Genome‐enabled prediction of reproductive traits in Nellore cattle using parametric models and machine learning methods

This study aimed to assess the predictive ability of different machine learning (ML) methods for genomic prediction of reproductive traits in Nellore cattle. The studied traits were age at first calving (AFC), scrotal circumference (SC), early pregnancy (EP) and stayability (STAY). The numbers of genotyped animals and SNP markers available were 2342 and 321 419 (AFC), 4671 and 309 486 (SC), 2681 and 319 619 (STAY) and 3356 and 319 108 (EP). Predictive ability of support vector regression (SVR), Bayesian regularized artificial neural network (BRANN) and random forest (RF) were compared with results obtained using parametric models (genomic best linear unbiased predictor, GBLUP, and Bayesian least absolute shrinkage and selection operator, BLASSO). A 5‐fold cross‐validation strategy was performed and the average prediction accuracy (ACC) and mean squared errors (MSE) were computed. The ACC was defined as the linear correlation between predicted and observed breeding values for categorical traits (EP and STAY) and as the correlation between predicted and observed adjusted phenotypes divided by the square root of the estimated heritability for continuous traits (AFC and SC). The average ACC varied from low to moderate depending on the trait and model under consideration, ranging between 0.56 and 0.63 (AFC), 0.27 and 0.36 (SC), 0.57 and 0.67 (EP), and 0.52 and 0.62 (STAY). SVR provided slightly better accuracies than the parametric models for all traits, increasing the prediction accuracy for AFC to around 6.3 and 4.8% compared with GBLUP and BLASSO respectively. Likewise, there was an increase of 8.3% for SC, 4.5% for EP and 4.8% for STAY, comparing SVR with both GBLUP and BLASSO. In contrast, the RF and BRANN did not present competitive predictive ability compared with the parametric models. The results indicate that SVR is a suitable method for genome‐enabled prediction of reproductive traits in Nellore cattle. Further, the optimal kernel bandwidth parameter in the SVR model was trait‐dependent, thus, a fine‐tuning for this hyper‐parameter in the training phase is crucial.     

Genetic relationship between growth and reproductive traits in Nellore cattle

The objective of this study was to evaluate the genetic relationship between postweaning weight gain (PWG), heifer pregnancy (HP), scrotal circumference (SC) at 18 months of age, stayability at 6 years of age (STAY) and finishing visual score at 18 months of age (PREC), and to determine the potential of these traits as selection criteria for the genetic improvement of growth and reproduction in Nellore cattle. The HP was defined as the observation that a heifer conceived and remained pregnant, which was assessed by rectal palpation at 60 days. The STAY was defined as whether or not a cow calved every year up to the age of 6 years, given that she was provided the opportunity to breed. The Bayesian linear-threshold analysis via the Gibbs sampler was used to estimate the variance and covariance components applying a multitrait model. Posterior mean estimates of direct heritability were 0.15 ± 0.00, 0.42 ± 0.02, 0.49 ± 0.01, 0.11 ± 0.01 and 0.19 ± 0.00 for PWG, HP, SC, STAY and PREC, respectively. The genetic correlations between traits ranged from 0.17 to 0.62. The traits studied generally have potential for use as selection criteria in genetic breeding programs. The genetic correlations between all traits show that selection for one of these traits does not imply the loss of the others.     

Two-trait random regression model to estimate the genetic association of scrotal circumference with female reproductive performance in Nelore cattle

In an attempt to determine when scrotal circumference (SC) could be a reasonable indicator of female reproductive performance, a series of two-trait random regression model (regression for SC on age at measurement) using Gibbs sampling was applied to field data of Nelore cattle raised in a tropical environment. The female traits evaluated were age at first calving (AFC), first calving interval (FCI), heifer pregnancy (HP), and stayability (STAY). The posterior means of heritability of female traits ranged from 0.15 for AFC to 0.46 for HP and were about 0.50 for SC. The posterior means of genetic correlations between SC and AFC, FCI, HP, STAY were up to −0.70, −0.25, 0.48, and 0.29, respectively. Genetically, SC could be a reasonable indicator of female puberty (e.g., HP) as long as it is measured at a young age (400–440 days). However, for female reproductive traits measured at an older age (e.g., STAY), SC is merely a modest or even poor indicator. The use of sire expected progeny differences for female reproductive traits will be more effective than the use of expected progeny differences for SC to improve the reproductive performance of female cattle.     

