Networks of inbreeding coefficients in a selected population of rabbits

Ballou's Ancestral Inbreeding Coefficient: Formulation and New Estimate with Higher Reliability

Inbreeding is unavoidable in small populations. However, the deleterious effects of inbreeding on fitness-related traits (inbreeding depression) may not be an inevitable phenomenon, since deleterious recessive alleles causing inbreeding depression might be purged from populations through inbreeding and selection. Inbreeding purging has been of great interest in conservation biology and animal breeding, because populations manifesting lower inbreeding depression could be created even with a small number of breeding animals, if inbreeding purging exists. To date, many studies intending to detect inbreeding purging in captive and domesticated animal populations have been carried out using pedigree analysis. Ballou's ancestral inbreeding coefficient (FBAL-ANC) is one of the most widely used measurements to detect inbreeding purging, but the theoretical basis for FBAL-ANC has not been fully established. In most of the published works, estimates from stochastic simulation (gene-dropping simulation) have been used. In this report, the author provides a mathematical basis for FBAL-ANC and proposes a new estimate by hybridizing stochastic and deterministic computation processes. A stochastic simulation suggests that the proposed method could considerably reduce the variance of estimates, compared to ordinary gene-dropping simulation, in which whole gene transmissions in a pedigree are stochastically determined. The favorable property of the proposed method results from the bypass of a part of the stochastic process in the ordinary gene-dropping simulation. Using the proposed method, the reliability of the estimates of FBAL-ANC could be remarkably enhanced. The relationship between FBAL-ANC and other pedigree-based parameters is also discussed.

A comparison of marker-based estimators of inbreeding and inbreeding depression

BACKGROUND

The availability of genome-wide marker data allows estimation of inbreeding coefficients (F, the probability of identity-by-descent, IBD) and, in turn, estimation of the rate of inbreeding depression (ΔID). We investigated, by computer simulations, the accuracy of the most popular estimators of inbreeding based on molecular markers when computing F and ΔID in populations under random mating, equalization of parental contributions, and artificially selected populations. We assessed estimators described by Li and Horvitz (F_LH1 and F_LH2), VanRaden (F_VR1 and F_VR2), Yang and colleagues (F_YA1 and F_YA2), marker homozygosity (F_HOM), runs of homozygosity (F_ROH) and estimates based on pedigree (F_PED) in comparison with estimates obtained from IBD measures (F_IBD).

RESULTS

If the allele frequencies of a base population taken as a reference for the computation of inbreeding are known, all estimators based on marker allele frequencies are highly correlated with F_IBD and provide accurate estimates of the mean ΔID. If base population allele frequencies are unknown and current frequencies are used in the estimations, the largest correlation with F_IBD is generally obtained by F_LH1 and the best estimator of ΔID is F_YA2. The estimators F_VR2 and F_LH2 have the poorest performance in most scenarios. The assumption that base population allele frequencies are equal to 0.5 results in very biased estimates of the average inbreeding coefficient but they are highly correlated with F_IBD and give relatively good estimates of ΔID. Estimates obtained directly from marker homozygosity (F_HOM) substantially overestimated ΔID. Estimates based on runs of homozygosity (F_ROH) provide accurate estimates of inbreeding and ΔID. Finally, estimates based on pedigree (F_PED) show a lower correlation with F_IBD than molecular estimators but provide rather accurate estimates of ΔID. An analysis of data from a pig population supports the main findings of the simulations.

CONCLUSIONS

When base population allele frequencies are known, all marker-allele frequency-based estimators of inbreeding coefficients generally show a high correlation with F_IBD and provide good estimates of ΔID. When base population allele frequencies are unknown, F_LH1 is the marker frequency-based estimator that is most correlated with F_IBD, and F_YA2 provides the most accurate estimates of ΔID. Estimates from F_ROH are also very precise in most scenarios. The estimators F_VR2 and F_LH2 have the poorest performances.

Comparative analysis of genomic inbreeding parameters and runs of homozygosity islands in several fancy and meat rabbit breeds

Runs of homozygosity (ROH) are defined as long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROH and their length are indicators of the level and origin of inbreeding. In this study, we analysed SNP chip datasets (obtained using the Axiom OrcunSNP Array) of a total of 702 rabbits from 12 fancy breeds and four meat breeds to identify ROH with different approaches and calculate several genomic inbreeding parameters. The highest average number of ROH per animal was detected in Belgian Hare (~150) and the lowest in Italian Silver (~106). The average length of ROH ranged from 4.001 ± 0.556 Mb in Italian White to 6.268 ± 1.355 Mb in Ermine. The same two breeds had the lowest (427.9 ± 86.4 Mb, Italian White) and the highest (921.3 ± 179.8 Mb, Ermine) average values of the sum of all ROH segments. More fancy breeds had a higher level of genomic inbreeding (as defined by ROH) than meat breeds. Several ROH islands contain genes involved in body size, body length, pigmentation processes, carcass traits, growth, and reproduction traits (e.g.: AOX1, GPX5, IFRD1, ITGB8, NELL1, NR3C1, OCA2, TRIB1, TRIB2). Genomic inbreeding parameters can be useful to overcome the lack of information in the management of rabbit genetic resources. ROH provided information to understand, to some extent, the genetic history of rabbit breeds and to identify signatures of selection in the rabbit genome.

