Standard Deviations: The Biological Bases of Transmission Ratio Distortion.

The rule of Mendelian inheritance is remarkably robust, but deviations from the equal transmission of alternative alleles at a locus [a.k.a. transmission ratio distortion (TRD)] are also commonly observed in genetic mapping populations. Such TRD reveals locus-specific selection acting at some point between the diploid heterozygous parents and progeny genotyping and therefore can provide novel insight into otherwise-hidden genetic and evolutionary processes. Most of the classic selfish genetic elements were discovered through their biasing of transmission, but many unselfish evolutionary and developmental processes can also generate TRD. In this review, we describe methodologies for detecting TRD in mapping populations, detail the arenas and genetic interactions that shape TRD during plant and animal reproduction, and summarize patterns of TRD from across the genetic mapping literature. Finally, we point to new experimental approaches that can accelerate both detection of TRD and characterization of the underlying genetic mechanisms.

Detecting inbreeding depression in structured populations.

Measuring inbreeding and its consequences on fitness is central for many areas in biology including human genetics and the conservation of endangered species. However, there is no consensus on the best method, neither for quantification of inbreeding itself nor for the model to estimate its effect on specific traits. We simulated traits based on simulated genomes from a large pedigree and empirical whole-genome sequences of human data from populations with various sizes and structures (from the 1,000 Genomes project). We compare the ability of various inbreeding coefficients ([Formula: see text]) to quantify the strength of inbreeding depression: allele-sharing, two versions of the correlation of uniting gametes which differ in the weight they attribute to each locus and two identical-by-descent segments-based estimators. We also compare two models: the standard linear model and a linear mixed model (LMM) including a genetic relatedness matrix (GRM) as random effect to account for the nonindependence of observations. We find LMMs give better results in scenarios with population or family structure. Within the LMM, we compare three different GRMs and show that in homogeneous populations, there is little difference among the different [Formula: see text] and GRM for inbreeding depression quantification. However, as soon as a strong population or family structure is present, the strength of inbreeding depression can be most efficiently estimated only if i) the phenotypes are regressed on [Formula: see text] based on a weighted version of the correlation of uniting gametes, giving more weight to common alleles and ii) with the GRM obtained from an allele-sharing relatedness estimator.

Assessing different metrics of pedigree and genomic inbreeding and inbreeding effect on growth, fertility, and feed efficiency traits in a closed-herd Nellore cattle population.

BACKGROUND: The selection of individuals based on their predicted breeding values and mating of related individuals can increase the proportion of identical-by-descent alleles. In this context, the objectives of this study were to estimate inbreeding coefficients based on alternative metrics and data sources such as pedigree (FPED), hybrid genomic relationship matrix H (FH), and ROH of different length (FROH); and calculate Pearson correlations between the different metrics in a closed Nellore cattle population selected for body weight adjusted to 378 days of age (W378). In addition to total FROH (all classes) coefficients were also estimated based on the size class of the ROH segments: FROH1 (1-2 Mb), FROH2 (2-4 Mb), FROH3 (4-8 Mb), FROH4 (8-16 Mb), and FROH5 (> 16 Mb), and for each chromosome (FROH_CHR). Furthermore, we assessed the effect of each inbreeding metric on birth weight (BW), body weights adjusted to 210 (W210) and W378, scrotal circumference (SC), and residual feed intake (RFI). We also evaluated the chromosome-specific effects of inbreeding on growth traits. RESULTS: The correlation between FPED and FROH was 0.60 while between FH and FROH and FH and FPED were 0.69 and 0.61, respectively. The annual rate of inbreeding was 0.16% for FPED, 0.02% for FH, and 0.16% for FROH. A 1% increase in FROH5 resulted in a reduction of up to -1.327 ± 0.495 kg in W210 and W378. Four inbreeding coefficients (FPED, FH, FROH2, and FROH5) had a significant effect on W378, with reductions of up to -3.810 ± 1.753 kg per 1% increase in FROH2. There was an unfavorable effect of FPED on RFI (0.01 ± 0.0002 kg dry matter/day) and of FROH on SC (-0.056 ± 0.022 cm). The FROH_CHR coefficients calculated for BTA3, BTA5, and BTA8 significantly affected the growth traits. CONCLUSIONS: Inbreeding depression was observed for all traits evaluated. However, these effects were greater for the criterion used for selection of the animals (i.e., W378). The increase in the genomic inbreeding was associated with a higher inbreeding depression on the traits evaluated when compared to pedigree-based inbreeding. Genomic information should be used as a tool during mating to optimize control of inbreeding and, consequently, minimize inbreeding depression in Nellore cattle.