Body condition score of Nellore beef cows: a heritable measure to improve the selection of reproductive and maternal traits

Despite the economic importance of beef cattle production in Brazil, female reproductive performance, which is strongly associated with production efficiency, is not included in the selection index of most breeding programmes due to low heritability and difficulty in measure. The body condition score (BCS) could be used as an indicator of these traits. However, so far little is known about the feasibility of using BCS as a selection tool for reproductive performance in beef cattle. In this study, we investigated the sources of variation in the BCS of Nellore beef cows, quantified its association with reproductive and maternal traits and estimated its heritability. BCS was analysed using a logistic model that included the following effects: contemporary group at weaning, cow weight and hip height, calving order, reconception together with the weight and scores of conformation and early finishing assigned to calves at weaning. In the genetic analysis, variance components of BCS were estimated through Bayesian inference by fitting an animal model that also included the aforementioned effects. The results showed that BCS was significantly associated with all of the reproductive and maternal variables analysed. The estimated posterior mean of heritability of BCS was 0.24 (highest posterior density interval at 95%: 0.093 to 0.385), indicating an involvement of additive gene action in its determination. The present findings show that BCS can be used as a selection criterion for Nellore females.     

Genetics of crossbred sow longevity

The aim of this study was to estimate genetic parameters for longevity from Swedish crossbred sows to investigate the possibilities of selecting for this trait. Data were collected from 16 commercial piglet-producing herds, on crossbred (Landrace × Yorkshire) sows farrowing in the period 1 January 2001 to 31 December 2004. The data set with records on 10 373 sows was split into two sets according to the breed of the sire, i.e. Landrace sires (LS) or Yorkshire sires (YS). Removal hazard during productive life (PL) was analysed with survival analysis, using a sire model. Stayability from first to second litter (STAY12), stayability from first to third litter (STAY13), length of productive life (LPL) and lifetime production (LTP) were analysed with linear models, using an animal model. Females after the worst sire had 1.7 times higher (progeny of LS) and 2.4 times higher (progeny of YS) risk of removal than females after the best sire. Heritability for PL was estimated at 0.06 (LS) and 0.12 (YS). The heritabilities for the linear longevity traits ranged from 0.03 to 0.08. Genetic correlations between the four linear longevity traits were all high and positive (0.6 to 1.0), as were the phenotypic correlations (0.5 to 0.8). The correlations (Spearman rank) between the sire's estimated breeding values for all the five longevity traits were all significant (P < 0.001) and moderate to strong in both data sets. Estimated breeding value (EBV) correlations between the five longevity traits and traits included in the present Swedish breeding evaluation (Quality Genetics (QG)) were significant in a few cases. Significant and favourable EBV correlations were found between age at first farrowing and both STAY12 and STAY13 (-0.20 and -0.31), as well as between litter weight at 3 weeks and LPL and LTP (0.13 to 0.20). Significant and unfavourable EBV correlations were found between age at 100 kg and STAY12 (0.32), as well as between the exterior conformation score from testing station and PL (-0.20). The level of the estimated heritabilities for longevity indicates that genetic improvement of sow longevity would be possible. However, overall, there was no strong indirect selection for sow longevity with the current Swedish breeding evaluation (QG).     

How to quantify (the response to) sexual selection on traits

Natural selection operates via fitness components like mating success, fecundity, and longevity, which can be understood as intermediaries in the causal process linking traits to fitness. In particular, sexual selection occurs when traits influence mating or fertilization success, which, in turn, influences fitness. We show how to quantify both these steps in a single path analysis, leading to better estimates of the strength of sexual selection. Our model controls for confounding variables, such as body size or condition, when estimating the relationship between mating and reproductive success. Correspondingly, we define the Bateman gradient and the Jones index using partial rather than simple regressions, which better captures how they are commonly interpreted. The model can be applied both to purely phenotypic data and to quantitative genetic parameters estimated using information on relatedness. The phenotypic approach breaks down selection differentials into a sexually selected and a “remainder” component. The quantitative genetic approach decomposes the estimated evolutionary response to selection analogously. We apply our method to analyze sexual selection in male dusky pipefish, Syngnathus floridae, and in two simulated datasets. We highlight conceptual and statistical limitations of previous path‐based approaches, which can lead to substantial misestimation of sexual selection.     

