Inbreeding depression due to recent and ancient inbreeding in Dutch Holstein-Friesian dairy cattle

Reproductive traits in Pura Raza Española mares manifest inbreeding depression from low levels of homozygosity

Inbreeding depression is a genetic phenomenon associated with the loss of fitness and mean phenotypic performance due to mating between relatives. Historically, inbreeding coefficients have been estimated from pedigree information. However, the onset of genomic selection programs provides large datasets of individuals genotyped using SNP arrays, enabling more precise assessment of an individual's genomic-level inbreeding using genomic data. One of the traits most sensitive to issues stemming from increased inbreeding is reproduction. This is particularly important in equine, in which fertility is only moderate compared to other livestock species. To explore this further, we evaluated the effect of inbreeding on five reproductive traits (age at first foaling (AFF), average interval between foalings (AIF), total number of foalings (NF), productive life (PL) and reproductive efficiency (RE)) in Pura Raza Español mares using genomic data. Residual predicted phenotypes were obtained by purging these traits through the REML (wgResidual) and ssGREML (gResidual) approaches in reproductive data of 29,847 PRE mares using the BLUPF90+ program. Next, we used pedigree-based (Fped) and ROH-based genomic (FROH) inbreeding coefficients derived from 1018 animals genotyped with 61,271 SNPs to estimate the inbreeding depression (linear regression). Our results indicated significant levels of inbreeding depression for all reproductive traits, with the exception of the AIF trait when Fped was used. However, all traits were negatively affected by the increase in genomic inbreeding, and FROH was found to capture more inbreeding depression than Fped. Likewise, REML models (ssGREML) using genomic data for estimated predicted residual phenotypes resulted in higher variance explained by the model compared with the models not using genomics (REML). Finally, a segmented regression analysis was conducted to evaluate the effect of inbreeding depression, revealing that the levels of genealogical and genomic homozygosity do not manifest uniformly in reproductive traits. In contrast, the levels of inbreeding depression ranged from low to high as homozygosity increased. This analysis also showed that reproductive traits are very sensitive to inbreeding depression, even with relatively low levels of homozygosity.

Impact of inbreeding on production, fertility, and health traits in German Holstein dairy cattle utilizing various inbreeding estimators

In dairy cattle production, it is important to understand how inbreeding affects production, fertility, and health traits. However, there is still limited use of genomic information to estimate inbreeding, despite advancements in genotyping technologies. To address this gap, we investigated the effect of inbreeding on German Holstein dairy cattle using both pedigree-based and genomic-based inbreeding estimators. We employed one method based on pedigree information (Fped) together with 6 genomic-based methods, including 3 genome-wide complex trait analysis software estimators (Fhat1, Fhat2, Fhat3), VanRaden's first method (FVR1, with observed allele frequencies, and FVR0.5, when allele frequencies are set to 0.5), and one based on runs of homozygosity (Froh). Data from 24,489 cows with both phenotypes and genotypes were used, with a pedigree including 232,780 animals born between 1970 and 2018. We analyzed the effects of inbreeding depression on production, fertility, and health traits separately, using single-trait linear animal models as well as threshold models to account for the binary nature of the health traits. For the health traits, we transformed solutions from the liability scale to a probability scale for easier interpretation. Our results showed that the mean inbreeding coefficients from all estimators ranged from -0.003 to 0.243, with negative values observed for most genomic-based methods. We found out that a 1% increase in inbreeding caused a depression ranging from 25.94 kg (Fhat1) to 40.62 kg (Fhat3), 1.18 kg (Fhat2) to 1.70 kg (Fhat3), 0.90 kg (Fhat2) to 1.45 kg (Froh and Fhat3), 0.19 (Fped) to 0.34 d (Fhat3) for 305-d milk yield, fat, protein, and calving interval, respectively. The health traits showed very slight gradual changes when inbreeding was increased steadily from 0% to 50%, with digital dermatitis showing a rather contrasting trend to that of mastitis, which increased the more an animal was inbred. Overall, our study highlights the importance of considering both pedigree-based and genomic-based inbreeding estimators when assessing the impact on inbreeding, emphasizing that not all inbreeding is harmful.

Inbreeding depression for producer-recorded udder, metabolic, and reproductive diseases in US dairy cattle

This study leveraged a growing dataset of producer-recorded phenotypes for mastitis, reproductive diseases (metritis and retained placenta), and metabolic diseases (ketosis, milk fever, and displaced abomasum) to investigate the potential presence of inbreeding depression for these disease traits. Phenotypic, pedigree, and genomic information were obtained for 354,043 and 68,292 US Holstein and Jersey cows, respectively. Total inbreeding coefficients were calculated using both pedigree and genomic information; the latter included inbreeding estimates obtained using a genomic relationship matrix and runs of homozygosity. We also generated inbreeding coefficients based on the generational inbreeding for recent and old pedigree inbreeding, for different run-of-homozygosity length classes, and for recent and old homozygous-by-descent segment-based inbreeding. Estimates on the liability scale revealed significant evidence of inbreeding depression for reproductive-disease traits, with an increase in total pedigree and genomic inbreeding showing a notable effect for recent inbreeding. However, we found inconsistent evidence for inbreeding depression for mastitis or any metabolic diseases. Notably, in Holsteins, the probability of developing displaced abomasum decreased with inbreeding, particularly for older inbreeding. Estimates of disease probability for cows with low, average, and high inbreeding levels did not significantly differ across any inbreeding coefficient and trait combination, indicating that although inbreeding may affect disease incidence, it likely plays a smaller role compared with management and environmental factors.

Exploring genomic inbreeding and selection signatures in a commercial Brangus herd through functional annotation

Composite breeds, including Brangus, are widely utilized in subtropical and tropical regions to harness the advantages of both Bos t. taurus and Bos t. indicus breeds. The formation and subsequent selection of composite breeds may result in discernible signatures of selection and shifts in genomic population structure. The objectives of this study were to 1) assess genomic inbreeding, 2) identify signatures of selection, 3) assign functional roles to these signatures in a commercial Brangus herd, and 4) contrast signatures of selection between selected and non-selected cattle from the same year. A total of 4035 commercial Brangus cattle were genotyped using the GGP-F250K array. Runs of Homozygosity (ROH) were used to identify signatures of selection and calculate genomic inbreeding. Quantitative trait loci (QTL) enrichment analysis and literature search identified phenotypic traits linked to ROH islands. Genomic inbreeding averaged 5%, primarily stemming from ancestors five or more generations back. A total of nine ROH islands were identified, QTL enrichment analysis revealed traits related to growth, milk composition, carcass, reproductive, and meat quality traits. Notably, the ROH island on BTA14 encompasses the pleiomorphic adenoma (PLAG1) gene, which has been linked to growth, carcass, and reproductive traits. Moreover, ROH islands associated with milk yield and composition were more pronounced in selected replacement heifers of the population, underscoring the importance of milk traits in cow-calf production. In summary, our research sheds light on the changing genetic landscape of the Brangus breed due to selection pressures and reveals key genomic regions impacting production traits.

Unraveling inbreeding patterns and selection signals in Alpine Grey cattle

Inbreeding plays a crucial role in livestock breeding, influencing genetic diversity and phenotypic traits. Genomic data have helped address limitations posed by incomplete pedigrees, providing deeper insights into breed genetic diversity. This study assesses inbreeding levels via pedigree and genomic approaches and analyzes old and recent inbreeding using runs of homozygosity (ROH), and selection signals in Alpine Grey cattle. Pedigree data from 165 575 individuals, analyzed with INBUPGF90 software, computed inbreeding coefficients. Genomic-based coefficients derived from PLINK v1.9. or DetectRUNS R package analyses of 1 180 individuals' genotypes. Common single nucleotide polymorphisms within ROH pinpointed genomic regions, aggregating into "ROH islands" indicative of selection pressure. Overlaps with USCS Genome Browser unveiled gene presence. Moderate correlations (0.20-0.54) existed between pedigree and genomic coefficients, with most genomic estimators having higher (>0.8) correlation values. Inbreeding averaged 0.04 in < 8 Mb ROH segments, and 0.03 in > 16 Mb segments; > 90% of ROHs were < 8 Mb, indicating ancient inbreeding prevalence. Recent inbreeding proved less detrimental than in cosmopolitan breeds. Two major ROH islands on chromosomes 6 and 7 harbored genes linked to immune response, disease resistance (PYURF, HERC3), and fertility (EIF4EBP3, SRA1). This study underscores the need for detailed inbreeding analyses to understand genetic characteristics and historical changes in local breeds like Alpine Grey cattle. Genomic insights, especially from ROH, facilitated overcoming pedigree limitations, illuminating breed genetic diversity. Our findings reveal ancient inbreeding's enduring genetic impact and ROH islands potential for selective sweeps, elucidating traits in Alpine Grey cattle.