Genomic Underpinnings of Population Persistence in Isle Royale Moose.

Island ecosystems provide natural laboratories to assess the impacts of isolation on population persistence. However, most studies of persistence have focused on a single species, without comparisons to other organisms they interact with in the ecosystem. The case study of moose and gray wolves on Isle Royale allows for a direct contrast of genetic variation in isolated populations that have experienced dramatically differing population trajectories over the past decade. Whereas the Isle Royale wolf population recently declined nearly to extinction due to severe inbreeding depression, the moose population has thrived and continues to persist, despite having low genetic diversity and being isolated for ∼120 years. Here, we examine the patterns of genomic variation underlying the continued persistence of the Isle Royale moose population. We document high levels of inbreeding in the population, roughly as high as the wolf population at the time of its decline. However, inbreeding in the moose population manifests in the form of intermediate-length runs of homozygosity suggestive of historical inbreeding and purging, contrasting with the long runs of homozygosity observed in the smaller wolf population. Using simulations, we confirm that substantial purging has likely occurred in the moose population. However, we also document notable increases in genetic load, which could eventually threaten population viability over the long term. Overall, our results demonstrate a complex relationship between inbreeding, genetic diversity, and population viability that highlights the use of genomic datasets and computational simulation tools for understanding the factors enabling persistence in isolated populations.

Genomic partitioning of inbreeding depression in humans.

Across species, offspring of related individuals often exhibit significant reduction in fitness-related traits, known as inbreeding depression (ID), yet the genetic and molecular basis for ID remains elusive. Here, we develop a method to quantify enrichment of ID within specific genomic annotations and apply it to human data. We analyzed the phenomes and genomes of ∼350,000 unrelated participants of the UK Biobank and found, on average of over 11 traits, significant enrichment of ID within genomic regions with high recombination rates (>21-fold; p < 10-5), with conserved function across species (>19-fold; p < 10-4), and within regulatory elements such as DNase I hypersensitive sites (∼5-fold; p = 8.9 × 10-7). We also quantified enrichment of ID within trait-associated regions and found suggestive evidence that genomic regions contributing to additive genetic variance in the population are enriched for ID signal. We find strong correlations between functional enrichment of SNP-based heritability and that of ID (r = 0.8, standard error: 0.1). These findings provide empirical evidence that ID is most likely due to many partially recessive deleterious alleles in low linkage disequilibrium regions of the genome. Our study suggests that functional characterization of ID may further elucidate the genetic architectures and biological mechanisms underlying complex traits and diseases.

Early-acting inbreeding depression can evolve as an inbreeding avoidance mechanism.

Despite the potential for mechanical, developmental and/or chemical mechanisms to prevent self-fertilization, incidental self-fertilization is inevitable in many predominantly outcrossing species. In such cases, inbreeding can compromise individual fitness. Unquestionably, much of this inbreeding depression is maladaptive. However, we show that when reproductive compensation allows for the replacement of inviable embryos lost early in development, selection can favour deleterious recessive variants that induce 'self-sacrificial' death of inbred embryos. Our theoretical results provide numerous testable predictions which could challenge the assumption that inbreeding depression is always maladaptive. Our work is applicable any species that cannot fully avoid inbreeding, exhibits substantial inbreeding depression, and has the potential to compensate embryos lost early in development. In addition to its general applicability, our theory suggests that self-sacrificial variants might be responsible for the remarkably low realized selfing rates of gymnosperms with high primary selfing rates, as gymnosperms exhibit strong inbreeding depression, have effective reproductive compensation mechanisms, and cannot evolve chemical self-incompatibility.

Inbreeding and high developmental temperatures affect cognition and boldness in guppies (Poecilia reticulata).

