Influence of different environmental challenges on the expression of reproductive traits in Holstein cattle in Southern Brazil.

The aim of this study was to assess the impact of genotype-environment interaction (GEI) on the manifestation of traits such as age at first calving (AFC), age at first service (AFS), and calving interval (CI) through the application of the reaction norm model in Holstein cattle raised in Paraná state, Brazil. Utilizing data from the milk testing service of the Paraná Association of Holstein Cattle Breeders (APCBRH), this study analyzed records from 179,492 animals undergoing their first, second, and third lactations from the years 2012 to 2022. These animals were part of 513 herds spread across 72 municipalities in Paraná. The environmental gradient was established by normalizing contemporary group solutions, derived from the animal model, with the 305-day-corrected milk yield serving as the dependent variable. Subsequently, reaction norms were determined utilizing a Random Regression Model. Spearman's correlation was then applied to compare the estimates of breeding values across different environmental gradients for the studied traits. The highest EG (+ 4) indicates the least challenging environments, where animals experience better environmental conditions. Conversely, lower EG (-4) values represent the most challenging environments, where animals endure worse conditions. The only trait that exhibited a moderate heritability magnitude was AFC (0.23) in the least challenging environmental condition. The other traits were classified as having low heritability magnitudes regardless of the evaluated environmental gradient. While minimal evidence was found for the influence of GEI on CI, a clear GEI effect was observed for AFC and AFS across all environmental gradients examined. A reversal in genotype ranking occurred under extreme environmental conditions. The findings suggest that the best-performing genotype under one environmental gradient may not necessarily excel under another.

Impact of heat stress on genetic evaluation of oocyte and embryo production in Gir dairy cattle.

Identifying and selecting genotypes tolerant to heat stress might improve reproductive traits in dairy cattle, including oocyte and embryo production. The temperature-humidity index (THI) was used, via random regression models, to investigate the impact of heat stress on genetic parameters and breeding values of oocyte and embryo production in Gir dairy cattle. We evaluated records of total oocytes (TO), viable oocytes (VO), cleaved embryos (CE), and viable embryos (VE) from dairy Gir donors. Twenty-four models were tested, considering age at ovum pick-up (AOPU) and THI means as a regressor in the genetic evaluation. We computed THI in eight periods, from 0 to 112 days before ovum pick-up, which were adjusted by different orders of Legendre polynomials (second, third, and fourth). The best-fit model according to Akaike's information criterion (AIC) and Model Posterior Probabilities (MPP) considered Legendre polynomials of third order and THI means of 112 days for TO, fourth order and 56 days for VO, second order and 28 days for CE, and second order and 42 days for VE, respectively. The heritability (h2) estimates across AOPU and THI scales ranged from 0.34 to 0.62 for TO, 0.31 to 0.58 for VO, 0.26 to 0.39 for CE, and 0.15 to 0.26 for VE, respectively. The fraction of the phenotypic variance explained by the permanent environment in different AOPU and THI scales ranged from 0.03 to 0.25 for TO, 0.05 to 0.26 for VO, 0.09 to 0.36 for CE, and 0.15 to 0.27 for VE, respectively. Spearman's rank correlation between the estimated breeding values in different AOPU and THI scale from the top 5% sires and females ranged from 0.18 to 0.90 for TO, 0.31 to 0.95 for VO, 0.14 to 0.85 for CE, and 0.47 to 0.94 for VE, respectively. The h2 estimates for all evaluated traits varied from moderate to high magnitude across AOPU and THI scales, indicating that genetic selection can result in rapid genetic progress for the evaluated traits. There was a reranking among the best animals in different AOPU and THI. It is possible to select dairy Gir cattle tolerant to heat stress to improve oocyte and embryo production.

Ridge regression and deep learning models for genome-wide selection of complex traits in New Mexican Chile peppers.

BACKGROUND: Genomewide prediction estimates the genomic breeding values of selection candidates which can be utilized for population improvement and cultivar development. Ridge regression and deep learning-based selection models were implemented for yield and agronomic traits of 204 chile pepper genotypes evaluated in multi-environment trials in New Mexico, USA. RESULTS: Accuracy of prediction differed across different models under ten-fold cross-validations, where high prediction accuracy was observed for highly heritable traits such as plant height and plant width. No model was superior across traits using 14,922 SNP markers for genomewide selection. Bayesian ridge regression had the highest average accuracy for first pod date (0.77) and total yield per plant (0.33). Multilayer perceptron (MLP) was the most superior for flowering time (0.76) and plant height (0.73), whereas the genomic BLUP model had the highest accuracy for plant width (0.62). Using a subset of 7,690 SNP loci resulting from grouping markers based on linkage disequilibrium coefficients resulted in improved accuracy for first pod date, ten pod weight, and total yield per plant, even under a relatively small training population size for MLP and random forest models. Genomic and ridge regression BLUP models were sufficient for optimal prediction accuracies for small training population size. Combining phenotypic selection and genomewide selection resulted in improved selection response for yield-related traits, indicating that integrated approaches can result in improved gains achieved through selection. CONCLUSIONS: Accuracy values for ridge regression and deep learning prediction models demonstrate the potential of implementing genomewide selection for genetic improvement in chile pepper breeding programs. Ultimately, a large training data is relevant for improved genomic selection accuracy for the deep learning models.

