A heuristic method to identify runs of homozygosity associated with reduced performance in livestock

Detection and evaluation of parameters influencing the identification of heterozygous-enriched regions in Holstein cattle based on SNP chip or whole-genome sequence data

BACKGROUND

A heterozygous-enriched region (HER) is a genomic region with high variability generated by factors such as balancing selection, introgression, and admixture processes. In this study, we evaluated the genomic background of HERs and the impact of different parameters (i.e., minimum number of SNPs in a HER, maximum distance between two consecutive SNPs, minimum length of a HER, maximum number of homozygous allowed in a HER) and scenarios [i.e., different SNP panel densities and whole-genome sequence (WGS)] on the detection of HERs. We also compared HERs characterized in Holstein cattle with those identified in Angus, Jersey, and Norwegian Red cattle using WGS data.

RESULTS

The parameters used for the identification of HERs significantly impact their detection. The maximum distance between two consecutive SNPs did not impact HERs detection as the same average of HERs (269.31 ± 787.00) was observed across scenarios. However, the minimum number of markers, maximum homozygous markers allowed inside a HER, and the minimum length size impacted HERs detection. For the minimum length size, the 10 Kb scenario showed the highest average number of HERs (1,364.69 ± 1,483.64). The number of HERs decreased as the minimum number of markers increased (621.31 ± 1,271.83 to 6.08 ± 21.94), and an opposite pattern was observed for the maximum homozygous markers allowed inside a HER (54.47 ± 195.51 to 494.89 ± 1,169.35). Forty-five HER islands located in 23 chromosomes with high Tajima's D values and differential among the observed and estimated heterozygosity were detected in all evaluated scenarios, indicating their ability to potentially detect regions under balancing selection. In total, 3,440 markers and 28 genes previously related to fertility (e.g., TP63, ZSCAN23, NEK5, ARHGAP44), immunity (e.g., TP63, IGC, ARHGAP44), residual feed intake (e.g., MAYO9A), stress sensitivity (e.g., SERPINA6), and milk fat percentage (e.g., NOL4) were identified. When comparing HER islands among breeds, there were substantial overlaps between Holstein with Angus (95.3%), Jersey (94.3%), and Norwegian Red cattle (97.1%), indicating conserved HER across taurine breeds.

CONCLUSIONS

The detection of HERs varied according to the parameters used, but some HERs were consistently identified across all scenarios. Heterozygous genotypes observed across generations and breeds appear to be conserved in HERs. The results presented could serve as a guide for defining HERs detection parameters and further investigating their biological roles in future studies.

Effect of Individual Rate of Inbreeding, Recent and Ancestral Inbreeding on Wool Quality, Muscling Conformation and Exterior in German Sheep Breeds

This study provides comprehensive results on the current status of inbreeding depression for traits upon which sheep are selected for the herdbook in Germany. A total of 30 sheep breeds from the OviCap national database met the inclusion criteria for the present analysis regarding the depth and completeness of pedigrees and the number of animals with phenotypic data. We analyzed heritabilities and inbreeding depression for the three breeding objective traits of wool quality, muscling conformation and exterior. Heritabilities were across all breeds of moderate size, with estimates of 0.18 for wool quality and muscling conformation and of 0.14 for exterior. The models employed to estimate linear regression slopes for individual and ancestral inbreeding rates also account for non-genetic effects and the additive genetic effect of the animal. Inbreeding depression was obvious for all three traits when we averaged the estimates across all 30 sheep breeds. Inbreeding depression was significant for wool quality for only a few breeds, whereas for muscling conformation, 14/30 breeds achieved significant estimates. A 1% increase in inbreeding decreased the mean of all three traits across all sheep breeds by 0.33% of their standard deviation. Positive effects due to ancestral inbreeding were only significant in very few breeds in the different traits. Across all 30 sheep breeds, there were indications that purging effects (a reduction in negative effects of inbreeding depression due to selection for heterozygotes) may play a role for the exterior. The results of this study should help for reviewing breeding programs, particularly for sheep breeds with critical effective population sizes and increasing rates of inbreeding, with regard to the selection policy and selection intensity applied.