Inbreeding impairs the cognitive abilities of humans, but its impact on cognition in other animals is poorly studied. For example, environmental stress (e.g. food limitation and extreme temperatures) often amplifies inbreeding depression in morphological traits, but whether cognition is similarly affected is unclear. We, therefore, tested if a higher temperature (30°C versus 26°C) during development exacerbates any difference in inhibitory control between inbred (f = 0.25) and outbred guppies (Poecilia reticulata). Inhibitory control is an aspect of cognition that is often measured in vertebrates using a detour test, in which animals have to navigate around a transparent barrier to reach a reward. We also tested if inbreeding and temperature affect 'boldness', which is a putative personality trait in guppies. Inbreeding lowered inhibitory control of guppies raised at the higher temperature but not those raised at the control temperature. Inbred fish were significantly less bold than outbred fish. In addition, males, but not females, raised at the higher temperature had significantly lower inhibitory control. There was no effect of temperature on the boldness of either sex. Our study is among the first to test if experimentally induced inbreeding impairs cognition in a non-domesticated vertebrate. We show that both inbreeding and higher temperatures during development can affect the behaviour and cognitive abilities of fish. These findings are noteworthy given the twin threats of rising global temperatures and more frequent inbreeding as habitat fragmentation reduces population sizes.

Genetic architecture of inbreeding depression may explain its persistence in a population of wild red deer.

Inbreeding depression is of major concern in declining populations, but relatively little is known about its genetic architecture in wild populations, such as the degree to which it is composed of large or small effect loci and their distribution throughout the genome. Here, we combine fitness and genomic data from a wild population of red deer to investigate the genomic distribution of inbreeding effects. Based on the runs of homozygosity (ROH)-based inbreeding coefficient, FROH, we use chromosome-specific inbreeding coefficients (FROHChr) to explore whether the effect of inbreeding varies between chromosomes. Under the assumption that within an individual the probability of being identical-by-descent is equal across all chromosomes, we used a multi-membership model to estimate the deviation of FROHChr from the average inbreeding effect. This novel approach ensures effect sizes are not overestimated whilst maximising the power of our available dataset of >3000 individuals genotyped on >35,000 autosomal SNPs. We find that most chromosomes confer a minor reduction in fitness-related traits, which when these effects are summed, results in the observed inbreeding depression in birth weight, survival and lifetime breeding success. However, no chromosomes had a significant detrimental effect compared to the overall effect of inbreeding, indicating no major effect loci. We conclude that in this population, inbreeding depression is likely the result of multiple mildly or moderately deleterious mutations spread across all chromosomes, which are difficult to detect with statistical confidence. Such mutations will be inefficiently purged, which may explain the persistence of inbreeding depression in this population.

Adaptive potential in the face of a transmissible cancer in Tasmanian devils.

Emerging infectious diseases (EIDs) not only cause catastrophic declines in wildlife populations but also generate selective pressures that may result in rapid evolutionary responses. One such EID is devil facial tumour disease (DFTD) in the Tasmanian devil. DFTD is almost always fatal and has reduced the average lifespan of individuals by around 2 years, likely causing strong selection for traits that reduce susceptibility to the disease, but population decline has also left Tasmanian devils vulnerable to inbreeding depression. We analysed 22 years of data from an ongoing study of a population of Tasmanian devils on Freycinet Peninsula, Tasmania, to (1) identify whether DFTD may be causing selection on body size, by estimating phenotypic and genetic correlations between DFTD and size traits, (2) estimate the additive genetic variance of susceptibility to DFTD, and (3) investigate whether size traits or susceptibility to DFTD were under inbreeding depression. We found a positive phenotypic relationship between head width and susceptibility to DFTD, but this was not underpinned by a genetic correlation. Conversely, we found a negative phenotypic relationship between body weight and susceptibility to DFTD, and there was evidence for a negative genetic correlation between susceptibility to DFTD and body weight. There was additive genetic variance in susceptibility to DFTD, head width and body weight, but there was no evidence for inbreeding depression in any of these traits. These results suggest that Tasmanian devils have the potential to respond adaptively to DFTD, although the realised evolutionary response will critically further depend on the evolution of DFTD itself.

Patterns and effects of gene flow on adaptation across spatial scales: implications for management.