Genomic Analysis of Inbreeding and Coancestry in Nordic Jersey and Holstein Dairy Cattle Populations

In recent years, Genomic Selection (GS) has accelerated genetic gain in dairy cattle breeds worldwide. Despite the evident genetic progress, several dairy populations have also encountered challenges such as heightened inbreeding rates and reduced effective population sizes. The challenge has been to find a balance between achieving substantial genetic gain while managing genetic diversity within the population, thereby mitigating the negative effects of inbreeding depression. This study aims to elucidate the impact of GS on pedigree and genomic rates of inbreeding (ΔF) and coancestry (ΔC) in Nordic Jersey (NJ) and Holstein (NH) cattle populations. Furthermore, key genetic metrics including the generation interval (L), effective population size (Ne), and future effective population size (FNe) were assessed between 2 time periods, before and after GS, and across distinct animal cohorts in both breeds: females, bulls, and approved semen-producing bulls (AI-sires). Analysis of ΔF and ΔC revealed distinct trends across the studied periods and animal groups. Notably, there was a consistent increase in yearly ΔF for most animal groups in both breeds. An exception was observed in NH AI-sires, which demonstrated a slight decrease in yearly ΔF. Moreover, NJ displayed minimal changes in yearly ΔC between the periods, whereas NH exhibited elevated ΔC values across all animal groups. Particularly striking was the substantial increase in yearly ΔC within the NH female population, surging from 0.02% to 0.39% between the periods. Implementation of GS resulted in a reduction of the generation interval across all animal cohorts in both NJ and NH breeds. However, the extent of reduction was more pronounced in males compared with females. This reduction in generation interval influenced generational changes in ΔF and ΔC. Bulls and AI-sires of both breeds exhibited reduced generational ΔF between periods, in contrast to females that demonstrated an opposing pattern. Between the periods, NJ maintained a relatively stable Ne, 29.4 before and 30.3 after GS, while NH experienced a notable decline from 54.3 to 42.8. Female groups in both breeds displayed a negative Ne trend, while males demonstrated either neutral or positive Ne developments. Regarding FNe, NJ exhibited positive FNe development with an increase from 40.7 to 57.2. The opposite was observed in NH, where FNe decreased from 198.8 to 42.7. In summary, it was evident that the genomic methods could detect differences between the populations and changes in ΔF and ΔC more efficiently than pedigree methods. GS implementation yielded positive outcomes within the NJ population regarding the rate of coancestry but the opposite was observed with NH. Moreover, analysis of ΔC data hints at the potential to decrease future ΔF through informed mating strategies. Conversely, NH faces more pressing concerns, even though ΔF remains comparatively modest in contrast to what has been observed in other Holstein populations. These findings underscore the necessity of genomic control of inbreeding and coancestry with strategic changes in the Nordic breeding schemes for dairy to ensure long-term sustainability in the forthcoming years.

Genetic Variation and Composition of Two Commercial Estonian Dairy Cattle Breeds Assessed by SNP Data

The aims of this study were to assess the genomic relatedness of Estonian and selected European dairy cattle breeds and to examine the within-breed diversity of two Estonian dairy breeds using genome-wide SNP data. This study was based on a genotyped heifer population of the Estonian Red (ER) and Estonian Holstein (EH) breeds, including about 10% of all female cattle born in 2017-2020 (sample sizes n = 215 and n = 2265, respectively). The within-breed variation study focused on the level of inbreeding using the ROH-based inbreeding coefficient. The genomic relatedness analyses were carried out among two Estonian and nine European breeds from the WIDDE database. Admixture analysis revealed the heterogeneity of ER cattle with a mixed pattern showing several ancestral populations containing a relatively low proportion (1.5-37.0%) of each of the reference populations used. There was a higher FROH in EH (FROH = 0.115) than in ER (FROH = 0.044). Compared to ER, the long ROHs of EH indicated more closely related parents. The paternal origin of the genetic material used in breeding had a low effect on the inbreeding level. However, among EH, the highest genomic inbreeding was estimated in daughters of USA-born sires.

Differential patterns in runs of homozygosity in two mice lines under divergent selection for environmental variability for birth weight

Runs of homozygosity (ROH) are defined as long continuous homozygous stretches in the genome which are assumed to originate from a common ancestor. It has been demonstrated that divergent selection for variability in mice is possible and that low variability in birth weight is associated with robustness. To analyse ROH patterns and ROH-based genomic inbreeding, two mouse lines that were divergently selected for birth weight variability for 26 generations were used, with: 752 individuals for the high variability line (H-Line), 766 individuals for the low variability line (L-Line) and 74 individuals as a reference population. Individuals were genotyped using the high density Affymetrix Mouse Diversity Genotyping Array. ROH were identified using both the sliding windows (SW) and the consecutive runs (CR) methods. Inbreeding coefficients were calculated based on pedigree (FPED ) information, on ROH identified using the SW method (FROHSW ) and on ROH identified using the CR method (FROHCR ). Differences in genomic inbreeding were not consistent across generations and these parameters did not show clear differences between lines. Correlations between FPED and FROH were high, particularly for FROHSW . Moreover, correlations between FROHSW and FPED were even higher when ROH were identified with no restrictions in the number of heterozygotes per ROH. The comparison of FROH estimates between either of the selected lines were based on significant differences at the chromosome level, mainly in chromosomes 3, 4, 6, 8, 11, 15 and 19. ROH-based inbreeding estimates that were computed using longer homozygous segments had a higher relationship with FPED . Differences in robustness between lines were not attributable to a higher homozygosis in the L-Line, but maybe to the different distribution of ROH at the chromosome level between lines. The analysis identified a set of genomic regions for future research to establish the genomic basis of robustness.

Genome-Wide Analysis of Milk Production Traits and Selection Signatures in Serbian Holstein-Friesian Cattle

To improve the genomic evaluation of milk-related traits in Holstein-Friesian (HF) cattle it is essential to identify the associated candidate genes. Novel SNP-based analyses, such as the genetic mapping of inherited diseases, GWAS, and genomic selection, have led to a new era of research. The aim of this study was to analyze the association of each individual SNP in Serbian HF cattle with milk production traits and inbreeding levels. The SNP 60 K chip Axiom Bovine BovMDv3 was deployed for the genotyping of 334 HF cows. The obtained genomic results, together with the collected phenotypic data, were used for a GWAS. Moreover, the identification of ROH segments was performed and served for inbreeding coefficient evaluation and ROH island detection. Using a GWAS, a polymorphism, rs110619097 (located in the intron of the CTNNA3 gene), was detected to be significantly (p < 0.01) associated with the milk protein concentration in the first lactation (adjusted to 305 days). The average genomic inbreeding value (FROH) was 0.079. ROH islands were discovered in proximity to genes associated with milk production traits and genomic regions under selection pressure for other economically important traits of dairy cattle. The findings of this pilot study provide useful information for a better understanding of the genetic architecture of milk production traits in Serbian HF dairy cows and can be used to improve lactation performances in Serbian HF cattle breeding programs.

Characterization of runs of Homozygosity revealed genomic inbreeding and patterns of selection in indigenous sahiwal cattle

Runs of homozygosity (ROH) are contiguous genomic regions, homozygous across all sites which arise in an individual due to the parents transmitting identical haplotypes to their offspring. The genetic improvement program of Sahiwal cattle after decades of selection needs re-assessment of breeding strategy and population phenomena. Hence, the present study was carried out to optimize input parameters in PLINK for ROH estimates, to explore ROH islands and assessment of pedigree and genome-based inbreeding in Sahiwal cattle. The sliding window approach with parameters standardized to define ROH for the specific population under study was used for the identification of runs. The optimum maximum gap, density, window-snp and window-threshold were 250 Kb, 120 Kb/SNP, 10, 0.05 respectively and ROH patterns were also characterized. ROH islands were defined as the short homozygous genomic regions shared by a large proportion of individuals in a population, containing significantly higher occurrences of ROH than the population specific threshold level. These were identified using the -homozyg-group function of the PLINK v1.9 program. Our results indicated that the Islands of ROH harbor a few candidate genes, ACAD11, RFX4, BANP, UBA5 that are associated with major economic traits. The average FPED (Pedigree based inbreeding coefficient), FROH (Genomic inbreeding coefficient), FHOM (Inbreeding estimated as the ratio of observed and expected homozygous genotypes), FGRM (Inbreeding estimated on genomic relationship method) and FGRM0.5 (Inbreeding estimated from the diagonal of a GRM with allele frequencies near to 0.5) were 0.009, 0.091, 0.035, -0.104 and -0.009, respectively. Our study revealed the optimum parameter setting in PLINK viz. maximal gaps between two SNPs, minimal density of SNPs in a segment (in kb/SNP) and scanning window size to identify ROH segments, which will enable ROH estimation more efficient and comparable across various SNP genotyping-based studies. The result further emphasized the significant role of genomics in unraveling population diversity, selection signatures and inbreeding in the ongoing Sahiwal breed improvement programs.

