scholarly journals Inbreeding Calculated with Runs of Homozygosity Suggests Chromosome-Specific Inbreeding Depression Regions in Line 1 Hereford

Animals ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 3105
Author(s):  
Bethany Pilon ◽  
Kelly Hinterneder ◽  
El Hamidi A. Hay ◽  
Breno Fragomeni
Keyword(s):  
Inbreeding Depression ◽  
Prediction Accuracy ◽  
Average Daily Gain ◽  
Pedigree Information ◽  
Cattle Population ◽  
Runs Of Homozygosity ◽  
Negative Effects ◽  
Prediction Ability ◽  
Phenotype Prediction ◽  
Inbreeding Coefficients

The goal of this study was to evaluate inbreeding in a closed beef cattle population and assess phenotype prediction accuracy using inbreeding information. Effects of inbreeding on average daily gain phenotype in the Line 1 Hereford cattle population were assessed in this study. Genomic data were used to calculate inbreeding based on runs of homozygosity (ROH), and pedigree information was used to calculate the probability of an allele being identical by descent. Prediction ability of phenotypes using inbreeding coefficients calculated based on pedigree information and runs of homozygosity over the whole genome was close to 0, even in the case of significant inbreeding coefficient effects. On the other hand, inbreeding calculated per individual chromosomes’ ROH yielded higher accuracies of prediction. Additionally, including only ROH from chromosomes with higher predicting ability further increased prediction accuracy. Phenotype prediction accuracy, inbreeding depression, and the effects of chromosome-specific ROHs varied widely across the genome. The results of this study suggest that inbreeding should be evaluated per individual regions of the genome. Moreover, mating schemes to avoid inbreeding depression should focus more on specific ROH with negative effects. Finally, using ROH as added information may increase prediction of the genetic merit of animals in a genomic selection program.

scholarly journals Runs of homozygosity and analysis of inbreeding depression

2020 ◽  
Vol 98 (12) ◽  
Author(s):  
Pattarapol Sumreddee ◽  
Sajjad Toghiani ◽  
El Hamidi Hay ◽  
Andrew Roberts ◽  
Samuel E Aggrey ◽  
...  
Keyword(s):  
Inbreeding Depression ◽  
Search Algorithm ◽  
Average Daily Gain ◽  
Pedigree Information ◽  
Accurate Estimation ◽  
Minimum Length ◽  
Runs Of Homozygosity ◽  
Deleterious Alleles ◽  
Genome Wide ◽  
Hereford Cattle

Abstract Pedigree information was traditionally used to assess inbreeding. The availability of high-density marker panels provides an alternative to assess inbreeding, particularly in the presence of incomplete and error-prone pedigrees. Assessment of autozygosity across chromosomal segments using runs of homozygosity (ROH) has emerged as a valuable tool to estimate inbreeding due to its general flexibility and ability to quantify the chromosomal contribution to genome-wide inbreeding. Unfortunately, the identification of ROH segments is sensitive to the parameters used during the search process. These parameters are heuristically set, leading to significant variation in the results. The minimum length required to identify an ROH segment has major effects on the estimation of inbreeding and inbreeding depression, yet it is arbitrarily set. To overcome this limitation, a search algorithm to approximate mutation enrichment was developed to determine the minimum length of ROH segments. It consists of finding genome segments with significant effect differences in trait means between animals with high and low burdens of autozygous intervals with a specific length. The minimum length could be determined heuristically as the smallest interval at which a significant signal is detected. The proposed method was tested in an inbred Hereford cattle population genotyped for 30,220 SNPs. Phenotypes recorded for six traits were used for the approximation of mutation loads. The estimated minimum length was around 1 Mb for yearling weight (YW) and average daily gain (ADG) and 4 Mb for birth weight and weaning weight. These trait-specific thresholds estimated using the proposed method could be attributed to a trait-dependent effect of homozygosity. The detection of significant inbreeding effects was well aligned with the estimated thresholds, especially for YW and ADG. Although highly deleterious alleles are expected to be more frequent in recent inbreeding (long ROH), short ROH segments (<5 Mb) could contain a large number of less deleterious mutations with substantial joint effects on some traits (YW and ADG). Our results highlight the importance of accurate estimation of the ROH-based inbreeding and the necessity to consider a trait-specific minimum length threshold for the identification of ROH segments in inbreeding depression analyses. These thresholds could be determined using the proposed method provided the availability of phenotypic information.