Genetic relationships among traits related to reproduction and growth of Nelore females

The objective of the study presented here was to analyze the genetic relationships among heifer pregnancy (HP), age at first calving (AFC), stayability (STAY), average annual productivity of the cow, in kilograms of weaned calf per cow per year (PRODAM), postweaning weight gain (PWG), and hip height (HH) of Nelore females from 12 Brazilian herds. (Co)variance components were obtained by six-trait animal model using Gibbs sampling. The posterior mean of the heritability estimates were 0.37, 0.18, 0.19, 0.16, 0.21, and 0.37 for HP, AFC, STAY, PRODAM, PWG, and HH, respectively. In general, the genetic correlations were strong between traits related to reproduction, for example, −0.85 between HP and AFC, and 0.94 between STAY and PRODAM. Weak genetic correlations were obtained between reproductive and growth traits (absolute values ranging from 0.02 to 0.30). Although weak, the genetic correlations between PWG and reproductive traits were favorable, whereas the genetic correlations between HH and reproductive traits were close to zero and slightly unfavorable for HP, AFC, and STAY. An increase of HH is therefore expected to have little or no negative effect on the reproductive performance of females. The posterior mean of genetic correlation between PWG and HH was moderate (0.50). On the basis of the heritability, genetic correlation estimates, and time to obtain data, HP and PRODAM seems to show the best potential as selection criteria to improve the productive and reproductive performance of Nelore females. In principle, it is possible to select for increased PWG without compromising the reproduction of Nelore females. However, selection for PWG may result in an increase of female HH as a correlated response, a fact that could increase management costs in advanced generations of selection. In the light of the results, all traits studied here can be used as selection criteria and there is no strong evidence of genetic antagonism among traits related to reproduction and growth of Nelore females.     

Genetic parameters and environmental effects on temperament score and reproductive traits of Nellore cattle

Animal temperament is a trait of economic relevance and its use as a selection criterion requires the identification of environmental factors that influence this trait, as well as the estimation of its genetic variability and interrelationship with other traits. The objectives of this study were to evaluate the effect of the covariates dam age at calving (ADC), long yearling age (YA) and long yearling weight (YW) on temperament score (T) and to estimate genetic parameters for T, scrotal circumference (SC) at long YA and age at first calving (AFC) in Nellore cattle participating in a selection program. The traits were analyzed by the restricted maximum likelihood method under a multiple-trait animal model. For all traits, contemporary group was included as a fixed effect and additive genetic and residual as random effects. In addition to these effects, YA, YW and ADC were considered for analyzing T. In the case of SC and AFC, the effect of long YW was included as a covariate. Genetic parameters were estimated for and between traits. The three covariates significantly influenced T. The heritability estimates for T, SC and AFC were 0.18 ± 0.02, 0.53 ± 0.04 and 0.23 ± 0.08, respectively. The genetic correlations between T and SC, and T and AFC were -0.07 ± 0.17 and -0.06 ± 0.19, respectively. The genetic correlation estimated between SC and AFC was -0.57 ± 0.16. In conclusion, a response to selection for T, SC and AFC is expected and selection for T does not imply correlated responses with the other traits.     

Quantitative genetics and sex-specific selection on sexually dimorphic traits in bighorn sheep

Sexual conflict at loci influencing traits shared between the sexes occurs when sex-specific selection pressures are antagonistic relative to the genetic correlation between the sexes. To assess whether there is sexual conflict over shared traits, we estimated heritability and intersexual genetic correlations for highly sexually dimorphic traits (horn volume and body mass) in a wild population of bighorn sheep (Ovis canadensis) and quantified sex-specific selection using estimates of longevity and lifetime reproductive success. Body mass and horn volume showed significant additive genetic variance in both sexes, and intersexual genetic correlations were 0.24+/-0.28 for horn volume and 0.63+/-0.30 for body mass. For horn volume, selection coefficients did not significantly differ from zero in either sex. For body weight, selection coefficients were positive in females but did not differ from zero in males. The absence of detectable sexually antagonistic selection suggests that currently there are no sexual conflicts at loci influencing horn volume and body mass.     