Inbreeding depression is associated with recent homozygous-by-descent segments in Belgian Blue beef cattle

BACKGROUND

Cattle populations harbor generally high inbreeding levels that can lead to inbreeding depression (ID). Here, we study ID with different estimators of the inbreeding coefficient F, evaluate their sensitivity to used allele frequencies (founder versus sample allele frequencies), and compare effects from recent and ancient inbreeding.

METHODS

We used data from 14,205 Belgian Blue beef cattle genotyped cows that were phenotyped for 11 linear classification traits. We computed estimators of F based on the pedigree information (FPED), on the correlation between uniting gametes (FUNI), on the genomic relationship matrix (FGRM), on excess homozygosity (FHET), or on homozygous-by-descent (HBD) segments (FHBD).

RESULTS

FUNI and FGRM were sensitive to used allele frequencies, whereas FHET and FHBD were more robust. We detected significant ID for four traits related to height and length; FHBD and FUNI presenting the strongest associations. Then, we took advantage of the classification of HBD segments in different age-related classes (the length of an HBD segment being inversely related to the number of generations to the common ancestors) to determine that recent HBD classes (common ancestors present approximately up to 15 generations in the past) presented stronger ID than more ancient HBD classes. We performed additional analyses to check whether these observations could result from a lower level of variation in ancient HBD classes, or from a reduced precision to identify these shorter segments.

CONCLUSIONS

Overall, our results suggest that mutational load decreases with haplotype age, and that mating plans should consider mainly the levels of recent inbreeding.

Characterizing and Eliminating the Inbreeding Load

The authors evaluated the relevant literature related to purging, which is the interaction between selection and inbreeding in which the population may eliminate its inbreeding load at least partially. According to the relevant literature, the inbreeding load and the process of purging were evaluated via pedigree methods based on ancestral inbreeding, the inbreeding-purging model, and expressed opportunity of purging, along with genomic methods. Most ancestral inbreeding-related studies were performed in zoos, where only a small proportion of the studied populations show signs of purging. The inbreeding-purging model was developed with Drosophila, and it was used to evaluate different zoo ungulates and Pannon white rabbits. Purging was detected in both studies. The expressed opportunity of purging was applied in Jersey cattle and Pannon white rabbits. In the Jersey cattle, it had an effect of 12.6% for fitness, while in the Pannon white rabbits, the inbreeding load was between 40% and 80% of its original value. The genomic studies also signalled purging, but they also made it clear that, contrary to the detected purging, the evaluated populations still suffered from inbreeding depression. Therefore, especially for domesticated animals, it can be concluded that deliberate inbreeding with the purpose of generating purging is not advocated.

Improving the nutritional values of yellow mealworm Tenebrio molitor (Coleoptera: Tenebrionidae) larvae as an animal feed ingredient: a review

Yellow mealworm larvae (YML; Tenebrio molitor) are considered as a valuable insect species for animal feed due to their high nutritional values and ability to grow under different substrates and rearing conditions. Advances in the understanding of entomophagy and animal nutrition over the past decades have propelled research areas toward testing multiple aspects of YML to exploit them better as animal feed sources. This review aims to summarize various approaches that could be exploited to maximize the nutritional values of YML as an animal feed ingredient. In addition, YML has the potential to be used as an antimicrobial or bioactive agent to improve animal health and immune function in production animals. The dynamics of the nutritional profile of YML can be influenced by multiple factors and should be taken into account when attempting to optimize the nutrient contents of YML as an animal feed ingredient. Specifically, the use of novel land-based and aquatic feeding resources, probiotics, and the exploitation of larval gut microbiomes as novel strategies can assist to maximize the nutritional potential of YML. Selection of relevant feed supplies, optimization of ambient conditions, the introduction of novel genetic selection procedures, and implementation of effective post-harvest processing may be required in the future to commercialize mealworm production. Furthermore, the use of appropriate agricultural practices and technological improvements within the mealworm production sector should be aimed at achieving both economic and environmental sustainability. The issues highlighted in this review could pave the way for future approaches to improve the nutritional value of YML.

Genetic and phenotypic parameters for sexual precocity and parasite resistance traits in Nellore cattle

Indicator traits of sexual precocity are widely used as selection criteria for the genetic improvement of beef cattle; however, the impact of selection for these traits on resistance to endoparasites and ectoparasites is unknown. Therefore, this study aimed to estimate the genetic and phenotypic parameters for indicator traits of sexual precocity and parasite resistance in Nellore cattle. The sexual precocity traits evaluated were probability of first calving (PFC) and scrotal circumference at 12 and 18 months of age (SC12 and SC18). The resistance-related traits included tick (TC), gastrointestinal nematode egg (NEC), and Eimeria spp. oocyst (EOC) counts. (Co)variance components were estimated by Bayesian inference using multitrait animal models. The mean heritabilities for PFC, SC12, SC18, TC, NEC, and EOC were 0.23, 0.38, 0.42, 0.14, 0.16, and 0.06, respectively, and suggest that selection will change the mean values of these traits over time. The genetic and phenotypic correlations for most pairs formed by a precocity and a resistance trait were not different from zero, suggesting that selection for sexual precocity traits will not result in changes in resistance traits. Thus, selection for indicator traits of sexual precocity does not elicit unfavorable correlated responses in resistance to endoparasites and ectoparasites, and joint selection aimed at improving these traits can be performed using multitrait selection methods, when necessary.

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.

Impact of Inbreeding and Ancestral Inbreeding on Longevity Traits in German Brown Cows

A recent study on the population structure of the German Brown population found increasing levels of classical and ancestral inbreeding coefficients. Thus, the aim of this study was to determine the effects of inbreeding depression and purging on longevity traits using classical and ancestral inbreeding coefficients according to Kalinowski (2002) (Fa_Kal, FNew), Ballou (1997) (Fa_Bal), and Baumung (2015) (Ahc). For this purpose, uncensored data of 480,440 cows born between 1990 and 2001 were available. We analyzed 17 longevity traits, including herd life, length of productive life, number of calvings, lifetime and effective lifetime production for milk, fat, and protein yield, the survival to the 2nd, 4th, 6th, 8th, and 10th lactation number, and the culling frequencies due to infertility, or udder and foot and leg problems. Inbreeding depression was significant and negative for all traits but for culling due to udder and to foot and leg problems. When expressed in percentages of genetic standard deviations, inbreeding depression per 1% increase in inbreeding was -3.61 to -10.98%, -2.42 to -2.99%, -2.21 to -4.58%, and 5.13% for lifetime production traits, lifetime traits, survival rates, and culling due to infertility, respectively. Heterosis and recombination effects due to US Brown Swiss genes were positive and counteracted inbreeding depression. The effects of FNew were not significantly different from zero, while Fa_Kal had negative effects on lifetime and lifetime production traits. Similarly, the interaction of F with Fa_Bal was significantly negative. Thus, purging effects could not be shown for longevity traits in German Brown. A possible explanation may be seen in the breed history of the German Brown, that through the introgression of US Brown Swiss bulls ancestral inbreeding increased and longevity decreased. Our results show, that reducing a further increase in inbreeding in mating plans is advisable to prevent a further decline in longevity due to inbreeding depression, as purging effects were very unlikely in this population.

Effects of type traits, inbreeding, and production on survival in US Jersey cattle

Greater longevity is associated with lower replacement costs, higher average milk production, and fewer replacement heifers needed. Longevity data are obtained late in life, and for this reason stayability, defined as the probability of survival from birth until a certain age, can be used as an alternative measure. The objective of this study was to evaluate the effects of different type traits, inbreeding, and production level on the stayability of Jersey cows to various ages, and to assess trends over time. Data consisted of 460,172 to 204,658 stayability records, depending on length of the opportunity period, for survival from birth until 36, 48, 60, 72, or 84 mo of age. Threshold models were used to analyze the stayability traits, including different type traits, inbreeding coefficient, and within-herd production level as explanatory variables. Heritability estimates for stayability traits ranged from 0.05 (36 mo) to 0.22 (84 mo). As expected, the probability of survival decreased as age increased. Highly productive cows were more likely to survive than their poor-producing contemporaries regardless of age and the type trait evaluated. Our data indicate that farmers' selection decisions tend to punish poor production at early ages and reward high production at later stages. Inbreeding negatively affected the probability of survival, especially when inbreeding coefficients exceeded 10%, and this impact was most noticeable at 48 mo of age or later. Some type traits, such as stature and foot angle, had little effect on the probability of survival. Other type traits, such as strength, dairy form, rump width, and rear legs, showed higher probability of survival at intermediate scores, whereas other type traits, such as fore udder attachment, rear udder height, udder depth, and final score, showed higher probability of survival at higher scores. Finally, our results indicate that the probability of survival has decreased in the last decade, probably due to a greater number of heifers available and, therefore, higher culling rates.