Genomic Scanning of Inbreeding Depression for Litter Size in Two Varieties of Iberian Pigs

Inbreeding depression is expected to be more pronounced in fitness-related traits, such as pig litter size. Recent studies have suggested that the genetic determinism of inbreeding depression may be heterogeneous across the genome. Therefore, the objective of this study was to conduct a genomic scan of the whole pig autosomal genome to detect the genomic regions that control inbreeding depression for litter size in two varieties of Iberian pigs (Entrepelado and Retinto). The datasets consisted of 2069 (338 sows) and 2028 (327 sows) records of litter size (Total Number Born and Number Born Alive) for the Entrepelado and Retinto varieties. All sows were genotyped using the Geneseek GGP PorcineHD 70 K chip. We employed the Unfavorable Haplotype Finder software to extract runs of homozygosity (ROHs) and conducted a mixed-model analysis to identify highly significant differences between homozygous and heterozygous sows for each specific ROH. A total of eight genomic regions located on SSC2, SSC5, SSC7, SSC8, and SSC13 were significantly associated with inbreeding depression, housing some relevant genes such as FSHR, LHCGR, CORIN, AQP6, and CEP120.

Identification of Homozygous Regions With Adverse Effects on the Five Economic Traits of Duroc Pigs

Runs of homozygosity (ROH) are widely used to estimate genomic inbreeding, which is linked to inbreeding depression on phenotypes. However, the adverse effects of specific homozygous regions on phenotypic characteristics are rarely studied in livestock. In this study, the 50 K SNP data of 3,770 S21 Duroc (American origin) and 2,096 S22 Duroc (Canadian origin) pigs were used to investigate the harmful ROH regions on five economic traits. The results showed that the two Duroc lines had different numbers and distributions of unfavorable ROHs, which may be related to the different selection directions and intensities between the two lines. A total of 114 and 58 ROH segments were found with significant adverse effects on the economic traits of S21 and S22 pigs, respectively. Serval pleiotropic ROHs were detected to reduce two or multiple phenotypic performances in two Duroc populations. Candidate genes in these shared regions were mainly related to growth, fertility, immunity, and fat deposition. We also observed that some ROH genotypes may cause opposite effects on different traits. This study not only enhances our understanding of the adverse effects of ROH on phenotypes, but also indicates that ROH information could be incorporated into breeding programs to estimate and control the detrimental effects of homozygous regions.

Fine-Scale Analysis of Runs of Homozygosity Islands Affecting Fertility in Mares

The loss of genetic variability in livestock populations bred under strict selection processes is a growing concern, as it may lead to increased inbreeding values and lower fertility, as a consequence of the “inbreeding depression” effect. This is particularly important in horses, where inbreeding levels tend to rise as individuals become more and more closely related. In this study, we evaluated the effect of increased inbreeding levels on mare fertility by combining an SNP-based genomic approach using runs of homozygosity and the estimation of genetic breeding values for reproductive traits in a large population of Pura Raza Española mares. Our results showed a negative correlation between whole-genome homozygosity and fertility estimated breeding values (EBVs) at the genome level (ρ = −0.144). However, the analysis at chromosome level revealed a wide variability, with some chromosomes showing higher correlations than others. Interestingly, the correlation was stronger (−0.241) when we repeated the analysis in a reduced dataset including the 10% most and least fertile individuals, where the latter showed an increase in average inbreeding values (F_ROH) of around 30%. We also found 41 genomic regions (ROHi, runs of homozygosity islands) where homozygosity increased 100-fold, 13 of which were significantly associated with fertility after cross-validation. These regions encompassed 17 candidate genes previously related to oocyte and embryo development in several species. Overall, we demonstrated the relationship between increased homozygosis at the genomic level and fertility in mares. Our findings may help to deal with the occurrence of inbreeding depression, as well as further our understanding of the mechanisms underlying fertility in mares.

Genomic Prediction Methods Accounting for Nonadditive Genetic Effects

The use of genomic information for prediction of future phenotypes or breeding values for the candidates to selection has become a standard over the last decade. However, most procedures for genomic prediction only consider the additive (or substitution) effects associated with polymorphic markers. Nevertheless, the implementation of models that consider nonadditive genetic variation may be interesting because they (1) may increase the ability of prediction, (2) can be used to define mate allocation procedures in plant and animal breeding schemes, and (3) can be used to benefit from nonadditive genetic variation in crossbreeding or purebred breeding schemes. This study reviews the available methods for incorporating nonadditive effects into genomic prediction procedures and their potential applications in predicting future phenotypic performance, mate allocation, and crossbred and purebred selection. Finally, a brief outline of some future research lines is also proposed.

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

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.