Genetic parameters and relationships between growth traits and scrotal circumference measured at different ages in Nellore cattle

Records from 106,212 Nellore animals, born between 1998 and 2006, were used to estimate (co)variance components and genetic parameters for birth weight (BW), average weight gains from birth to weaning (GBW), average weight gains from weaning to after yearling (GWAY), weaning hip height (WHH), postweaning hip height (PHH) and scrotal circumferences at 9 (SC9), 12 (SC12) and 15 (SC15) months of age. (Co)variance components were estimated by an animal model using multi-trait analysis. Heritability estimates for BW, GBW, GWAY, WHH, PHH, SC9, SC12 and SC15 were 0.31 ± 0.01; 0.25 ± 0.02; 0.30 ± 0.04; 0.51 ± 0.04; 0.54 ± 0.04; 0.39 ± 0.01; 0.41 ± 0.01 and 0.44 ± 0.02, respectively. Genetic correlations between growth traits ranged from 0.09 ± 0.01 to 0.88 ± 0.01, thereby implying that, at any age, selection to increase average weight gains will also increase stature. Genetic correlations between BW and average weight gains with scrotal circumferences were all positive and moderate (0.15 ± 0.03 to 0.38 ± 0.01). On the other hand, positive and low genetic associations were estimated between hip height and scrotal circumference at different ages (0.09 ± 0.01 to 0.17 ± 0.02). The results of this study pointed out that selection to larger scrotal circumferences in males will promote changes in average weight gains. In order to obtain Nellore cattle with the stature and size suitable for the production system, both weight gain and hip height should be included in a selection index.     

Genomic reaction norm models exploiting genotype × environment interaction on sexual precocity indicator traits in Nellore cattle

Brazilian beef cattle are raised predominantly on pasture in a wide range of environments. In this scenario, genotype by environment (G×E) interaction is an important source of phenotypic variation in the reproductive traits. Hence, the evaluation of G×E interactions for heifer’s early pregnancy (HP) and scrotal circumference (SC) traits in Nellore cattle, belonging to three breeding programs, was carried out to determine the animal’s sensitivity to the environmental conditions (EC). The dataset consisted of 85 874 records for HP and 151 553 records for SC, from which 1800 heifers and 3343 young bulls were genotyped with the BovineHD BeadChip. Genotypic information for 826 sires was also used in the analyses. EC levels were based on the contemporary group solutions for yearling body weight. Linear reaction norm models (RNM), using pedigree information (RNM_A) or pedigree and genomic information (RNM_H), were used to infer G×E interactions. Two validation schemes were used to assess the predictive ability, with the following training populations: (a) forward scheme—dataset was split based on year of birth from 2008 for HP and from 2011 for SC; and (b) environment-specific scheme—low EC (−3.0 and −1.5) and high EC (1.5 and 3.0). The inclusion of the H matrix in RNM increased the genetic variance of the intercept and slope by 18.55 and 23.00% on average respectively, and provided genetic parameter estimates that were more accurate than those considering pedigree only. The same trend was observed for heritability estimates, which were 0.28–0.56 for SC and 0.26–0.49 for HP, using RNM_H, and 0.26–0.52 for SC and 0.22–0.45 for HP, using RNM_A. The lowest correlation observed between unfavorable (−3.0) and favorable (3.0) EC levels were 0.30 for HP and −0.12 for SC, indicating the presence of G×E interaction. The G×E interaction effect implied differences in animals’ genetic merit and re-ranking of animals on different environmental conditions. SNP marker–environment interaction was detected for Nellore sexual precocity indicator traits with changes in effect and variance across EC levels. The RNM_H captured G×E interaction effects better than RNM_A and improved the predictive ability by around 14.04% for SC and 21.31% for HP. Using the forward scheme increased the overall predictive ability for SC (20.55%) and HP (11.06%) compared with the environment-specific scheme. The results suggest that the inclusion of genomic information combined with the pedigree to assess the G×E interaction leads to more accurate variance components and genetic parameter estimates.     