scholarly journals 205 Runs of homozygosity and analysis of inbreeding depression

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 39-40
Author(s):  
Pattarapol Sumreddee ◽  
Sajjad Toghiani ◽  
Andrew J Roberts ◽  
El H Hay ◽  
Samuel E Aggrey ◽  
...  
Keyword(s):  
Inbreeding Depression ◽  
Clustering Algorithm ◽  
Search Algorithm ◽  
Pedigree Information ◽  
Minimum Length ◽  
Runs Of Homozygosity ◽  
Model Based Clustering ◽  
Genome Wide ◽  
Hereford Cattle ◽  
Density Marker

Abstract Pedigree information was traditionally used to assess inbreeding. Availability of high-density marker panels provides an alternative to assess inbreeding, particularly in the presence of incomplete and error-prone pedigrees. Assessment of autozygosity across chromosomal segments using runs of homozygosity (ROH) is emerging as a valuable tool to estimate inbreeding due to its general flexibility and ability to quantify chromosomal contribution to genome-wide inbreeding. Unfortunately, identifying ROH segments is sensitive to the parameters used during the search process. These parameters are heuristically set, leading to significant variation in the results. The minimum length required to identify a ROH segment has major effects on the estimation of inbreeding, yet it is arbitrarily set. Understanding the rise, purging, and the effects of deleterious mutations requires the ability to discriminate between ancient and recent inbreeding. However, thresholds to discriminate between short and long ROH segments are largely unknown. To address these questions, an inbred Hereford cattle population of 785 animals genotyped for 30,220 SNPs was used. A search algorithm to approximate mutation loads was used to determine the minimum length of ROH segments. It consisted of finding genome segments with significant differences in trait means between animals with high and low autozygosity intervals at certain threshold values. The minimum length was around 1 Mb for weaning and yearling weights and ADG, and 2.5 Mb for birth weight. Using a model-based clustering algorithm, a mixture of three Gaussian distributions was clearly separable, resulting in three classes of short (< 6.16 Mb), medium (6.16–12.57 Mb), and long (>12.27 Mb) ROH segments, representing ancient, intermediate, and recent inbreeding. Contribution of ancient, intermediate and recent to genome-wide inbreeding was 37.4%, 40.1% and 22.5%, respectively. Inbreeding depression analyses showed a greater damaging effect of recent inbreeding, likely due to purging of old highly deleterious haplotypes.

scholarly journals Associations of autozygosity with a broad range of human phenotypes

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
David W Clark ◽  
Yukinori Okada ◽  
Kristjan H S Moore ◽  
Dan Mason ◽  
Nicola Pirastu ◽  
...  
Keyword(s):  
Reproductive Success ◽  
Inbreeding Depression ◽  
Social Factors ◽  
Genetic Variants ◽  
Runs Of Homozygosity ◽  
Sibling Pairs ◽  
Full Sibling ◽  
Inbreeding Coefficients ◽  
Genomic Inbreeding ◽  
Close Relatives

Abstract In many species, the offspring of related parents suffer reduced reproductive success, a phenomenon known as inbreeding depression. In humans, the importance of this effect has remained unclear, partly because reproduction between close relatives is both rare and frequently associated with confounding social factors. Here, using genomic inbreeding coefficients (FROH) for >1.4 million individuals, we show that FROH is significantly associated (p < 0.0005) with apparently deleterious changes in 32 out of 100 traits analysed. These changes are associated with runs of homozygosity (ROH), but not with common variant homozygosity, suggesting that genetic variants associated with inbreeding depression are predominantly rare. The effect on fertility is striking: FROH equivalent to the offspring of first cousins is associated with a 55% decrease [95% CI 44–66%] in the odds of having children. Finally, the effects of FROH are confirmed within full-sibling pairs, where the variation in FROH is independent of all environmental confounding.

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

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&lt; Fi ≤ 6.25, 6.25&lt; 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.