Relationship between age, scrotal circumference, postweaning weight and semen quality in Nellore and Caracu bulls: a cross sectional study.

The aim of this study was to investigate the relationship between age, scrotal circumference, postweaning weight and semen quality in Nellore and Caracu bulls selected for postweaning weight. Data from the andrological evaluation of 836 bulls born between 2000 and 2019, including 583 Nellore animals (Bos indicus) and 253 Caracu animals (Bos taurus), were used. The bulls were divided into categories of age at the time of assessment: category 1 consisted of animals aged 20 to 23 months (22 ± 0.76 months, 518 ± 94.17 kg), category 2 consisted of animals aged 24 to 35 months (30 ± 4.42 months, 679 ± 137.19 kg), and category 3 consisted of animals ≥ 36 months (60 ± 14.12 months, 907 ± 161.73 kg). The statistical model included the effects of breed, age category, date of semen collection, and breed x age category interaction. Heritability estimates for scrotal circumference at 13 months of age (SC1year) and semen quality traits were obtained for the sample of Nellore animals. Most semen quality traits improved with increasing age in both Nellore and Caracu animals. High heritability was observed for SC1year (0.45), while sperm motility, vigor, turbulence, and major, minor and total sperm defects exhibited low heritability (0.11, 0.019, 0.047, 0.017, 0.017 and 0.019, respectively). Spearman correlations of breeding values for postweaning weight (W378) and SC1year with the semen quality traits were low. Nellore and Caracu bulls have similar semen quality that improves with increasing age. In the Nellore breed, the heritability of SC is high, while semen quality traits exhibit low heritability. Selection for higher postweaning weight does not phenotypically affect the semen quality of bulls at breeding age.

Genomic Prediction of Resistance to Tan Spot, Spot Blotch and Septoria Nodorum Blotch in Synthetic Hexaploid Wheat.

Genomic prediction combines molecular and phenotypic data in a training population to predict the breeding values of individuals that have only been genotyped. The use of genomic information in breeding programs helps to increase the frequency of favorable alleles in the populations of interest. This study evaluated the performance of BLUP (Best Linear Unbiased Prediction) in predicting resistance to tan spot, spot blotch and Septoria nodorum blotch in synthetic hexaploid wheat. BLUP was implemented in single-trait and multi-trait models with three variations: (1) the pedigree relationship matrix (A-BLUP), (2) the genomic relationship matrix (G-BLUP), and (3) a combination of the two matrices (A+G BLUP). In all three diseases, the A-BLUP model had a lower performance, and the G-BLUP and A+G BLUP were statistically similar (p ≥ 0.05). The prediction accuracy with the single trait was statistically similar (p ≥ 0.05) to the multi-trait accuracy, possibly due to the low correlation of severity between the diseases.

SNP- and haplotype-based single-step genomic predictions for body weight, wool, and reproductive traits in North American Rambouillet sheep.