Identification of unique ROH regions with unfavorable effects on production and fertility traits in Canadian Holsteins

Background

The advent of genomic information and the reduction in the cost of genotyping have led to the use of genomic information to estimate genomic inbreeding as an alternative to pedigree inbreeding. Using genomic measures, effects of genomic inbreeding on production and fertility traits have been observed. However, there have been limited studies on the specific genomic regions causing the observed negative association with the trait of interest. Our aim was to identify unique run of homozygosity (ROH) genotypes present within a given genomic window that display negative associations with production and fertility traits and to quantify the effects of these identified ROH genotypes.

Methods

In total, 50,575 genotypes based on a 50K single nucleotide polymorphism (SNP) array and 259,871 pedigree records were available. Of these 50,575 genotypes, 46,430 cows with phenotypic records for production and fertility traits and having a first calving date between 2008 and 2018 were available. Unique ROH genotypes identified using a sliding-window approach were fitted into an animal mixed model as fixed effects to determine their effect on production and fertility traits.

Results

In total, 133 and 34 unique ROH genotypes with unfavorable effects were identified for production and fertility traits, respectively, at a 1% genome-wise false discovery rate. Most of these ROH regions were located on bovine chromosomes 8, 13, 14 and 19 for both production and fertility traits. For production traits, the average of all the unfavorably identified unique ROH genotypes effects were estimated to decrease milk yield by 247.30 kg, fat yield by 11.46 kg and protein yield by 8.11 kg. Similarly, for fertility traits, an average 4.81-day extension in first service to conception, a 0.16 increase in number of services, and a − 0.07 incidence in 56-day non-return rate were observed. Furthermore, a ROH region located on bovine chromosome 19 was identified that, when homozygous, had a negative effect on production traits. Signatures of selection proximate to this region have implicated GH1 as a potential candidate gene, which encodes the growth hormone that binds the growth hormone receptor. This observed negative effect could be a consequence of unfavorable alleles in linkage disequilibrium with favorable alleles.

Conclusions

ROH genotypes with unfavorable effects on production and fertility traits were identified within and across multiple traits on most chromosomes. These identified ROH genotypes could be included in mate selection programs to minimize their frequency in future generations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-021-00660-z.

How Depressing Is Inbreeding? A Meta-Analysis of 30 Years of Research on the Effects of Inbreeding in Livestock

Inbreeding depression has been widely documented for livestock and other animal and plant populations. Inbreeding is generally expected to have a stronger unfavorable effect on fitness traits than on other traits. Traditionally, the degree of inbreeding depression in livestock has been estimated as the slope of the linear regression of phenotypic values on pedigree-based inbreeding coefficients. With the increasing availability of SNP-data, pedigree inbreeding can now be replaced by SNP-based measures. We performed a meta-analysis of 154 studies, published from 1990 to 2020 on seven livestock species, and compared the degree of inbreeding depression (1) across different trait groups, and (2) across different pedigree-based and SNP-based measures of inbreeding. Across all studies and traits, a 1% increase in pedigree inbreeding was associated with a median decrease in phenotypic value of 0.13% of a trait’s mean, or 0.59% of a trait’s standard deviation. Inbreeding had an unfavorable effect on all sorts of traits and there was no evidence for a stronger effect on primary fitness traits (e.g., reproduction/survival traits) than on other traits (e.g., production traits or morphological traits). p-values of inbreeding depression estimates were smaller for SNP-based inbreeding measures than for pedigree inbreeding, suggesting more power for SNP-based measures. There were no consistent differences in p-values for percentage of homozygous SNPs, inbreeding based on runs of homozygosity (ROH) or inbreeding based on a genomic relationship matrix. The number of studies that directly compares these different measures, however, is limited and comparisons are furthermore complicated by differences in scale and arbitrary definitions of particularly ROH-based inbreeding. To facilitate comparisons across studies in future, we provide the dataset with inbreeding depression estimates of 154 studies and stress the importance of always reporting detailed information (on traits, inbreeding coefficients, and models used) along with inbreeding depression estimates.

Inbreeding depression across the genome of Dutch Holstein Friesian dairy cattle

BACKGROUND

Inbreeding depression refers to the decrease in mean performance due to inbreeding. Inbreeding depression is caused by an increase in homozygosity and reduced expression of (on average) favourable dominance effects. Dominance effects and allele frequencies differ across loci, and consequently inbreeding depression is expected to differ along the genome. In this study, we investigated differences in inbreeding depression across the genome of Dutch Holstein Friesian cattle, by estimating dominance effects and effects of regions of homozygosity (ROH).