Genome-wide assessment and mapping of inbreeding depression identifies candidate genes associated with semen traits in Holstein bulls

BACKGROUND

The reduction in phenotypic performance of a population due to mating between close relatives is called inbreeding depression. The genetic background of inbreeding depression for semen traits is poorly understood. Thus, the objectives were to estimate the effect of inbreeding and to identify genomic regions underlying inbreeding depression of semen traits including ejaculate volume (EV), sperm concentration (SC), and sperm motility (SM). The dataset comprised ~ 330 K semen records from ~ 1.5 K Holstein bulls genotyped with 50 K single nucleotide polymorphism (SNP) BeadChip. Genomic inbreeding coefficients were estimated using runs of homozygosity (i.e., F_ROH > 1 Mb) and excess of SNP homozygosity (F_SNP). The effect of inbreeding was estimated by regressing phenotypes of semen traits on inbreeding coefficients. Associated variants with inbreeding depression were also detected by regressing phenotypes on ROH state of the variants.

RESULTS

Significant inbreeding depression was observed for SC and SM (p < 0.01). A 1% increase in F_ROH reduced SM and SC by 0.28% and 0.42% of the population mean, respectively. By splitting F_ROH into different lengths, we found significant reduction in SC and SM due to longer ROH, which is indicative of more recent inbreeding. A genome-wide association study revealed two signals positioned on BTA 8 associated with inbreeding depression of SC (p < 0.00001; FDR < 0.02). Three candidate genes of GALNTL6, HMGB2, and ADAM29, located in these regions, have established and conserved connections with reproduction and/or male fertility. Moreover, six genomic regions on BTA 3, 9, 21 and 28 were associated with SM (p < 0.0001; FDR < 0.08). These genomic regions contained genes including PRMT6, SCAPER, EDC3, and LIN28B with established connections to spermatogenesis or fertility.

CONCLUSIONS

Inbreeding depression adversely affects SC and SM, with evidence that longer ROH, or more recent inbreeding, being especially detrimental. There are genomic regions associated with semen traits that seems to be especially sensitive to homozygosity, and evidence to support some from other studies. Breeding companies may wish to consider avoiding homozygosity in these regions for potential artificial insemination sires.

Reintroducing genetic diversity in populations from cryopreserved material: the case of Abondance, a French local dairy cattle breed

BACKGROUND

Genetic diversity is a necessary condition for populations to evolve under natural adaptation, artificial selection, or both. However, genetic diversity is often threatened, in particular in domestic animal populations where artificial selection, genetic drift and inbreeding are strong. In this context, cryopreserved genetic resources are a promising option to reintroduce lost variants and to limit inbreeding. However, while the use of ancient genetic resources is more common in plant breeding, it is less documented in animals due to a longer generation interval, making it difficult to fill the gap in performance due to continuous selection. This study investigates one of the only concrete cases available in animals, for which cryopreserved semen from a bull born in 1977 in a lost lineage was introduced into the breeding scheme of a French local dairy cattle breed, the Abondance breed, more than 20 years later.

RESULTS

We found that this re-introduced bull was genetically distinct with respect to the current population and thus allowed part of the genetic diversity lost over time to be restored. The expected negative gap in milk production due to continuous selection was absorbed in a few years by preferential mating with elite cows. Moreover, the re-use of this bull more than two decades later did not increase the level of inbreeding, and even tended to reduce it by avoiding mating with relatives. Finally, the reintroduction of a bull from a lost lineage in the breeding scheme allowed for improved performance for reproductive abilities, a trait that was less subject to selection in the past.

CONCLUSIONS

The use of cryopreserved material is an efficient way to manage the genetic diversity of an animal population, by mitigating the effects of both inbreeding and strong selection. However, attention should be paid to mating of animals to limit the disadvantages associated with incorporating original genetic material, notably a discrepancy in the breeding values for selected traits or an increase in inbreeding. Therefore, careful characterization of the genetic resources available in cryobanks could help to ensure the sustainable management of populations, in particular local or small populations. These results could also be transferred to the conservation of wild threatened populations.

State of Vyatka horse population in regions of Russia

The current state of Vyatka horse breed gene pool was studied in the research. It was revealed that the main array of the breeding stock is concentrated in three populations of three regions - the Udmurt Republic, the Kirov region, the Central Federal District. The purpose of the research was to assess the state of gene pool of Vyatka breed in modern conditions. Population of breeding stock horses both in agricultural enterprises and on private farms was analyzed in the territory of three regions of the Russian Federation: the Udmurt Republic, the Kirov Region, the Central Federal District. According to the genetic characteristics, horses in each population were divided into groups based on the relation degree: group 1 - outbred, group 2 - with distant Fx inbreeding (0.21.55 %), group 3 - with moderate Fx inbreeding (1.5612.5 %), group 4 - with close Fx inbreeding (12.625 %). The coefficient of inbreeding was estimated according to the Wright-Kislovsky formula. The most typical horses with an inherent conformation were outbred horses from the population of the Central Federal District. Monitoring the quantitative composition of the breed showed that the number of mares increased from 73 to 287 heads over the period from 1995 to 2021. However, a sharp decrease in the number of mares (222 heads) was recorded at the beginning of 2022. This tendency creates certain difficulties in the selection process. The largest number of mares is concentrated in the Central Federal District - 83 heads nowadays. At the present stage of work with Vyatka breed the analysis of genetic diversity showed that 43.3 % of the representatives were outbred, it was based on the study of the increase in homozygosity of individuals in a limited gene pool. Representatives of the Vyatka breed were obtained in equal proportions by remote and moderate inbreeding - 28.1 and 27 %, respectively. The most typical with the correct conformation were outbred horses from the population of the Central Federal District.

Pedigree and genome-based patterns of homozygosity in the South African Ayrshire, Holstein, and Jersey breeds

The erosion of genetic diversity limits long-term genetic gain and impedes the sustainability of livestock production. In the South African (SA) dairy industry, the major commercial dairy breeds have been applying estimated breeding values (EBVs) and/or have been participating in Multiple Across Country Evaluations (MACE). The transition to genomic estimated breeding values (GEBVs) in selection strategies requires monitoring of the genetic diversity and inbreeding of current genotyped animals, especially considering the comparatively small population sizes of global dairy breeds in SA. This study aimed to perform a homozygosity-based evaluation of the SA Ayrshire (AYR), Holstein (HST), and Jersey (JER) dairy cattle breeds. Three sources of information, namely 1) single nucleotide polymorphism (SNP) genotypes (3,199 animals genotyped for 35,572 SNPs) 2) pedigree records (7,885 AYR; 28,391 HST; 18,755 JER), and 3) identified runs of homozygosity (ROH) segments were used to quantify inbreeding related parameters. The lowest pedigree completeness was for the HST population reducing from a value of 0.990 to 0.186 for generation depths of one to six. Across all breeds, 46.7% of the detected ROH were between 4 megabase pairs (Mb) and 8 Mb in length. Two conserved homozygous haplotypes were identified in more than 70% of the JER population on Bos taurus autosome (BTA) 7. The JER breed displayed the highest level of inbreeding across all inbreeding coefficients. The mean (± standard deviation) pedigree-based inbreeding coefficient (FPED) ranged from 0.051 (±0.020) for AYR to 0.062 (±0.027) for JER, whereas SNP-based inbreeding coefficients (FSNP) ranged from 0.020 (HST) to 0.190 (JER) and ROH-based inbreeding coefficients, considering all ROH segment coverage (FROH), ranged from 0.053 (AYR) to 0.085 (JER). Within-breed Spearman correlations between pedigree-based and genome-based estimates ranged from weak (AYR: 0.132 between FPED and FROH calculated for ROH &lt;4Mb in size) to moderate (HST: 0.584 between FPED and FSNP). Correlations strengthened between FPED and FROH as the ROH length category was considered lengthened, suggesting a dependency on breed-specific pedigree depth. The genomic homozygosity-based parameters studied proved useful in investigating the current inbreeding status of reference populations genotyped to implement genomic selection in the three most prominent South African dairy cattle breeds.