Rambouillet sheep are commonly raised in extensive grazing systems in the US, mainly for wool and meat production. Genomic evaluations in US sheep breeds, including Rambouillet, are still incipient. Therefore, we aimed to evaluate the feasibility of performing genomic prediction of breeding values for various traits in Rambouillet sheep based on single nucleotide polymorphisms (SNP) or haplotypes (fitted as pseudo-SNP) under a single-step GBLUP approach. A total of 28,834 records for birth weight (BWT), 23,306 for postweaning weight (PWT), 5,832 for yearling weight (YWT), 9,880 for yearling fibre diameter (YFD), 11,872 for yearling greasy fleece weight (YGFW), and 15,984 for number of lambs born (NLB) were used in this study. Seven hundred forty-one individuals were genotyped using a moderate (50 K; n = 677) or high (600 K; n = 64) density SNP panel, in which 32 K SNP in common between the two SNP panels (after genotypic quality control) were used for further analyses. Single-step genomic predictions using SNP (H-BLUP) or haplotypes (HAP-BLUP) from blocks with different linkage disequilibrium (LD) thresholds (0.15, 0.35, 0.50, 0.65, and 0.80) were evaluated. We also considered different blending parameters when constructing the genomic relationship matrix used to predict the genomic-enhanced estimated breeding values (GEBV), with alpha equal to 0.95 or 0.50. The GEBV were compared to the estimated breeding values (EBV) obtained from traditional pedigree-based evaluations (A-BLUP). The mean theoretical accuracy ranged from 0.499 (A-BLUP for PWT) to 0.795 (HAP-BLUP using haplotypes from blocks with LD threshold of 0.35 and alpha equal to 0.95 for YFD). The prediction accuracies ranged from 0.143 (A-BLUP for PWT) to 0.330 (A-BLUP for YGFW) while the prediction bias ranged from -0.104 (H-BLUP for PWT) to 0.087 (HAP-BLUP using haplotypes from blocks with LD threshold of 0.15 and alpha equal to 0.95 for YGFW). The GEBV dispersion ranged from 0.428 (A-BLUP for PWT) to 1.035 (A-BLUP for YGFW). Similar results were observed for H-BLUP or HAP-BLUP, independently of the LD threshold to create the haplotypes, alpha value, or trait analysed. Using genomic information (fitting individual SNP or haplotypes) provided similar or higher prediction and theoretical accuracies and reduced the dispersion of the GEBV for body weight, wool, and reproductive traits in Rambouillet sheep. However, there were no clear improvements in the prediction bias when compared to pedigree-based predictions. The next step will be to enlarge the training populations for this breed to increase the benefits of genomic predictions.

Overview of the use of genomic data in animal breeding / Panorama do uso de dados genômicos no melhoramento genético animal

ABSTRACT: The use of molecular information in breeding programs contributed to important advances in the improvement of traits of economic interest in livestock production. The advent of single nucleotide polymorphism (SNP) panels applied to genome-wide selection (GWS) and genome-wide association studies (GWAS), along with computational advances (e.g., use of powerful software and robust analyses) allowed a better understanding of the genetic architecture of farm animals and increased the selection efficiency. In this context, the statistic method single-step GBLUP has been frequently used to perform GWS, and more recently GWAS analyses, providing accurate predictions and QTL detection, respectively. Nevertheless, in developing countries, species such as sheep and goats, whose genomic data are more difficult to be obtained, the use of data simulation has been efficient in the study of the major factors involved in the selection process, such as size of training population, density of SNP chips, and genotyping strategies. The effects of these factors are directly associated with the prediction accuracy of genomic breeding values. In this review we showed important aspects of the use of genomics in the genetic improvement of production traits of animals, the main methods currently used for prediction and estimation of molecular marker effects, the importance of data simulation for validation of those methods, as well as the advantages, challenges and limitations of the use of GWS and GWAS in the current scenario of livestock production.

RESUMO: Em programas de melhoramento genético, o uso de informações moleculares garantiu importantes avanços para a melhoria de características de interesse econômico, no âmbito da produção animal. O advento da tecnologia de painéis de SNPs aplicados à seleção genômica ampla (GWS) e associação genômica ampla (GWAS), aliado ao avanço computacional, com o uso de softwares e análises robustas, permitiram melhor compreensão sobre a arquitetura genética dos animais de produção e, consequentemente, maior eficiência na seleção. Nesse contexto, o método estatístico single-step GBLUP tem sido utilizado, frequentemente, na execução da GWS e, mais recentemente, em GWAS, possibilitando predições acuradas e detecção de QTLs, respectivamente. No entanto, em países em desenvolvimento e, em espécies como os ovinos e caprinos, que existe maior dificuldade para a aquisição de dados genômicos, o uso da simulação de dados tem se mostrado eficiente para estudar os principais fatores envolvidos no processo de seleção, como o tamanho da população de treinamento, densidade de chipde SNPs e estratégias de genotipagem, cujos efeitos estão diretamente associados à acurácia da predição de valores genéticos genômicos. Nesta revisão, serão abordados pontos importantes sobre o uso da genômica no melhoramento genético de características produtivas em animais, principais métodos de predição e estimação de efeitos de marcadores moleculares na atualidade, a importância da simulação de dados para a validação desses métodos, bem como as vantagens, os desafios e as limitações no cenário atual da produção animal com o uso da seleção e associação genômica ampla.

Overview of the use of genomic data in animal breeding / Panorama do uso de dados genômicos no melhoramento genético animal

The use of molecular information in breeding programs contributed to important advances in the improvement of traits of economic interest in livestock production. The advent of single nucleotide polymorphism (SNP) panels applied to genome-wide selection (GWS) and genome-wide association studies (GWAS), along with computational advances (e.g., use of powerful software and robust analyses) allowed a better understanding of the genetic architecture of farm animals and increased the selection efficiency. In this context, the statistic method single-step GBLUP has been frequently used to perform GWS, and more recently GWAS analyses, providing accurate predictions and QTL detection, respectively. Nevertheless, in developing countries, species such as sheep and goats, whose genomic data are more difficult to be obtained, the use of data simulation has been efficient in the study of the major factors involved in the selection process, such as size of training population, density of SNP chips, and genotyping strategies. The effects of these factors are directly associated with the prediction accuracy of genomic breeding values. In this review we showed important aspects of the use of genomics in the genetic improvement of production traits of animals, the main methods currently used for prediction and estimation of molecular marker effects, the importance of data simulation for validation of those methods, as well as the advantages, challenges and limitations of the use of GWS and GWAS in the current scenario of livestock production.