Gene flow can have rapid effects on adaptation and is an important evolutionary tool available when undertaking biological conservation and restoration. This tool is underused partly because of the perceived risk of outbreeding depression and loss of mean fitness when different populations are crossed. In this article, we briefly review some theory and empirical findings on how genetic variation is distributed across species ranges, describe known patterns of gene flow in nature with respect to environmental gradients, and highlight the effects of gene flow on adaptation in small or stressed populations in challenging environments (e.g., at species range limits). We then present a case study involving crosses at varying spatial scales among mountain populations of a trigger plant (Stylidium armeria: Stylidiaceae) in the Australian Alps to highlight how some issues around gene flow effects can be evaluated. We found evidence of outbreeding depression in seed production at greater geographic distances. Nevertheless, we found no evidence of maladaptive gene flow effects in likelihood of germination, plant performance (size), and performance variance, suggesting that gene flow at all spatial scales produces offspring with high adaptive potential. This case study demonstrates a path to evaluating how increasing sources of gene flow in managed wild and restored populations could identify some offspring with high fitness that could bolster the ability of populations to adapt to future environmental changes. We suggest further ways in which managers and researchers can act to understand and consider adaptive gene flow in natural and conservation contexts under rapidly changing conditions.

Simulation analyses of the evolution of intra-inflorescence flowering patterns assuming selection on anthesis interval among individual flowers.

What conditions select flowering patterns within inflorescences, or variation in the anthesis interval within inflorescences among plants? Under what conditions are gradual blooming and simultaneous blooming, both traits related to floral display size, advantageous? We constructed a simulation model in which the opening times and longevities of individual flowers within inflorescences, the sizes of attractive structures of individual flowers, and the numbers of ovules and pollen grains produced by individual flowers evolve. Individual plants in the population compete for pollinators, and plants are selected by pollinators according to their floral display sizes and amounts of resources allocated to attractive structures. We found that, if the proportion of pollen on a pollinator deposited on a stigma was low, gradual blooming did not evolve even if inbreeding depression was greater than 0.5. This is because the amount of outcross-pollen on pollinators decreased at a low rate during flower visits within a single inflorescence, and the selfing rate was suppressed to a low level even if the floral display size was large. On the other hand, if the proportion of pollen deposition was high, gradual blooming evolved even if inbreeding depression was smaller than 0.5. This may be because gradual blooming can enhance pollen delivery to other plants by reducing the loss of self-pollen by geitonogamy. On the other hand, allocation ratios among floral organs (female and male organs and attractive structures) were independent of the degree of simultaneous and gradual blooming within inflorescences. We concluded that the evolution of gradual blooming is more strongly affected by the proportion of pollen on a pollinator deposited on a stigma than by inbreeding depression.

Fisher's automatic advantage of self-fertilization does not apply in cleistogamous species.

PREMISE: In hermaphroditic plants, the evolution of self-fertilization is driven by two major forces; the cost of outcrossing or Fisher's automatic advantage of selfing and inbreeding depression. Seminal theoretical works have established that an inbreeding depression threshold of 0.5 governs the evolution. Below that threshold, selfing evolves, above that, outcrossing evolves. Does this threshold apply to cleistogamous plants? METHODS: I developed a model using a Lloydian approach to analyze the evolution of cleistogamy. RESULTS: I showed that the inbreeding depression threshold does not apply in cleistogamous species, and that because cleistogamous (closed) flowers do not export pollen, Fisher's advantage of selfing is totally cancelled. CONCLUSIONS: In line with model predictions, I discuss the fact that cleistogamous species often exhibit low inbreeding depression in empirical studies.

Optimal outbreeding is shaped during larval life-history in the splash pool copepod Tigriopus californicus.

Inbreeding and outbreeding depression are dynamic forms of selection critical to mating system evolution and the efficacy of conservation biology. Most evidence on how the relative severity and timing of these forces are shaped is confined to self-fertilization, distant outcrossing, and intermediate 'optimal outcrossing' in hermaphrodites. We tested the notion that closed population demographics may reduce and delay the costs of inbreeding relative to distant outbreeding in an intertidal copepod with separate sexes and a biphasic larval / post-metamorphic life-history (Tigriopus californicus). At three lifecycle stages (fecundity, metamorphosis, and post-metamorphosis), we quantified the effects of inbreeding and outbreeding in crosses with varying degrees of recent common ancestry. Although inbreeding and outbreeding depression have distinct genetic mechanisms, both manifested the same stage-specific consequences for fitness. Inbreeding and outbreeding depression were not apparent for fecundity, post-metamorphic survival, sex ratio, or the ability to acquire mates, but inbreeding between full siblings and outbreeding between interpopulation hybrids reduced the fraction of offspring that completed metamorphosis by 32% and 47%, respectively. On average, the effects of inbreeding on metamorphic rate were weaker and nearly twice as variable among families than those of outbreeding, suggesting genetic load was less pervasive than the incompatibilities accrued between divergent populations. Overall, our results indicate the transition from larval to juvenile life stages is markedly susceptible to both inbreeding and outbreeding depression in T. californicus. We suggest stage-specific selection acting concurrently with the timing of metamorphosis may be an instrumental factor shaping reproductive optima in species with complex life-histories.