METHODS

Genotype (75 k) and phenotype data of 38,792 cows were used. For nine yield, fertility and udder health traits, GREML models were run to estimate genome-wide inbreeding depression and estimate additive, dominance and ROH variance components. For this purpose, we introduced a ROH-based relationship matrix. Additive, dominance and ROH effects per SNP were obtained through back-solving. In addition, a single SNP GWAS was performed to identify significant additive, dominance or ROH associations.

RESULTS

Genome-wide inbreeding depression was observed for all yield, fertility and udder health traits. For example, a 1% increase in genome-wide homozygosity was associated with a decrease in 305-d milk yield of approximately 99 kg. For yield traits only, including dominance and ROH effects in the GREML model resulted in a better fit (P < 0.05) than a model with only additive effects. After correcting for the effect of genome-wide homozygosity, dominance and ROH variance explained less than 1% of the phenotypic variance for all traits. Furthermore, dominance and ROH effects were distributed evenly along the genome. The most notable region with a favourable dominance effect for yield traits was on chromosome 5, but overall few regions with large favourable dominance effects and significant dominance associations were detected. No significant ROH-associations were found.

CONCLUSIONS

Inbreeding depression was distributed quite equally along the genome and was well captured by genome-wide homozygosity. These findings suggest that, based on 75 k SNP data, there is little benefit of accounting for region-specific inbreeding depression in selection schemes.

The usage of Mate Select, a web-based selection tool for pedigree dogs for promoting sustainable breeding

BACKGROUND

Inbreeding is a phenomenon that accumulates through the mating of relatives within closed populations, such as pedigree dog breeds, and results in reduced genetic variation within breeds, and may lead to poorer health and fertility from inbreeding depression. The impact of inbreeding is driven by the selection and mating of parents, but information on choices to reduce inbreeding is difficult to assess for individual breeders. Tools to inform dog breeders on the current state of the inbreeding and the relationships among possible parents are potentially useful for providing guidance towards choices that are more beneficial to the breed. However, their utility depends on their usage and this study examines the usage of Mate Select, a web-based tool offered by The Kennel Club, covering 222 breeds for a period of 7 years following its launch in 2011.

RESULTS

The average usage was 2830 searches/week in 2012 with a slight fall of 2.2% per year (P < 0.001) to 2480 searches/week in 2018. Of these, 4% originated from outside the UK, across all continents except Antarctica, with the majority coming from English speaking countries. Searches/week showed a cyclical pattern with two cycles of 26.0 and 50.1 weeks. Since Mate Select's launch there has been a steady increase in searches from mobile devices, from 11% in 2012 to 43% in 2018. For the 197 breeds with at least 10 dams registered with the Kennel Club during the study period, there was a relationship between usage and registrations, with the average number of searches as a multiple of the number of dams increasing from 2 to 10 for breeds with up to 70 dams and declining towards 2 again for the largest breeds with approximately 20,000 registered dams. However, there remained substantial variation among breeds of similar size, and breeds for which EBVs had become available during the study period had a 2.46 fold greater frequency of searches per registered bitch (P < 0.001), but this was not linked directly to the publication of EBVs.

CONCLUSIONS

Mate Select has sustained and substantial usage, although there is also substantial variation in usage among breeds, which offers an opportunity to develop further guidance.

Symposium review: Exploiting homozygosity in the era of genomics-Selection, inbreeding, and mating programs

The advent of genomic selection paved the way for an unprecedented acceleration in genetic progress. The increased ability to select superior individuals has been coupled with a drastic reduction in the generation interval for most dairy populations, representing both an opportunity and a challenge. Homozygosity is now rapidly accumulating in dairy populations. Currently, inbreeding depression is managed mostly by culling at the farm level and by controlling the overall accumulation of homozygosity at the population level. A better understanding of how homozygosity and recessive load are related will guarantee continued genetic improvement while curtailing the accumulation of harmful recessives and maintaining enough genetic variability to ensure the possibility of selection in the face of changing environmental conditions. In this review, we present a snapshot of the current dairy selection structure as it relates to response to selection and accumulation of homozygosity, briefly outline the main approaches currently used to manage inbreeding and overall variability, and present some approaches that can be used in the short term to control accumulation of harmful recessives while maintaining sustained selection pressure.

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.