Fine-tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book: the case of the Pura Raza Española horse

BACKGROUND

Estimating inbreeding, which is omnipresent and inevitable in livestock populations, is a primary goal for management and animal breeding especially for those interested in mitigating the negative consequences of inbreeding. Inbreeding coefficients have been historically estimated by using pedigree information; however, over the last decade, genome-base inbreeding coefficients have come to the forefront in this field. The Pura Raza Española (PRE) horse is an autochthonous Spanish horse breed which has been recognised since 1912. The total PRE population (344,718 horses) was used to estimate Classical (F), Ballou's ancestral, Kalinowski's ancestral, Kalinowski's new and the ancestral history coefficient values. In addition, genotypic data from a selected population of 805 PRE individuals was used to determine the individual inbreeding coefficient using SNP-by-SNP-based techniques (methods of moments -F_HOM-, the diagonal elements of the genomic -F_G-, and hybrid matrixes -F_H-) and ROH measures (F_RZ). The analyse of both pedigree and genomic based inbreeding coefficients in a large and robust population such as the PRE horse, with proven parenteral information for the last 40 years and a high degree of completeness (over 90% for the last 70 years) will allow us to understand PRE genetic variability better and the correlations between the estimations will give the data greater reliability.

RESULTS

The mean values of the pedigree-based inbreeding coefficients ranged from 0.01 (F for the last 3 generations -F3-) to 0.44 (ancestral history coefficient) and the mean values of genomic-based inbreeding coefficients varied from 0.05 (F_RZ for three generations, F_H and F_HOM) to 0.11 (F_RZ for nine generations). Significant correlations were also found between pedigree and genomic inbreeding values, which ranged between 0.58 (F3 with F_HOM) and 0.79 (F with F_RZ). In addition, the correlations between F_RZ estimated for the last 20 generations and the pedigree-based inbreeding highlight the fact that fewer generations of genomic data are required when comparing total inbreeding values, and the opposite when ancient values are calculated.

CONCLUSIONS

Ultimately, our results show that it is still useful to work with a deep and reliable pedigree in pedigree-based genetic studies with very large effective population sizes. Obtaining a satisfactory parameter will always be desirable, but the approximation obtained with a robust pedigree will allow us to work more efficiently and economically than with massive genotyping.

Trends in genetic diversity and the effect of inbreeding in American Angus cattle under genomic selection

Background

While the adoption of genomic evaluations in livestock has increased genetic gain rates, its effects on genetic diversity and accumulation of inbreeding have raised concerns in cattle populations. Increased inbreeding may affect fitness and decrease the mean performance for economically important traits, such as fertility and growth in beef cattle, with the age of inbreeding having a possible effect on the magnitude of inbreeding depression. The purpose of this study was to determine changes in genetic diversity as a result of the implementation of genomic selection in Angus cattle and quantify potential inbreeding depression effects of total pedigree and genomic inbreeding, and also to investigate the impact of recent and ancient inbreeding.

Results

We found that the yearly rate of inbreeding accumulation remained similar in sires and decreased significantly in dams since the implementation of genomic selection. Other measures such as effective population size and the effective number of chromosome segments show little evidence of a detrimental effect of using genomic selection strategies on the genetic diversity of beef cattle. We also quantified pedigree and genomic inbreeding depression for fertility and growth. While inbreeding did not affect fertility, an increase in pedigree or genomic inbreeding was associated with decreased birth weight, weaning weight, and post-weaning gain in both sexes. We also measured the impact of the age of inbreeding and found that recent inbreeding had a larger depressive effect on growth than ancient inbreeding.

Conclusions

In this study, we sought to quantify and understand the possible consequences of genomic selection on the genetic diversity of American Angus cattle. In both sires and dams, we found that, generally, genomic selection resulted in decreased rates of pedigree and genomic inbreeding accumulation and increased or sustained effective population sizes and number of independently segregating chromosome segments. We also found significant depressive effects of inbreeding accumulation on economically important growth traits, particularly with genomic and recent inbreeding.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-021-00644-z.