The difficulty of detecting inbreeding depression and its effect on conservation decisions.

Statistical inferences about inbreeding depression are often derived from analyses with low power and a high risk of failing to detect inbreeding depression. That risk is widely appreciated by scientists familiar with the relevant statistical and genetical theory, but may be overlooked and underappreciated by decision-makers. Consequently, there is value in demonstrating this risk using a real example. We use data from the wolf population on Isle Royale to demonstrate the difficulty of making reliable statistical inferences about inbreeding depression. This wolf population is known-by other methods-to have gone effectively extinct due to deleterious genetic processes associated with inbreeding. Beyond that demonstration, we use two case-studies-wolves on Isle Royale and vaquita (porpoises) from the Gulf of California, Mexico-to show how statistical inferences about inbreeding depression can affect conservation decisions. According to most decision theory, decisions depend importantly on: 1) probabilities that certain states exist (e.g. inbreeding depression is present) and 2) the utility assigned to various outcomes (e.g. the value of acting to mitigate inbreeding when it is present). The probabilities are provided by statistical inference; whereas utilities are almost entirely determined by normative values and judgements. Our analysis suggests that decisions to mitigate inbreeding depression are often driven more by utilities (normative values) than probabilities (statistical inferences). As such, advocates for mitigating inbreeding depression will benefit from better communicating to decision-makers the value of populations persisting and the extent to which decisions should depend on normative values.

The impact of identity by descent on fitness and disease in dogs.

Domestic dogs have experienced population bottlenecks, recent inbreeding, and strong artificial selection. These processes have simplified the genetic architecture of complex traits, allowed deleterious variation to persist, and increased both identity-by-descent (IBD) segments and runs of homozygosity (ROH). As such, dogs provide an excellent model for examining how these evolutionary processes influence disease. We assembled a dataset containing 4,414 breed dogs, 327 village dogs, and 380 wolves genotyped at 117,288 markers and data for clinical and morphological phenotypes. Breed dogs have an enrichment of IBD and ROH, relative to both village dogs and wolves, and we use these patterns to show that breed dogs have experienced differing severities of bottlenecks in their recent past. We then found that ROH burden is associated with phenotypes in breed dogs, such as lymphoma. We next test the prediction that breeds with greater ROH have more disease alleles reported in the Online Mendelian Inheritance in Animals (OMIA). Surprisingly, the number of causal variants identified correlates with the popularity of that breed rather than the ROH or IBD burden, suggesting an ascertainment bias in OMIA. Lastly, we use the distribution of ROH across the genome to identify genes with depletions of ROH as potential hotspots for inbreeding depression and find multiple exons where ROH are never observed. Our results suggest that inbreeding has played a large role in shaping genetic and phenotypic variation in dogs and that future work on understudied breeds may reveal new disease-causing variation.

The inflated significance of neutral genetic diversity in conservation genetics.

The current rate of species extinction is rapidly approaching unprecedented highs, and life on Earth presently faces a sixth mass extinction event driven by anthropogenic activity, climate change, and ecological collapse. The field of conservation genetics aims at preserving species by using their levels of genetic diversity, usually measured as neutral genome-wide diversity, as a barometer for evaluating population health and extinction risk. A fundamental assumption is that higher levels of genetic diversity lead to an increase in fitness and long-term survival of a species. Here, we argue against the perceived importance of neutral genetic diversity for the conservation of wild populations and species. We demonstrate that no simple general relationship exists between neutral genetic diversity and the risk of species extinction. Instead, a better understanding of the properties of functional genetic diversity, demographic history, and ecological relationships is necessary for developing and implementing effective conservation genetic strategies.