Heritability estimates and genetic correlations for body weight and scrotal circumference adjusted to 12 and 18 months of age for male Nellore cattle

Heritability estimates and genetic correlations were obtained for body weight and scrotal circumference, adjusted, respectively, to 12 (BW12 and SC12) and 18 (BW18 and SC18) months of age, for 10 742 male Nellore cattle. The adjustments to SC12 and SC18 were made using a nonlinear logistic function, while BW12 and BW18 were obtained by linear adjustment. The contemporary groups (CGs) were defined from animals born on the same farm, in the same year and birth season. The mean heritability estimates obtained using the restricted maximum likelihood method in bi-trait analysis were 0.25, 0.25, 0.29 and 0.42 for BW12, BW18, SC12 and SC18, respectively. The genetic correlations were 0.30 ± 0.11, 0.21 ± 0.13, 0.21 ± 0.11, -0.08 ± 0.15, 0.16 ± 0.12 and 0.89 ± 0.04 between the traits BW12 and BW18; BW12 and SC12; BW12 and SC18; BW18 and SC12; BW18 and SC18; and SC12 and SC18. The heritability for SC18 was considerably greater than for SC12, suggesting that this should be included as a selection criterion. The genetic correlation between BW18 and SC12 was close to zero, indicating that these traits did not influence each other. The contrary occurred between SC12 and SC18, indicating that selection using one of these could alter the other. Because of the mean magnitudes of heritabilities in the various measurements of weight and scrotal perimeter, it is suggested that the practice of individual selection for these traits is possible.     

Genetic relationship between milk urea nitrogen and reproductive performance in Holstein dairy cows

The objective of this study was to describe the genetic and phenotypic relationship between milk urea nitrogen (MUN) and reproductive traits in Iranian Holstein dairy cows. Test-day MUN data obtained from 57 301 dairy cows on 20 large dairy herds in Iran between January 2005 and June 2009. Genetic parameters for MUN and reproductive traits were estimated with a five-trait model using ASREML program. Random regression test-day models were used to estimate heritabilities separately for MUN from first, second and third lactations. Regression curves were modeled using Legendre polynomials of order 3. Herd-year-season along with age at calving was included as fixed effects in all models for reproductive traits. Heritabilities for MUN and reproductive traits were estimated separately for first lactation, second lactation and third lactation. The estimated heritabilities for MUN varied from 0.18 to 0.22. The heritability estimate was low for reproductive traits, which ranged from 0.02 to 0.06 for different traits and across parities. Except for days open, phenotypic and genetic correlations of MUN with reproductive performance traits were close to zero. Genetic correlations between MUN and days open were 0.23, 0.35 and 0.45 in first, second and third lactation, respectively. However, the phenotypic correlation between MUN at different parities was moderate (0.28 to 0.35), but the genetic correlation between MUN at different parities was high and ranged from 0.84 to 0.97. This study shows a limited application of MUN for use in selection programs to improve reproductive performance.     

Bayesian inference in genetic parameter estimation of visual scores in Nellore beef-cattle

The aim of this study was to estimate the components of variance and genetic parameters for the visual scores which constitute the Morphological Evaluation System (MES), such as body structure (S), precocity (P) and musculature (M) in Nellore beef-cattle at the weaning and yearling stages, by using threshold Bayesian models. The information used for this was gleaned from visual scores of 5,407 animals evaluated at the weaning and 2,649 at the yearling stages. The genetic parameters for visual score traits were estimated through two-trait analysis, using the threshold animal model, with Bayesian statistics methodology and MTGSAM (Multiple Trait Gibbs Sampler for Animal Models) threshold software. Heritability estimates for S, P and M were 0.68, 0.65 and 0.62 (at weaning) and 0.44, 0.38 and 0.32 (at the yearling stage), respectively. Heritability estimates for S, P and M were found to be high, and so it is expected that these traits should respond favorably to direct selection. The visual scores evaluated at the weaning and yearling stages might be used in the composition of new selection indexes, as they presented sufficient genetic variability to promote genetic progress in such morphological traits.     