The role of inbreeding depression on productive performance in the Italian Holstein breed

Inbreeding depression has become an urgent issue in cosmopolitan breeds where the massive genetic progress achieved in the latest generations is counterbalanced by a dramatic loss of genetic diversity causing increased health issues. Thus, the aim of this study was to estimate inbreeding depression on productive traits in Holstein dairy cattle. More precisely, we aimed to i) determine the level of inbreeding in 27,735 Italian Holstein dairy cows using pedigree and genotype data, ii) quantify the effect of inbreeding on 305-d in milk yield (MY; kg), fat yield (FY; kg), and protein yield (PY; kg) based on different statistical approaches, iii) determine if recent inbreeding has a more harmful impact than ancestral ones, and iv) quantify chromosomal homozygosity effect on productive traits. Quality control was performed on the autosomal chromosomes resulting in a final dataset of 84,443 single nucleotide polymorphisms. Four statistical models were used to evaluate the presence of inbreeding depression, which included linear regression analysis and division of FPED and FROH into percentile classes. Moreover, FROH was partitioned into i) length classes to assess the role of recent and ancestral inbreeding and ii) chromosome-specific contributions (FROH-CHR). Results evidenced that inbreeding negatively impacted the productive performance of Italian Holstein Friesian cows. However, differences between the estimated FPED and FROH coefficients resulted in different estimates of inbreeding depression. For instance, a 1% increase in FPED and FROH was associated with a decrease in MY of about 44 and 61 kg (P < 0.01). Further, when considering the extreme inbreeding percentile classes moving from the 5th lowest to the 95th highest, there was a reduction of -263 kg and -561 kg per lactation for FPED and FROH. Increased inbreeding, estimated by FPED and FROH, had also a negative effect on PY and FY, either fit as a regressor or percentile classes. When evaluating the impact of inbreeding based on runs of homozygosity (ROH) length classes, longer ROH (over 8 Mb) had a negative effect in all traits, indicating that recent inbreeding might be more harmful than the ancestral one. Finally, results within chromosome homozygosity highlighted specific chromosomes with a more deleterious effect on productive traits.

Analysis of runs of homozygosity of cattle living in different climate zones

Aim of this study was to analyze the distribution and characteristics of runs of homozygosity in Bos taurus taurus and Bos taurus indicus breeds, as well as their crosses, farmed all around the world. With this aim in view, we used single-nucleotide polymorphisms (SNP) genotypes for 3,263 cattle belonging to 204 different breeds. After quality control, 23,311 SNPs were retained for the analysis. Animals were divided into seven different groups: 1) continental taurus, 2) temperate taurus, 3) temperate indicus, 4) temperate composite, 5) tropical taurus, 6) tropical indicus, and 7) tropical composite. The climatic zones were created according to the latitude of the breeds' country of origin: i) continental, latitude ≥ 45°; ii) temperate, 45°< Latitude >23.26°; iii) tropics, latitude ≤ 23.26°. Runs of homozygosity were computed as 15 SNPs spanning in at least 2 Mb; number of ROH per animal (nROH), average ROH length (meanMb), and ROH-based inbreeding coefficients (FROH) were also computed. Temperate indicus showed the largest nROH, whereas Temperate taurus the lowest value. Moreover, the largest meanMb was observed for Temperate taurus, whereas the lowest value for Tropics indicus. Temperate indicus breeds showed the largest FROH values. Genes mapped in the identified ROH were reported to be associated with the environmental adaptation, disease resistance, coat color determinism, and production traits. Results of the present study confirmed that runs of homozygosity could be used to identify genomic signatures due to both artificial and natural selection.

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.

Cow reproduction rates with varying inbreeding degrees

The evaluation of the breeding work results carried out, the identification of optimal systems for the animals selection, including related ones, have always been relevant. The purpose was to study the influence of various inbreeding degrees on reproductive abilities and their selection and genetic parameters in Holstein cows. The research was carried out on the basis of Pushkinskoe Breeding Plant, Nizhny Novgorod region. At the earliest age, heifers were inseminated in the group with recent inbreeding (14.87 months), for this reason they had the lowest weight at the first insemination - 4 25.7 kg. Cows in the group with recent inbreeding had the shortest service period (108.9 days), the longest service period was in the group with close inbreeding (152.6 days). The variability of live weight during the first insemination and fertilization in all groups was at a low level (Cv = 5,228,25 %). The duration of the service period after first lactation in all groups, except for the group of close inbreeding, had a variation of about 45 %, in the group with close inbreeding it was 1.5 times higher. Despite its small number, the group of close inbreeding turned out to be the most variable in all indicators. An increase in the age of the first fertilization of heifers in the group of close inbreeding leads to an increase in the duration of the service period (r = 0.335). However, there is practically no connection between these indicators in the other groups. Many of the studied indicators had a weak positive or negative relationship with each other. Among the resulting young, more than half were heifers, in groups with different inbreeding degrees this indicator varied from 63.3 to 66.7 %, in the group with outbred animals it was 69.4 %. Twins were registered 2 times and only in the group with a recent inbreeding degree. Stillbirth in all groups was at a fairly low level - 5 .76.7 %, in the group with a close inbreeding degree no cases of stillborn calves were detected. The birth of calves with congenital deformities and pathologies from related mating was not observed. Thus, in the conducted studies, inbreeding had no negative impact on the cows reproductive qualities even to a close degree.

Genetic and Genomic Characterization of a New Beef Cattle Composite Breed (Purunã) Developed for Production in Pasture-Based Systems

Purunã is a composite beef cattle breed, developed in Southern Brazil by crossing the Angus, Charolais, Canchim, and Caracu breeds. The goal of this study was to perform the first genetic characterization of the Purunã breed, based on both pedigree and genomic information. For this, 100 randomly selected animals were genotyped, and 11,205 animals born from 1997 to 2019 had pedigree information. The genetic analyses performed were principal component analysis, admixture, phylogenic tree, pedigree and genomic inbreeding, linkage disequilibrium (LD), effective population size (Ne), consistency of the gametic phase, runs of homozygosity (ROH), heterozygosity-enriched regions (HERs), and functional analyses of the ROH and HER regions identified. Our findings indicate that Purunã is more genetically related to the Charolais, Canchim, and Angus breeds than Caracu or Nellore. The levels of inbreeding were shown to be small based on all the metrics evaluated and ranged from −0.009 to 0.029. A low (−0.12–0.31) correlation of the pedigree-based inbreeding compared to all the genomic inbreeding coefficients evaluated was observed. The LD average was 0.031 (±0.0517), and the consistency of the gametic phase was shown to be low for all the breed pairs, ranging from 0.42 to 0.27 to the distance of 20 Mb. The Ne values based on pedigree and genomic information were 158 and 115, respectively. A total of 1,839 ROHs were found, and the majority of them are of small length (&lt;4 Mb). An important homozygous region was identified on BTA5 with pathways related to behavioral traits (sensory perception, detection of stimulus, and others), as well as candidate genes related to heat tolerance (MY O 1A), feed conversion rate (RDH5), and reproduction (AMDHD1). A total of 1,799 HERs were identified in the Purunã breed with 92.3% of them classified within the 0.5–1 Mb length group, and 19 HER islands were identified in the autosomal genome. These HER islands harbor genes involved in growth pathways, carcass weight (SDCBP), meat and carcass quality (MT2A), and marbling deposition (CISH). Despite the genetic relationship between Purunã and the founder breeds, a multi-breed genomic evaluation is likely not feasible due to their population structure and low consistency of the gametic phase among them.

Breeding Sustainable Beef Cows: Reducing Weight and Increasing Productivity

Programs for sustainable beef production are established, but the specific role of beef cows in these systems is not well defined. This work characterized cows for two traits related to sustainability, cow weight (CW) and cumulative weight weaned (WtW). Cow weight indicates nutrient requirements and enteric methane emissions. Cumulative weight weaned reflects reproductive performance and avoidance of premature culling for characteristics related to animal health, welfare, and worker safety. Both traits were evaluated with random regression models with records from a crossbred population representing 18 breeds that conduct US national cattle evaluations. The genomic REML analyses included additive and dominance components, with relationships among 22,776 animals constructed from genotypes of 181,286 potentially functional variants imputed from a low-pass sequence. Projected to 8 years of age, the additive heritability estimate for CW was 0.57 and 0.11 for WtW. Dominance heritability was 0.02 for CW and 0.19 for WtW. Many variants with significant associations with CW were within previously described quantitative trait loci (QTL) for growth-related production, meat, and carcass traits. Significant additive WtW variants were covered by QTL for traits related to reproduction and structural soundness. All breeds contributed to groups of cows with high and low total genetic values (additive + dominance effects) for both traits. The high WtW cows and cows above the WtW mean but below the CW mean had larger heterosis values and fewer bases in runs of homozygosity. The high additive heritability of CW and dominance effects on WtW indicate that breeding to improve beef cow sustainability should involve selection to reduce CW and mate selection to maintain heterosis and reduce runs of homozygosity.

