Intra-chromosomal estimates of inbreeding and coancestry in the Spanish Holstein cattle population

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.

The value of genomic relationship matrices to estimate levels of inbreeding

BACKGROUND

Genomic relationship matrices are used to obtain genomic inbreeding coefficients. However, there are several methodologies to compute these matrices and there is still an unresolved debate on which one provides the best estimate of inbreeding. In this study, we investigated measures of inbreeding obtained from five genomic matrices, including the Nejati-Javaremi allelic relationship matrix (FNEJ), the Li and Horvitz matrix based on excess of homozygosity (FL&H), and the VanRaden (methods 1, FVR1, and 2, FVR2) and Yang (FYAN) genomic relationship matrices. We derived expectations for each inbreeding coefficient, assuming a single locus model, and used these expectations to explain the patterns of the coefficients that were computed from thousands of single nucleotide polymorphism genotypes in a population of Iberian pigs.

RESULTS

Except for FNEJ, the evaluated measures of inbreeding do not match with the original definitions of inbreeding coefficient of Wright (correlation) or Malécot (probability). When inbreeding coefficients are interpreted as indicators of variability (heterozygosity) that was gained or lost relative to a base population, both FNEJ and FL&H led to sensible results but this was not the case for FVR1, FVR2 and FYAN. When variability has increased relative to the base, FVR1, FVR2 and FYAN can indicate that it decreased. In fact, based on FYAN, variability is not expected to increase. When variability has decreased, FVR1 and FVR2 can indicate that it has increased. Finally, these three coefficients can indicate that more variability than that present in the base population can be lost, which is also unreasonable. The patterns for these coefficients observed in the pig population were very different, following the derived expectations. As a consequence, the rate of inbreeding depression estimated based on these inbreeding coefficients differed not only in magnitude but also in sign.

CONCLUSIONS

Genomic inbreeding coefficients obtained from the diagonal elements of genomic matrices can lead to inconsistent results in terms of gain and loss of genetic variability and inbreeding depression estimates, and thus to misleading interpretations. Although these matrices have proven to be very efficient in increasing the accuracy of genomic predictions, they do not always provide a useful measure of inbreeding.

Identification of runs of homozygosity affecting female fertility and milk production traits in Finnish Ayrshire cattle

Inbreeding gives rise to continuous lengths of homozygous genotypes called runs of homozygosity (ROH) that occur when identical haplotypes are inherited from both parents. ROHs are enriched for deleterious recessive alleles and can therefore be linked to inbreeding depression, defined as decreased phenotypic performance of the animals. However, not all ROHs within a region are expected to have harmful effects on the trait of interest. We aimed to identify ROHs that unfavourably affect female fertility and milk production traits in the Finnish Ayrshire population. The estimated effect of ROHs with the highest statistical significance varied between parities from 9 to 17 days longer intervals from calving to first insemination, from 13 to 38 days longer intervals from first to last insemination and from 0.3 to 1.0 more insemination per conception. Similarly, for milk production traits ROHs were associated with a reduction of 208 kg for milk yield, 7 kg for protein yield and 16 kg for fat yield. We also found regions where ROHs displayed unfavourable effects across multiple traits. Our findings can be exploited for more efficient control of inbreeding depression, for example by minimizing the occurrence of unfavourable haplotypes as homozygous state in breeding programmes.

Trends in genome-wide and region-specific genetic diversity in the Dutch-Flemish Holstein-Friesian breeding program from 1986 to 2015

Background

In recent decades, Holstein–Friesian (HF) selection schemes have undergone profound changes, including the introduction of optimal contribution selection (OCS; around 2000), a major shift in breeding goal composition (around 2000) and the implementation of genomic selection (GS; around 2010). These changes are expected to have influenced genetic diversity trends. Our aim was to evaluate genome-wide and region-specific diversity in HF artificial insemination (AI) bulls in the Dutch-Flemish breeding program from 1986 to 2015.

Methods

Pedigree and genotype data (~ 75.5 k) of 6280 AI-bulls were used to estimate rates of genome-wide inbreeding and kinship and corresponding effective population sizes. Region-specific inbreeding trends were evaluated using regions of homozygosity (ROH). Changes in observed allele frequencies were compared to those expected under pure drift to identify putative regions under selection. We also investigated the direction of changes in allele frequency over time.