150 Runs of Homozygosity Analysis and their Possible Influence on Sperm Motility in Highly Consanguineous Bulls

2018 ◽  
Vol 30 (1) ◽  
pp. 215
Author(s):  
E. Terán ◽  
D. Goszczynski ◽  
A. Molina ◽  
P. Ross ◽  
J. Dorado ◽  
...  
Keyword(s):  
Sperm Motility ◽  
Inbreeding Depression ◽  
Sperm Quality ◽  
Average Length ◽  
Snp Array ◽  
Gene Clusters ◽  
Enrichment Score ◽  
Cattle Population ◽  
Runs Of Homozygosity ◽  
Pedigree Data

Inbreeding depression is associated with emergence of deleterious effects and loss of genetic variability. Widespread use of genotyping technologies and new approaches for identification of runs-of-homozygosity (ROH) provide valuable tools to better understand the effects of inbreeding depression. We have previously demonstrated that inbreeding affects sperm motility patterns in cattle (Dorado et al. 2016 Reprod. Fertil. Dev. 29, 712-720; 10.1071/RD15324), with an increase in individuals presenting a hyperactivated-like motility. In this study, we characterised ROH patterns and performed gene ontology analysis of a large, highly consanguineous cattle population. Thirty-three Retinta bulls [average inbreeding percentage FPED = 16.57% (10.25 to 30.62%)] were genotyped using the Axiom® BOS 1 High-Density SNP Array (Thermo Fisher Scientific, Waltham, MA, USA). The ROH were estimated using CGATOH package and classified upon their length into 5 categories: 1-2, 2-4, 4-8, 8-16, and >16 Mb, which are inversely related to inbreeding events occurring 50 to 3 generations before, respectively. The ROH showed an average length of 3.73 Mb (1.48 to 6.71 Mb). Total FROH was partially explained by the increase in ROH fragments longer than 8 Mb, which is consistent with recent inbreeding events that occurred in this population in the last 6 generations. Additionally, the distribution of ROH varied notably between chromosomes. For instance, >16 Mb runs (very recent inbreeding event) were absent in BTA26 and BTA29, whereas certain loci on BTA7, BTA13, and BTA24 showed >16 Mb runs in 9 animals. To identify candidate biological functions affected by inbreeding, we performed functional analysis of the genome areas covered by ROH >8 Mb (our pedigree data covered 5.87 equivalent complete generations) using the Functional Annotation Clustering tool implemented in DAVID. Candidate regions were defined by occurring in ROH >8 in more than 6 animals and by a distance <1 Mb between adjacent single nucleotide polymorphisms. Eight significant gene clusters (enrichment score >1.30; P < 0.05) were identified, with 2 of these clusters related to sperm motility. One of these clusters (score 1.72) contained 23 genes coding microtubule-related proteins, which are associated with cellular movement structures such as flagella. The other cluster (score 1.42), included 4 genes related to dynein and motile cilium assembly ATPase complexes, associated with movement of eukaryotic flagella. We observed an additional cluster representing an ATP-binding feature, which included 77 genes (score 1.43). These results indicate that inbreeding could affect sperm motility by altering microtubule structure and motility. However, the fact that ROH were unevenly distributed across the genome, even in a highly inbred cattle population, also suggests that different metabolic pathways could be affected in individuals with similar inbreeding values. Therefore, the use of inbreeding coefficients as predictors for sperm quality should be approached carefully.

scholarly journals Effect of inbreeding on lean meat percentage and average daily gain in Hungarian Landrace pigs

2008 ◽  
Vol 51 (6) ◽  
pp. 541-548
Author(s):  
Z. Vígh ◽  
P. Gyovai ◽  
L. Csató ◽  
Á. Bokor ◽  
J. Farkas ◽  
...  
Keyword(s):  
Inbreeding Depression ◽  
Model Comparison ◽  
Mean Squared Error ◽  
Average Daily Gain ◽  
Lean Meat ◽  
Inbreeding Coefficients ◽  
Squared Error ◽  
Near Future ◽  
Best Fit ◽  
Daily Gain