Runs of Homozygosity and Quantitative Trait Locus/Association for Semen Parameters in Selected Chinese and South African Beef Cattle

In this study, runs of homozygosity (ROH) and quantitative trait locus/association (QTL) for semen parameters in selected Chinese and South African beef cattle breed were estimated. The computed results showed 7516 ROH were observed between classes 0−5 Mb with no ROH observed in classes >40 Mb. Distribution of ROH showed high level of genomic coverage for ANG, NGU, CSI, and BEL breeds. Approximately 13 genomic regions with QTL were controlling sperm motility, sperm concentration, semen volume, sperm count, sperm head abnormalities, sperm tail abnormalities, sperm integrity, and percentage of abnormal sperm traits. Nine candidate genes, CDF9, MARCH1, WDR19, SLOICI, ST7, DOP1B, CFAF9, INHBA, and ADAMTS1, were suggested to be associated with above mentioned QTL traits. The results for inbreeding coefficient showed moderate correlation between FROH vs FHOM at 0.603 and high correlation between FROH 0−5 Mb 0.929, and lowest correlation for 0−>40 Mb 0.400. This study suggested recent inbreeding in CSI, BEL, ANG, BON, SIM, and NGU breeds. Furthermore, it highlighted varied inbreeding levels and identified QTL for semen traits and genes of association. These results can assist in implementation of genetic improvement strategies for bulls and provide awareness and proper guidelines in developing breeding programs.

Genetic Diversity and Trends of Ancestral and New Inbreeding in Deutsch Drahthaar Assessed by Pedigree Data

Simple Summary

Deutsch Drahthaar (DD) is the most popular hunting dog in Germany, fulfilling all aspects of hunting including searching for trails. This breed was newly created at the beginning of the 20th century from a large number existing versatile hunting dog breeds. The aim of the breed was, and still is, to achieve the best performance in all aspects of hunting. We analyzed pedigrees of DD using demographic measures to quantify genetic diversity such as probabilities of gene origin and degrees of ancestral and individual inbreeding. A large number of genetically diverse founder dogs should open up the opportunity of creating a breed with a high genetic diversity and a low increase of inbreeding per generation. On the other hand, intense use of top sires and dams from a limited number of breeding lines may accelerate breeding progress in hunting abilities but reduce genetic diversity. Monitoring genetic diversity should help to maintain a high diversity of breeding populations. Our analysis of pedigree data from 101,887 DD dogs revealed inbreeding measures (coefficient of inbreeding F = 0.042, individual rate of inbreeding ΔF_i = 0.00551) and effective population size (Ne = 92) in the mean range compared to a wide range of other dog breeds. Ancestral inbreeding had a strong increasing trend, whereas trends in individual inbreeding and rate of individual inbreeding were slightly negative.

Abstract

Loss of genetic diversity and high inbreeding rates confer an increased risk of congenital anomalies and diseases and thus impacting dog breeding. In this study, we analyzed recent and ancestral inbreeding as well as other measures of genetic variability in the Deutsch Drahthaar (DD) dog population. Analyses included pedigree data from 101,887 animals and a reference population with 65,927 dogs born between 2000 and 2020. The mean equivalent complete generations was 8.6 with 69% known ancestors in generation 8. The mean realized effective population size was 92 with an increasing trend from 83 to 108 over birth years. The numbers of founders, effective founders and effective ancestors, as well as founder genomes, were 814, 66, 38 and 16.15, respectively. Thirteen ancestors explained 50% of the genetic diversity. The mean coefficient of inbreeding and individual rate of inbreeding (ΔF_i) were 0.042 and 0.00551, respectively, with a slightly decreasing trend in ΔF_i. Exposure of ancestors to identical-by-descent alleles explored through ancestral coefficients of inbreeding showed a strong increasing trend. Comparisons between new and ancestral inbreeding coefficients according to Kalinowski et al. showed an average relative contribution of 62% of new inbreeding to individual inbreeding. Comparisons among average coancestry within the parental population and average inbreeding in the reference population were not indicative of genetic substructures. In conclusion, the creation of the DD dog breed about 120 years ago resulted in a popular breed with considerable genetic diversity without substructuring into lines or subpopulations. The trend of new inbreeding was declining, while ancestral inbreeding through ancestors who were autozygous at least once in previous generations was increasing.

Characterization of runs of homozygosity, heterozygosity-enriched regions, and population structure in cattle populations selected for different breeding goals

Background

A decline in the level of genetic diversity in livestock can result in reduced response to selection, greater incidence of genetic defects, and inbreeding depression. In this context, various metrics have been proposed to assess the level of genetic diversity in selected populations. Therefore, the main goals of this study were to: 1) investigate the population structure of 16 cattle populations from 15 different pure breeds or composite populations, which have been selected for different breeds goals; and, 2) identify and compare runs of homozygosity (ROH) and heterozygosity-enriched regions (HER) based on different single nucleotide polymorphism (SNP) panels and whole-genome sequence data (WGS), followed by functional genomic analyses.

Results

A total of 24,187 ROH were found across all cattle populations, with 55% classified in the 2-4 Mb size group. Fourteen homozygosity islands were found in five populations, where four ROH islands located on BTA1, BTA5, BTA16, and BTA19 overlapped between the Brahman (BRM) and Gyr (GIR) breeds. A functional analysis of the genes found in these islands revealed candidate genes known to play a role in the melanogenesis, prolactin signaling, and calcium signaling pathways. The correlations between inbreeding metrics ranged from 0.02 to 0.95, where the methods based on homozygous genotypes (F_HOM), uniting of gametes (F_UNI), and genotype additive variance (F_GRM) showed strong correlations among them. All methods yielded low to moderate correlations with the inbreeding coefficients based on runs of homozygosity (F_ROH). For the HER, 3576 runs and 26 islands, distributed across all autosomal chromosomes, were found in regions containing genes mainly related to the immune system, indicating potential balancing selection. Although the analyses with WGS did not enable detection of the same island patterns, it unraveled novel regions not captured when using SNP panel data.

Conclusions

The cattle populations that showed the largest amount of ROH and HER were Senepol (SEN) and Montana (MON), respectively. Overlapping ROH islands were identified between GIR and BRM breeds, indicating a possible historical connection between the populations. The distribution and pattern of ROH and HER are population specific, indicating that different breeds have experienced divergent selection processes or different genetic processes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08384-0.

A review of inbreeding depression in dairy cattle: current status, emerging control strategies, and future prospects

Dairy cattle breeding has historically focused on relatively small numbers of elite bulls as sires of sons. In recent years, even if generation intervals were reduced and more diverse sires of sons could have been selected, genomic selection has not fundamentally changed the fact that a large number of individuals are being analyzed. However, a relatively small number of elite bulls are still siring those animals. Therefore inbreeding-derived negative consequences in the gene pool have brought concern. The detrimental effects of non-additive genetic changes such as inbreeding depression and dominance have been widely disseminated while seriously affecting bioeconomically important parameters because of an antagonistic relationship between dairy production and reproductive traits. Therefore, the estimation of benefits and limitations of inbreeding and variance of the selection response deserves to be evaluated and discussed to preserve genetic variability, a significant concern in the selection of individuals for reproduction and production. Short-term strategies for genetic merit improvement through modern breeding programs have severely lowered high-producing dairy cattle fertility potential. Since the current selection programs potentially increase long-term costs, genetic diversity has decreased globally as a consequence. Therefore, a greater understanding of the potential that selection programs have for supporting long-term genetic sustainability and genetic diversity among dairy cattle populations should be prioritized in managing farm profitability. The present review provides a broad approach to current inbreeding-derived problems, identifying critical points to be solved and possible alternative strategies to control selection against homozygous haplotypes while maintaining sustained selection pressure. Moreover, this manuscript explores future perspectives, emphasizing theoretical applications and critical points, and strategies to avoid the adverse effects of inbreeding in dairy cattle. Finally, this review provides an overview of challenges that will soon require multidisciplinary approaches to managing dairy cattle populations, intending to combine increases in productive trait phenotypes with improvements in reproductive, health, welfare, linear conformation, and adaptability traits into the foreseeable future.

Genetic load: genomic estimates and applications in non-model animals

Genetic variation, which is generated by mutation, recombination and gene flow, can reduce the mean fitness of a population, both now and in the future. This 'genetic load' has been estimated in a wide range of animal taxa using various approaches. Advances in genome sequencing and computational techniques now enable us to estimate the genetic load in populations and individuals without direct fitness estimates. Here, we review the classic and contemporary literature of genetic load. We describe approaches to quantify the genetic load in whole-genome sequence data based on evolutionary conservation and annotations. We show that splitting the load into its two components - the realized load (or expressed load) and the masked load (or inbreeding load) - can improve our understanding of the population genetics of deleterious mutations.