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.

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 and runs of homozygosity islands in Asturiana de los Valles cattle breed after 30 years of selection.

Inbreeding depression results in a decrease in the average phenotypic values of affected traits. It has been traditionally estimated from pedigree-based inbreeding coefficients. However, with the development of single-nucleotide polymorphism arrays, novel methods were developed for calculating the inbreeding coefficient, and consequently, inbreeding depression. The aim of the study was to analyse inbreeding depression in 6 growth and 2 reproductive traits in the Asturiana de los Valles cattle breed using both genealogical and molecular information. The pedigree group comprised 225,848 records and an average equivalent number of complete generations of 2.3. The molecular data comprised genotypes of 2693 animals using the Affymetrix medium-density chip. Using the pedigree information, three different inbreeding coefficients were estimated for the genotyped animals: the full pedigree coefficient (FPED), and the recent and ancient inbreeding coefficients based on the information of the last three generations (FPED<3G) and until the last three generations (FPED>3G), respectively. Using the molecular data, seven inbreeding coefficients were calculated. Four of them were estimated based on runs of homozygosity (ROH), considering (1) the total length (FROH), (2) segments shorter than 4 megabases (FROH<4), (3) between 4 and 17 megabases (FROH4-17), and (4) longer than 17 Mb (FROH>17). Additionally, the three inbreeding coefficients implemented in the Plink software (FHAT1-3) were estimated. Inbreeding depression was estimated using linear mixed-effects model with inbreeding coefficients used as covariates. All analysed traits (birth weight, preweaning average daily gain, weaning weight adjusted at 180 days, carcass weight, calving ease, age at first calving, calving interval) showed a statistically significant non-zero effect of inbreeding depression estimated from the pedigree group, except for the Postweaning Average Daily Gain trait. When inbreeding coefficients were based on the genomic group, statistically significant inbreeding depression was observed for two traits, Preweaning Average Daily Gain and Weaning Weight based on FROH, FROH>17, and FHAT3 inbreeding coefficients. Nevertheless, similar to inbreeding depression estimated based on pedigree information, estimates of inbreeding depression based on genomic information had no relevant economic impact. Despite this, from a long-term perspective, genotyped data could be included to maximize genetic progress in genetic programs following an optimal genetic contribution strategy and to consider individual inbreeding load instead global inbreeding. ROH islands were identified on chromosomes 2, 3, 8, 10, and 16. Such regions contain several candidate genes for growth development, intramuscular fat, body weight and lipid metabolism that are related to production traits selected in Asturiana de los Valles breed.

Effects of inbreeding on production traits and genetic evaluations in Guzerá beef cattle raised under tropical conditions.

The objectives of this study were to evaluate the influence of inbreeding on growth traits and body measurements, as well as on the estimation of genetic parameters and genetic trends in Guzerá cattle. Phenotypic records of 4,212 animals selected for postweaning weight from Guzerá Breeding Program of Advanced Beef Cattle Research Center were utilized. The pedigree file contained records from 7,213 animals born from 1928 to 2019. The traits analyzed were: birth weight (BW), weights adjusted to 210, 378 and 550 days of age (W210, W378 and W550, respectively), chest girth at 378 and 550 days of age (CG378 and CG550), scrotal circumference (SC), and hip height at 378 and 550 days of age (HH378 and H550). Linear regression was used to evaluate the effects of inbreeding on traits. Genetic parameters were obtained using models including or not the effect of inbreeding as a covariate. Inbreeding had negative effects (P ≤ 0.01) on BW (-0.09 kg), W378 (-2.86 kg), W550 (-2.95 kg), HH378 (-0.10 cm), and H550 (-0.29 cm). The lowest and highest heritability estimates were obtained for W210 (0.21 ± 0.07) and HH550 (0.57 ± 0.06), respectively. The genetic correlations were strong and positive between all traits, ranging from 0.44 ± 0.08 (SC x HH) to 0.99 ± 0.01 (W378 x W550). Spearman correlations between EBVs obtained with or without inbreeding effect ranged from 0.968 to 0.995 (P < 0.01). The results indicate loss of productive performance in inbred animals. However, the inclusion of inbreeding coefficient in genetic evaluation models did not alter the magnitude of genetic parameters or genetic trends for the traits studied.