Abstract. Pedigree and field test data – collected between 1994–2005 – were analyzed in a group of 132,548 Hungarian Landrace pigs. The analysed traits were average daily gain (ADG) and lean meat percentage (LMP). In the present study inbreeding coefficients, pedigree completeness (complete generation equivalents) and inbreeding depression for ADG and LMP were estimated. Increasing the number of generations that were considered in the pedigree the estimated inbreeding coefficients did not change after the 5th generation, but pedigree completeness was continuously increased. The estimated inbreeding depression for ADG and LMP were different applying 40 different models but the magnitude of the differences was small. The model comparison showed that the models containing litter and year-month effects had the best fit (smallest mean squared error). Increasing the inbreeding coefficient by 10 % decreased ADG by 4.01 g and practically did not affect LMP (0.003 %). It can be concluded that the estimated inbreeding depression was small and substantial depression can not be expected in the near future. However, the low level of inbreeding of the studied population can partly be explained by the short pedigrees. This suggests that Hungarian pig breeders may often import breeding animals or carry out herd replacements rather than applying continuous within group selection.

scholarly journals Correlation of Genomic and Pedigree Inbreeding Coefficients in Small Cattle Populations

Animals ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 3234
Author(s):  
José Cortes-Hernández ◽  
Adriana García-Ruiz ◽  
Carlos Gustavo Vásquez-Peláez ◽  
Felipe de Jesus Ruiz-Lopez
Keyword(s):  
Inbreeding Coefficient ◽  
Pedigree Information ◽  
Genomic Relationship Matrix ◽  
Relationship Matrix ◽  
Genomic Relationship ◽  
Runs Of Homozygosity ◽  
Inbreeding Coefficients ◽  
Improvement Programs ◽  
Genomic Inbreeding ◽  
Holstein Population

This study aimed to identify inbreeding coefficient (F) estimators useful for improvement programs in a small Holstein population through the evaluation of different methodologies in the Mexican Holstein population. F was estimated as follows: (a) from pedigree information (Fped); (b) through runs of homozygosity (Froh); (c) from the number of observed and expected homozygotic SNP in the individuals (Fgeno); (d) through the genomic relationship matrix (Fmg). The study included information from 4277 animals with pedigree records and 100,806 SNP. The average and standard deviation values of F were 3.11 ± 2.30 for Fped, −0.02 ± 3.55 for Fgeno, 2.77 ± 0.71 for Froh and 3.03 ± 3.05 for Fmg. The correlations between coefficients varied from 0.30 between Fped and Froh, to 0.96 between Fgeno and Fmg. Differences in the level of inbreeding among the parent’s country of origin were found regardless of the method used. The correlations among genomic inbreeding coefficients were high; however, they were low with Fped, so further research on this topic is required.

Additional nutritional considerations for preconditioning beef calves.

EDIS ◽  
2017 ◽  
Vol 2017 (4) ◽  
Author(s):  
Philipe Moriel
Keyword(s):  
Average Daily Gain ◽  
Beef Steers ◽  
Labor Costs ◽  
Vaccine Response ◽  
Negative Effects ◽  
Beef Calves ◽  
Supplemental Feed ◽  
Concentrate Supplementation ◽  
Protein Supply ◽  
Daily Gain

Calves can be preconditioned using a wide variety of supplemental feed ingredients. However, feed ingredient selection is not the only factor to consider during a preconditioning process. Increasing the protein supply to stressed, preconditioning beef steers led to greater growth performance, and increased immune response to vaccination during a 42-day preconditioning period. Producers should not reduce the frequency of concentrate supplementation during the entire preconditioning period as it might lead to poorer vaccine response and average daily gain (consequently, less calf value at sale). However, a gradual reduction of frequency of supplementation is a supplementation strategy that can overcome these negative effects on growth and immunity, and allows producers to save on feeding and labor costs without producing lighter calves that have weaker immune responses.  

scholarly journals Grid search approach to discriminate between old and recent inbreeding using phenotypic, pedigree and genomic information

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Pattarapol Sumreddee ◽  
El Hamidi Hay ◽  
Sajjad Toghiani ◽  
Andrew Roberts ◽  
Samuel E. Aggrey ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Growth Traits ◽  
Average Daily Gain ◽  
Recent Common Ancestor ◽  
Pedigree Information ◽  
Grid Search ◽  
Genomic Information ◽  
The Impact ◽  
Daily Gain ◽  
Harmful Effects