Genetic Diversity in the Italian Holstein Dairy Cattle Based on Pedigree and SNP Data Prior and After Genomic Selection

Genetic diversity has become an urgent matter not only in small local breeds but also in more specialized ones. While the use of genomic data in livestock breeding programs increased genetic gain, there is increasing evidence that this benefit may be counterbalanced by the potential loss of genetic variability. Thus, in this study, we aimed to investigate the genetic diversity in the Italian Holstein dairy cattle using pedigree and genomic data from cows born between 2002 and 2020. We estimated variation in inbreeding, effective population size, and generation interval and compared those aspects prior to and after the introduction of genomic selection in the breed. The dataset contained 84,443 single-nucleotide polymorphisms (SNPs), and 74,485 cows were analyzed. Pedigree depth based on complete generation equivalent was equal to 10.67. A run of homozygosity (ROH) analysis was adopted to estimate SNP-based inbreeding (F_ROH). The average pedigree inbreeding was 0.07, while the average F_ROH was more than double, being equal to 0.17. The pattern of the effective population size based on pedigree and SNP data was similar although different in scale, with a constant decrease within the last five generations. The overall inbreeding rate (ΔF) per year was equal to +0.27% and +0.44% for F_ped and F_ROH throughout the studied period, which corresponded to about +1.35% and +2.2% per generation, respectively. A significant increase in the ΔF was found since the introduction of genomic selection in the breed. This study in the Italian Holstein dairy cattle showed the importance of controlling the loss of genetic diversity to ensure the long-term sustainability of this breed, as well as to guarantee future market demands.

Temporal and region‐specific variations in genome‐wide inbreeding effects on female size and reproduction traits of rainbow trout

Recent studies have shown that current levels of inbreeding, estimated by runs of homozygosity (ROH), are moderate to high in farmed rainbow trout lines. Based on ROH metrics, the aims of our study were to (i) quantify inbreeding effects on female size (postspawning body weight, fork length) and reproduction traits (spawning date, coelomic fluid weight, spawn weight, egg number, average egg weight) in rainbow trout, and (ii) identify both the genomic regions and inbreeding events affecting performance. We analysed the performance of 1346 females under linear animal models including random additive and dominance genetics effects, with fixed covariates accounting for inbreeding effects at different temporal and genomic scales. A significant effect of genome‐wide inbreeding (F) was only observed for spawning date and egg weight, with performance variations of +12.3% and −3.8%, respectively, for 0.1 unit increase in F level. At different local genomic scales, we observed highly variable inbreeding effects on the seven traits under study, ranging from increasing to decreasing trait values. As widely reported in the literature, the main scenario observed during this study was a negative impact of recent inbreeding. However, other scenarios such as positive effects of recent inbreeding or negative impacts of old inbreeding were also observed. Although partial dominance appeared to be the main hypothesis explaining inbreeding depression for all the traits studied, the overdominance hypothesis might also play a significant role in inbreeding depression affecting fecundity (egg number and mass) traits in rainbow trout. These findings suggest that region‐specific inbreeding can strongly impact performance without necessarily observing genome‐wide inbreeding effects. They shed light on the genetic architecture of inbreeding depression and its evolution along the genome over time. The use of region‐specific metrics may enable breeders to more accurately manage the trade‐off between genetic merit and the undesirable side effects associated with inbreeding.

Runs of homozygosity analysis reveals consensus homozygous regions affecting production traits in Chinese Simmental beef cattle

BACKGROUND

Genomic regions with a high frequency of runs of homozygosity (ROH) are related to important traits in farm animals. We carried out a comprehensive analysis of ROH and evaluated their association with production traits using the BovineHD (770 K) SNP array in Chinese Simmental beef cattle.

RESULTS

We detected a total of 116,953 homozygous segments with 2.47Gb across the genome in the studied population. The average number of ROH per individual was 99.03 and the average length was 117.29 Mb. Notably, we detected 42 regions with a frequency of more than 0.2. We obtained 17 candidate genes related to body size, meat quality, and reproductive traits. Furthermore, using Fisher's exact test, we found 101 regions were associated with production traits by comparing high groups with low groups in terms of production traits. Of those, we identified several significant regions for production traits (P < 0.05) by association analysis, within which candidate genes including ECT2, GABRA4, and GABRB1 have been previously reported for those traits in beef cattle.

CONCLUSIONS

Our study explored ROH patterns and their potential associations with production traits in beef cattle. These results may help to better understand the association between production traits and genome homozygosity and offer valuable insights into managing inbreeding by designing reasonable breeding programs in farm animals.

Familial follicular cell thyroid carcinomas in a large number of Dutch German longhaired pointers

Thyroid carcinomas (TCs) originating from follicular cells of the thyroid gland occur in both humans and dogs, and they have highly similar histomorphologic patterns. In dogs, TCs have not been extensively investigated, especially concerning the familial origin of TCs. Here, we report familial thyroid follicular cell carcinomas (FCCs) confirmed by histology in 54 Dutch origin German longhaired pointers. From the pedigree, 45 of 54 histopathologically confirmed cases are closely related to a pair of first‐half cousins in the past, indicating a familial disease. In addition, genetics contributed more to the thyroid FCC than other factors by an estimated heritability of 0.62 based on pedigree. The age of diagnosis ranged between 4.5 and 13.5 years, and 76% of cases were diagnosed before 10 years of age, implying an early onset of disease. We observed a significant higher pedigree‐based inbreeding coefficient in the affected dogs (mean F, 0.23) compared to unaffected dogs (mean F, 0.14), suggesting the contribution of inbreeding to tumour development. The unique occurrence of familial thyroid FCC in this dog population and the large number of affected dogs make this population an important model to identify the genetic basis of familial thyroid FCC in this breed and may contribute to the research into pathogenesis, prevention and treatment in humans.

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.

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

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.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07872-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.

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.

Genome-wide scan reveals genetic divergence in Italian Holstein cows bred within PDO cheese production chains

Dairy cattle breeds have been exposed to intense artificial selection for milk production traits over the last fifty years. In Italy, where over 80% of milk is processed into cheese, selection has also focused on cheese-making traits. Due to a deep-rooted tradition in cheese-making, currently fifty Italian cheeses are marked with the Protected Designation of Origin (PDO) label as they proved traditional land of origin and procedures for milk transformation. This study aimed to explore from a genetic point of view if the presence of such diverse productive contexts in Italy have shaped in a different manner the genome of animals originally belonging to a same breed. We analyzed high density genotype data from 1000 Italian Holstein cows born between 2014 and 2018. Those animals were either farmed in one of four Italian PDO consortia or used for drinkable milk production only. Runs of Homozygosity, Bayesian Information Criterion and Discriminant Analysis of Principal Components were used to evaluate potential signs of genetic divergence within the breed. We showed that the analyzed Italian Holstein cows have genomic inbreeding level above 5% in all subgroups, reflecting the presence of ongoing artificial selection in the breed. Our study provided a comprehensive representation of the genetic structure of the Italian Holstein breed, highlighting the presence of potential genetic subgroups due to divergent dairy farming systems. This study can be used to further investigate genetic variants underlying adaptation traits in these subgroups, which in turn might be used to design more specialized breeding programs.

Genome-wide association study and inbreeding depression on body size traits in Qira black sheep (Ovis aries)

Qira black sheep is a famous indigenous sheep breed in China. The objectives of this study are to identify candidate genes related to body size, and to estimate the level of inbreeding depression on body size based on runs of homozygosity in Qira black sheep. Here, 188 adult Qira black sheep were genotyped with a high density (630 K) SNP chip and genome-wide association study for body weight and body size traits (including withers height, body slanting length, tail length, chest girth, chest width, and chest depth) were performed using an additive linear model. In consequence, 12 genome- and chromosome-wide significant SNPs and, accordingly, six candidate genes involved in muscle differentiation, metabolism and cell processes were identified. Of them, ZNF704 (zinc finger protein 704) was identified for body weight; AK2 (adenylate kinase 2) and PARK2 (parkin RBR E3 ubiquitin protein ligase) for tail length; MOCOS (molybdenum cofactor sulfurase) and ELP2 (elongator acetyltransferase complex subunit 2) for chest width; and MFAP1 (microfibril associated protein 1) for chest girth. Additionally, inbreeding depressions on body size were observed in the current herd. These results will provide insightful understandings into the genetic mechanisms of adult body size, and into the conservation and utilization of Qira black sheep.

High-Level Gene Flow Restricts Genetic Differentiation in Dairy Cattle Populations in Thailand: Insights from Large-Scale Mt D-Loop Sequencing

Domestication and artificial selection lead to the development of genetically divergent cattle breeds or hybrids that exhibit specific patterns of genetic diversity and population structure. Recently developed mitochondrial markers have allowed investigation of cattle diversity worldwide; however, an extensive study on the population-level genetic diversity and demography of dairy cattle in Thailand is still needed. Mitochondrial D-loop sequences were obtained from 179 individuals (hybrids of Bos taurus and B. indicus) sampled from nine different provinces. Fifty-one haplotypes, of which most were classified in haplogroup "I", were found across all nine populations. All sampled populations showed severely reduced degrees of genetic differentiation, and low nucleotide diversity was observed in populations from central Thailand. Populations that originated from adjacent geographical areas tended to show high gene flow, as revealed by patterns of weak network structuring. Mismatch distribution analysis was suggestive of a stable population, with the recent occurrence of a slight expansion event. The results provide insights into the origins and the genetic relationships among local Thai cattle breeds and will be useful for guiding management of cattle breeding in Thailand.

