larger litter size than M. pennsylvanicus, the latter species used more energy to raise a litter than C. gapperi. Only one of three measures of physiological reproductive effort showed a significant difference between species. We conclude that there is no clear pattern between reproductive traits and habitat. Many traits appear to vary with body weight.

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