Abstract Background Although inbreeding caused by the mating of animals related through a recent common ancestor is expected to have more harmful effects on phenotypes than ancient inbreeding (old inbreeding), estimating these effects requires a clear definition of recent (new) and ancient (old) inbreeding. Several methods have been proposed to classify inbreeding using pedigree and genomic data. Unfortunately, these methods are largely based on heuristic criteria such as the number of generations from a common ancestor or length of runs of homozygosity (ROH) segments. To mitigate these deficiencies, this study aimed to develop a method to classify pedigree and genomic inbreeding into recent and ancient classes based on a grid search algorithm driven by the assumption that new inbreeding tends to have a more pronounced detrimental effect on traits. The proposed method was tested using a cattle population characterized by a deep pedigree. Results Effects of recent and ancient inbreeding were assessed on four growth traits (birth, weaning and yearling weights and average daily gain). Thresholds to classify inbreeding into recent and ancient classes were trait-specific and varied across traits and sources of information. Using pedigree information, inbreeding generated in the last 10 to 11 generations was considered as recent. When genomic information (ROH) was used, thresholds ranged between four to seven generations, indicating, in part, the ability of ROH segments to characterize the harmful effects of inbreeding in shorter periods of time. Nevertheless, using the proposed classification method, the discrimination between new and old inbreeding was less robust when ROH segments were used compared to pedigree. Using several model comparison criteria, the proposed approach was generally better than existing methods. Recent inbreeding appeared to be more harmful across the growth traits analyzed. However, both new and old inbreeding were found to be associated with decreased yearling weight and average daily gain. Conclusions The proposed method provided a more objective quantitative approach for the classification of inbreeding. The proposed method detected a clear divergence in the effects of old and recent inbreeding using pedigree data and it was superior to existing methods for all analyzed traits. Using ROH data, the discrimination between old and recent inbreeding was less clear and the proposed method was superior to existing approaches for two out of the four analyzed traits. Deleterious effects of recent inbreeding were detected sooner (fewer generations) using genomic information than pedigree. Difference in the results using genomic and pedigree information could be due to the dissimilarity in the number of generations to a common ancestor. Additionally, the uncertainty associated with the identification of ROH segments and associated inbreeding could have an effect on the results. Potential biases in the estimation of inbreeding effects may occur when new and old inbreeding are discriminated based on arbitrary thresholds. To minimize the impact of inbreeding, mating designs should take the different inbreeding origins into consideration.

scholarly journals Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Jingru Zhou ◽  
Yingping Zhuang ◽  
Jianye Xia
Keyword(s):  
Aspergillus Niger ◽  
Large Scale ◽  
Measurement Techniques ◽  
Metabolic Model ◽  
System Level ◽  
Metabolic Phenotype ◽  
Omics Data ◽  
Prediction Ability ◽  
Phenotype Prediction ◽  
Genome Scale

Abstract Background Genome-scale metabolic model (GSMM) is a powerful tool for the study of cellular metabolic characteristics. With the development of multi-omics measurement techniques in recent years, new methods that integrating multi-omics data into the GSMM show promising effects on the predicted results. It does not only improve the accuracy of phenotype prediction but also enhances the reliability of the model for simulating complex biochemical phenomena, which can promote theoretical breakthroughs for specific gene target identification or better understanding the cell metabolism on the system level. Results Based on the basic GSMM model iHL1210 of Aspergillus niger, we integrated large-scale enzyme kinetics and proteomics data to establish a GSMM based on enzyme constraints, termed a GEM with Enzymatic Constraints using Kinetic and Omics data (GECKO). The results show that enzyme constraints effectively improve the model’s phenotype prediction ability, and extended the model’s potential to guide target gene identification through predicting metabolic phenotype changes of A. niger by simulating gene knockout. In addition, enzyme constraints significantly reduced the solution space of the model, i.e., flux variability over 40.10% metabolic reactions were significantly reduced. The new model showed also versatility in other aspects, like estimating large-scale $$k_{{cat}}$$ k cat values, predicting the differential expression of enzymes under different growth conditions. Conclusions This study shows that incorporating enzymes’ abundance information into GSMM is very effective for improving model performance with A. niger. Enzyme-constrained model can be used as a powerful tool for predicting the metabolic phenotype of A. niger by incorporating proteome data. In the foreseeable future, with the fast development of measurement techniques, and more precise and rich proteomics quantitative data being obtained for A. niger, the enzyme-constrained GSMM model will show greater application space on the system level.

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