Artificial selection on male longevity influences age-dependent reproductive effort in the black field cricket Teleogryllus commodus

Although the trade-off between reproductive effort and longevity is central to both sexual selection and evolutionary theories of aging, there has been little synthesis between these fields. Here, we selected directly on adult longevity of male field crickets Teleogryllus commodus and measured the correlated responses of age-dependent male reproductive effort, female lifetime fecundity, and several other life-history traits. Male longevity responded significantly to five generations of divergent selection. Males from downward-selected lines commenced calling sooner and reached their peak calling effort at a younger age. They called more per night and, despite living less than half as long, called more overall than males selected for increased longevity. Females from the downward-selected lines lived significantly shorter lives than females from the upward-selected lines but still produced the same number of offspring. Nymph survival, development time, and body size and weight at eclosion did not show significant correlated response to selection on male longevity, despite evidence for substantial genetic variation in each of these traits. Collectively, our findings directly support the antagonistic pleiotropy model of aging and suggest an important role for sexual selection in the aging process.     

Live fast, die young: trade-offs between fitness components and sexually antagonistic selection on weaponry in Soay sheep

Males are predicted to compete for reproductive opportunities, with sexual selection driving the evolution of large body size and weaponry through the advantage they confer for access to females. Few studies have explored potential trade-offs of investment in secondary sexual traits between different components of fitness or tested for sexually antagonistic selection pressures. These factors may provide explanations for observed polymorphisms in both form and quality of secondary sexual traits. We report here an analysis of selection on horn phenotype in a feral population of Soay sheep (Ovis aries) on the island of Hirta, St. Kilda, Scotland. Soay sheep display a phenotypic polymorphism for horn type with males growing either normal or reduced (scurred) horns, and females growing either normal, scurred, or no (polled) horns; further variation in size exists within horn morphs. We show that horn phenotype and the size of the trait displayed is subject to different selection pressures in males and females, generating sexually antagonistic selection. Furthermore, there was evidence of a trade-off between breeding success and longevity in normal-horned males, with both the normal horn type and larger horn size being associated with greater annual breeding success but reduced longevity. Therefore, selection through lifetime breeding success was not found to act upon horn phenotype in males. In females, a negative association of annual breeding success within the normal-horned phenotype did not result in a significant difference in lifetime fitness when compared to scurred individuals, as no significant difference in longevity was found. However, increased horn size within this group was negatively associated with breeding success and longevity. Females without horns (polled) suffered reduced longevity and thus reduced lifetime breeding success relative the other horn morphs. Our results therefore suggest that trade-offs between different components of fitness and antagonistic selection between the sexes may maintain genetic variation for secondary sexual traits within a population.     

Accuracy of genomic predictions in Bos indicus (Nellore) cattle

Background

Nellore cattle play an important role in beef production in tropical systems and there is great interest in determining if genomic selection can contribute to accelerate genetic improvement of production and fertility in this breed. We present the first results of the implementation of genomic prediction in a Bos indicus (Nellore) population.

Methods

Influential bulls were genotyped with the Illumina Bovine HD chip in order to assess genomic predictive ability for weight and carcass traits, gestation length, scrotal circumference and two selection indices. 685 samples and 320 238 single nucleotide polymorphisms (SNPs) were used in the analyses. A forward-prediction scheme was adopted to predict the genomic breeding values (DGV). In the training step, the estimated breeding values (EBV) of bulls were deregressed (dEBV) and used as pseudo-phenotypes to estimate marker effects using four methods: genomic BLUP with or without a residual polygenic effect (GBLUP20 and GBLUP0, respectively), a mixture model (Bayes C) and Bayesian LASSO (BLASSO). Empirical accuracies of the resulting genomic predictions were assessed based on the correlation between DGV and dEBV for the testing group.

Results

Accuracies of genomic predictions ranged from 0.17 (navel at weaning) to 0.74 (finishing precocity). Across traits, Bayesian regression models (Bayes C and BLASSO) were more accurate than GBLUP. The average empirical accuracies were 0.39 (GBLUP0), 0.40 (GBLUP20) and 0.44 (Bayes C and BLASSO). Bayes C and BLASSO tended to produce deflated predictions (i.e. slope of the regression of dEBV on DGV greater than 1). Further analyses suggested that higher-than-expected accuracies were observed for traits for which EBV means differed significantly between two breeding subgroups that were identified in a principal component analysis based on genomic relationships.