Sperm morphometry is affected by increased inbreeding in the Retinta cattle breed: A molecular approach

The effect of inbreeding depression on sperm motility is well documented, but its influence on sperm morphometry has been scarcely examined to date. Here, we combined the use of computer-assisted sperm morphometry analysis (CASMA) with a SNP-based genomic approach to determine and characterize the effect of inbreeding on the sperm shape of a highly inbred cattle population. We determined seven morphometric parameters on frozen-thawed sperm samples of 57 Retinta bulls: length (L, µm), width (W, µm), area (A, µm² ), perimeter (P, µm), ellipticity (ELI; L/W), elongation (L-W)/(L + W) and perimeter-to-area shape factor (p2a; P² /4 × π × A). The comparison of highly inbred (HI) and lowly inbreed (LI) individuals based on runs of homozygosity (ROH) inbreeding values (F _ROH ) showed no differences between groups. An additional two-step unsupervised sperm subpopulation analysis based on morphometric parameters showed significant differences in the abundance of different sperm subpopulations between groups (p < 0.05). This analysis revealed that HI bulls harbored a higher percentage of narrow-head sperm as opposed to the higher percentage of large- and round-headed sperm detected in LI. A further genomic characterization revealed 23 regions differentially affected by inbreeding in both groups, detecting six genes (SPAG6, ARMC3, PARK7, VAMP3, DYNLRB2, and PHF7) previously related to different spermatogenesis-associated processes.

Association of inbreeding and regional equine leucocyte antigen homozygosity with the prevalence of insect bite hypersensitivity in Old Kladruber horse

Inbreeding depression is the reduction of performance caused by mating of close relatives. In livestock populations, inbreeding depression has been traditionally estimated by regression of phenotypes on pedigree inbreeding coefficients. This estimation can be improved by utilising genomic inbreeding coefficients. Here we estimate inbreeding depression for insect bite hypersensitivity (IBH) prevalence, the most common allergic horse disease worldwide, in Old Kladruber horse. In a deep pedigree with 3214 horses (187 genotyped), we used a generalised linear mixed model with IBH phenotype from 558 horses examined between 1996 and 2009 (1368 records). In addition to the classical pedigree information, we used the single-step approach that enabled joint use of pedigree and genomic information to estimate inbreeding depression overall genome and equine leucocyte antigen (ELA) class II region. Significant inbreeding depression was observed in all models fitting overall inbreeding coefficients (odds ratio between 1.018 and 1.074, P < 0.05) with the exception of Kalinowski's new inbreeding (P = 0.0516). The increase of ELA class II inbreeding was significantly associated with increased prevalence of IBH (odds ratio 1.018; P = 0.027). However, when fitted jointly with the overall inbreeding coefficient, the effect of ELA class II inbreeding was not significant (odds ratio 1.016; P = 0.062). Overall, the higher ELA class II and/or overall inbreeding (pedigree or genomic) was associated with increased prevalence of IBH in Old Kladruber horses. The single-step approach provides an efficient use of all the available pedigree, genomic, and phenotype information for estimation of overall and regional inbreeding effects.

Genomic inbreeding and selection signatures in the local dairy breed Icelandic Cattle

Icelandic Cattle is the only dairy cattle breed native to Iceland. It currently numbers ca. 26 000 breeding females. We used 50k genotypes of over 8000 Icelandic Cattle to estimate genomic and pedigree-based inbreeding and to detect selection signatures using the integrated haplotype score. We used 47 Icelandic bulls genotyped with a 770k SNP chip to estimate LD decay for comparison with other Nordic dairy cattle breeds. We detected ROHs on the autosomes and computed ROH-based autosomal inbreeding coefficients. Average inbreeding coefficients according to pedigree and ROHs were 0.0621 and 0.101. Effective population sizes for the years 2009-2017 according to pedigree, ROHs, genomic relationship matrix, excess of homozygosity and individual increase in inbreeding were 81, 65, 60, 58 and 92 respectively. We identified three regions and six candidate genes that showed a signature of selection according to the integrated haplotype score (P < 0.05) on chromosomes 1, 16 and 23. The LD structure of Icelandic Cattle is shaped by a long period of isolation and a small founder population. The estimate of LD at distances closer than 0.3 Mb is lower in Icelandic Cattle than in Danish Jersey, but is higher than in Danish Holstein and Red Nordic Dairy Cattle breeds. Our findings show that inbreeding rates in Icelandic Cattle currently are sustainable according to FAO guidelines, and our results do not indicate severe historical inbreeding.

Assessing the genetic background and genomic relatedness of red cattle populations originating from Northern Europe

Background

Local cattle breeds need special attention, as they are valuable reservoirs of genetic diversity. Appropriate breeding decisions and adequate genomic management of numerically smaller populations are required for their conservation. At this point, the analysis of dense genome-wide marker arrays provides encompassing insights into the genomic constitution of livestock populations. We have analyzed the genetic characterization of ten cattle breeds originating from Germany, The Netherlands and Denmark belonging to the group of red dairy breeds in Northern Europe. The results are intended to provide initial evidence on whether joint genomic breeding strategies of these populations will be successful.

Results

Traditional Danish Red and Groningen White-Headed were the most genetically differentiated breeds and their populations showed the highest levels of inbreeding. In contrast, close genetic relationships and shared ancestry were observed for the populations of German Red and White Dual-Purpose, Dutch Meuse-Rhine-Yssel, and Dutch Deep Red breeds, reflecting their common histories. A considerable amount of gene flow from Red Holstein to German Angler and to German Red and White Dual-Purpose was revealed, which is consistent with frequent crossbreeding to improve productivity of these local breeds. In Red Holstein, marked genomic signatures of selection were reported on chromosome 18, suggesting directed selection for important breeding goal traits. Furthermore, tests for signatures of selection between Red Holstein, Red and White Dual-Purpose, and Meuse-Rhine-Yssel uncovered signals for all investigated pairs of populations. The corresponding genomic regions, which were putatively under different selection pressures, harboured various genes which are associated with traits such as milk and beef production, mastitis and female fertility.

Conclusions

This study provides comprehensive knowledge on the genetic constitution and genomic connectedness of divergent red cattle populations in Northern Europe. The results will help to design and optimize breeding strategies. A joint genomic evaluation including some of the breeds studied here seems feasible.

Runs of homozygosity and analysis of inbreeding depression

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.

Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions

Understanding the biological mechanisms of climatic adaptation is of paramount importance for the optimization of breeding programs and conservation of genetic resources. The aim of this study was to investigate genetic diversity and unravel genomic regions potentially under selection for heat and/or cold tolerance in thirty-two worldwide cattle breeds, with a focus on Chinese local cattle breeds adapted to divergent climatic conditions, Datong yak (Bos grunniens; YAK), and Bali (Bos javanicus) based on dense SNP data. In general, moderate genetic diversity levels were observed in most cattle populations. The proportion of polymorphic SNP ranged from 0.197 (YAK) to 0.992 (Mongolian cattle). Observed and expected heterozygosity ranged from 0.023 (YAK) to 0.366 (Sanhe cattle; SH), and from 0.021 (YAK) to 0.358 (SH), respectively. The overall average inbreeding (±SD) was: 0.118 ± 0.028, 0.228 ± 0.059, 0.194 ± 0.041, and 0.021 ± 0.004 based on the observed versus expected number of homozygous genotypes, excess of homozygosity, correlation between uniting gametes, and runs of homozygosity (ROH), respectively. Signatures of selection based on multiple scenarios and methods (F ST, HapFLK, and ROH) revealed important genomic regions and candidate genes. The candidate genes identified are related to various biological processes and pathways such as heat-shock proteins, oxygen transport, anatomical traits, mitochondrial DNA maintenance, metabolic activity, feed intake, carcass conformation, fertility, and reproduction. This highlights the large number of biological processes involved in thermal tolerance and thus, the polygenic nature of climatic resilience. A comprehensive description of genetic diversity measures in Chinese cattle and YAK was carried out and compared to 24 worldwide cattle breeds to avoid potential biases. Numerous genomic regions under positive selection were detected using three signature of selection methods and candidate genes potentially under positive selection were identified. Enriched function analyses pinpointed important biological pathways, molecular function and cellular components, which contribute to a better understanding of the biological mechanisms underlying thermal tolerance in cattle. Based on the large number of genomic regions identified, thermal tolerance has a complex polygenic inheritance nature, which was expected considering the various mechanisms involved in thermal stress response.