Results

Effective population size estimates for the 1986–2015 period ranged from 69 to 102. Two major breakpoints were observed in genome-wide inbreeding and kinship trends. Around 2000, inbreeding and kinship levels temporarily dropped. From 2010 onwards, they steeply increased, with pedigree-based, ROH-based and marker-based inbreeding rates as high as 1.8, 2.1 and 2.8% per generation, respectively. Accumulation of inbreeding varied substantially across the genome. A considerable fraction of markers showed changes in allele frequency that were greater than expected under pure drift. Putative selected regions harboured many quantitative trait loci (QTL) associated to a wide range of traits. In consecutive 5-year periods, allele frequencies changed more often in the same direction than in opposite directions, except when comparing the 1996–2000 and 2001–2005 periods.

Conclusions

Genome-wide and region-specific diversity trends reflect major changes in the Dutch-Flemish HF breeding program. Introduction of OCS and the shift in breeding goal were followed by a drop in inbreeding and kinship and a shift in the direction of changes in allele frequency. After introduction of GS, rates of inbreeding and kinship increased substantially while allele frequencies continued to change in the same direction as before GS. These results provide insight in the effect of breeding practices on genomic diversity and emphasize the need for efficient management of genetic diversity in GS schemes.

Electronic supplementary material

The online version of this article (10.1186/s12711-018-0385-y) contains supplementary material, which is available to authorized users.

Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep

Background

Because very large numbers of single nucleotide polymorphisms (SNPs) are now available throughout the genome, they are particularly suitable for the detection of genomic regions where a reduction in heterozygosity has occurred and they offer new opportunities to improve the accuracy of inbreeding (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$F$$\end{document}F) estimates. Runs of homozygosity (ROH) are contiguous lengths of homozygous segments of the genome where the two haplotypes inherited from the parents are identical. Here, we investigated the occurrence and distribution of ROH using a medium-dense SNP panel to characterize autozygosity in 516 Valle del Belice sheep and to identify the genomic regions with high ROH frequencies.

Results

We identified 11,629 ROH and all individuals displayed at least one ROH longer than 1 Mb. The mean value of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$F$$\end{document}F estimated from ROH longer than1 Mb was 0.084 ± 0.061. ROH that were shorter than 10 Mb predominated. The highest and lowest coverages of Ovis aries chromosomes (OAR) by ROH were on OAR24 and OAR1, respectively. The number of ROH per chromosome length displayed a specific pattern, with higher values for the first three chromosomes. Both number of ROH and length of the genome covered by ROH varied considerably between animals. Two hundred and thirty-nine SNPs were considered as candidate markers that may be under directional selection and we identified 107 potential candidate genes. Six genomic regions located on six chromosomes, corresponding to ROH islands, are presented as hotspots of autozygosity, which frequently coincided with regions of medium recombination rate. According to the KEGG database, most of these genes were involved in multiple signaling and signal transduction pathways in a wide variety of cellular and biochemical processes. A genome scan revealed the presence of ROH islands in genomic regions that harbor candidate genes for selection in response to environmental stress and which underlie local adaptation.

Conclusions

These results suggest that natural selection has, at least partially, a role in shaping the genome of Valle del Belice sheep and that ROH in the ovine genome may help to detect genomic regions involved in the determinism of traits under selection.

Electronic supplementary material

The online version of this article (10.1186/s12711-017-0360-z) contains supplementary material, which is available to authorized users.

Estimation of inbreeding depression on female fertility in the Finnish Ayrshire population

Single nucleotide polymorphism (SNP) data enable the estimation of inbreeding at the genome level. In this study, we estimated inbreeding levels for 19,075 Finnish Ayrshire cows genotyped with a low-density SNP panel (8K). The genotypes were imputed to 50K density, and after quality control, 39,144 SNPs remained for the analysis. Inbreeding coefficients were estimated for each animal based on the percentage of homozygous SNPs (F_PH ), runs of homozygosity (F_ROH ) and pedigree (F_PED ). Phenotypic records were available for 13,712 animals including non-return rate (NRR), number of inseminations (AIS) and interval from first to last insemination (IFL) for heifers and up to three parities for cows, as well as interval from calving to first insemination (ICF) for cows. Average F_PED was 0.02, F_ROH 0.06 and F_PH 0.63. A correlation of 0.71 was found between F_PED and F_ROH , 0.66 between F_PED and F_PH and 0.94 between F_ROH and F_PH . Pedigree-based inbreeding coefficients did not show inbreeding depression in any of the traits. However, when F_ROH or F_PH was used as a covariate, significant inbreeding depression was observed; a 10% increase in F_ROH was associated with 5 days longer IFL0 and IFL1, 2 weeks longer IFL3 and 3 days longer ICF2 compared to non-inbred cows.