Conclusions

Bayesian regression models are of interest for future applications of genomic selection in this population, but further improvements are needed to reduce deflation of their predictions. Recurrent updates of the training population would be required to enable accurate prediction of the genetic merit of young animals. The technical feasibility of applying genomic prediction in a Bos indicus (Nellore) population was demonstrated. Further research is needed to permit cost-effective selection decisions using genomic information.     

A genome‐wide scan for selection signatures in Nellore cattle

Brazilian Nellore cattle (Bos indicus) have been selected for growth traits for over more than four decades. In recent years, reproductive and meat quality traits have become more important because of increasing consumption, exports and consumer demand. The identification of genome regions altered by artificial selection can potentially permit a better understanding of the biology of specific phenotypes that are useful for the development of tools designed to increase selection efficiency. Therefore, the aims of this study were to detect evidence of recent selection signatures in Nellore cattle using extended haplotype homozygosity methodology and BovineHD marker genotypes (>777 000 single nucleotide polymorphisms) as well as to identify corresponding genes underlying these signals. Thirty‐one significant regions (P < 0.0001) of possible recent selection signatures were detected, and 19 of these overlapped quantitative trait loci related to reproductive traits, growth, feed efficiency, meat quality, fatty acid profiles and immunity. In addition, 545 genes were identified in regions harboring selection signatures. Within this group, 58 genes were associated with growth, muscle and adipose tissue metabolism, reproductive traits or the immune system. Using relative extended haplotype homozygosity to analyze high‐density single nucleotide polymorphism marker data allowed for the identification of regions potentially under artificial selection pressure in the Nellore genome, which might be used to better understand autozygosity and the effects of selection on the Nellore genome.     

Quantitative genetic insights into the coevolutionary dynamics of male and female genitalia

The spectacular variability that typically characterizes male genital traits has largely been attributed to the role of sexual selection. Among the evolutionary mechanisms proposed to account for this diversity, two processes in particular have generated considerable interest. On the one hand, females may exploit postcopulatory mechanisms of selection to favour males with preferred genital traits (cryptic female choice; CFC), while on the other hand females may evolve structures or behaviours that mitigate the direct costs imposed by male genitalia (sexual conflict; SC). A critical but rarely explored assumption underlying both processes is that male and female reproductive traits coevolve, either via the classic Fisherian model of preference-trait coevolution (CFC) or through sexually antagonistic selection (SC). Here, we provide evidence for this prediction in the guppy (Poecilia reticulata), a polyandrous livebearing fish in which males transfer sperm internally to females via consensual and forced matings. Our results from a paternal half-sibling breeding design reveal substantial levels of additive genetic variation underlying male genital size and morphology—two traits known to predict mating success during non-consensual matings. Our subsequent finding that physically interacting female genital traits exhibit corresponding levels of genetic (co)variation reveals the potential intersexual coevolutionary dynamics of male and female genitalia, thereby fulfilling a fundamental assumption underlying CFC and SC theory.     

SEXUAL SIZE DIMORPHISM AND SELECTION IN THE WILD IN THE WATERSTRIDER AQUARIUS REMIGIS: LIFETIME FECUNDITY SELECTION ON FEMALE TOTAL LENGTH AND ITS COMPONENTS

Darwin's fecundity advantage model is often cited as the cause of female biased size dimorphism, however, the empirical studies of lifetime selection on male and female body size that would be required to demonstrate this are few. As a component of a study relating sexual size dimorphism to lifetime selection in natural populations of the female size-biased waterstrider Aquarius remigis (Hemiptera: Gerridae), we estimated coefficients for daily fecundity selection, longevity selection, and lifetime fecundity selection acting on female body size and components of body size for two consecutive generations. Daily fecundity was estimated using females confined in field enclosures and reproductive survival was estimated by twice-weekly recaptures. We found that daily fecundity selection favored females with longer total length through direct selection acting on abdomen length. Longevity selection favored females with smaller total length. When daily fecundity and reproductive longevity were combined to estimate lifetime fecundity we found significant balancing selection acting on total length in both years. The relationship between daily fecundity and reproductive longevity also reveals a significant cost of reproduction in one of two years. We relate these selection estimates to previous estimates of sexual selection on male body size and consider the relationship between contemporary selection and sexual size dimorphism.