Em programas de melhoramento genético, o uso de informações moleculares garantiu importantes avanços para a melhoria de características de interesse econômico, no âmbito da produção animal. O advento da tecnologia de painéis de SNPs aplicados à seleção genômica ampla (GWS) e associação genômica ampla (GWAS), aliado ao avanço computacional, com o uso de softwares e análises robustas, permitiram melhor compreensão sobre a arquitetura genética dos animais de produção e, consequentemente, maior eficiência na seleção. Nesse contexto, o método estatístico single-step GBLUP tem sido utilizado, frequentemente, na execução da GWS e, mais recentemente, em GWAS, possibilitando predições acuradas e detecção de QTLs, respectivamente. No entanto, em países em desenvolvimento e, em espécies como os ovinos e caprinos, que existe maior dificuldade para a aquisição de dados genômicos, o uso da simulação de dados tem se mostrado eficiente para estudar os principais fatores envolvidos no processo de seleção, como o tamanho da população de treinamento, densidade de chipde SNPs e estratégias de genotipagem, cujos efeitos estão diretamente associados à acurácia da predição de valores genéticos genômicos. Nesta revisão, serão abordados pontos importantes sobre o uso da genômica no melhoramento genético de características produtivas em animais, principais métodos de predição e estimação de efeitos de marcadores moleculares na atualidade, a importância da simulação de dados para a validação desses métodos, bem como as vantagens, os desafios e as limitações no cenário atual da produção animal com o uso da seleção e associação genômica ampla.

Weak genotype x environment interaction suggests that measuring scrotal circumference at 12 and 18 mo of age is helpful to select precocious Brahman cattle.

The aim of this study was to evaluate the genotype x environment interaction (GxE) for scrotal circumference (SC) measured at different ages using pedigree-based (A-1) and pedigree and genomic-based (H-1) relationship matrices. Data from 1,515 Brahman bulls, from the Cooperative Research Centre for Beef Genetic Technologies (Beef CRC) experimental dataset, were used in this study. SC was adjusted to age and body weight measured at 6 mo (SC6), 12 mo (SC12), 18 mo (SC18), and 24 mo of age (SC24). Body weight (BW) measured at 6 mo (BW6), 12 mo (BW12), 18 mo (BW18), and 24 mo of age (BW24) was used as criteria to describe the environment for SC in each age. All the animals measured were genotyped using medium-density SNP chips ("50k" or "70k" SNP) and their genotype were imputed using a reference panel with 729,068 SNP. The environment gradient (EG) was obtained by standardizing the solutions of the contemporary groups obtained by Animal Model with BW as the dependent variable. Then, the reaction norms (RN) were determined through a Random Regression Model. The breeding values (EBV) were estimated using either A-1 or H-1. The rank correlation was obtained using Spearman's correlation among the EBV estimated for the traits in analysis. For SC6 and SC24, higher estimates of heritability (h²) were obtained using A-1, when compared with those observed with H-1. In those ages, the improvement of the environment decreases the h² coefficient. On the other hand, the h² for SC12 and SC18 increased as the environment became more favorable, regardless of the matrix used. The RN for SC6 and SC24 estimated using A-1 and H-1 showed a decrease of variance from the worst to the best environment, an indication of existence of GxE. On the other hand, for SC12 and SC18, there were no significant differences between the EBV estimated in the lower and in the higher environments, regardless of the kinship matrix used, suggesting absence of GxE on those ages. Spearman's correlation among EBV estimated using A-1 and H-1 in different EG was practically equal to unity for all traits evaluated. In our study, there was weak evidence of GxE effect on SC in ages suitable for selection for sexual precocity. So, the absence of GxE at 12 and 18 mo means that these ages are advantageous for measuring SC to selection for sexual precocity. The advantage is that no changes in classification were observed when the sires were evaluated in different environments.

Beef production systems rely on efficient cow-calf operations, that is, farms where the cow herd has a high level of fertility and pregnancies are common. Bull fertility also plays an important role in terms of pregnancy rates. To increase herd fertility, cattle breeders and genetic selection programs use some indicator traits that are related to fertility. A common indicator trait used is scrotal circumference (SC), which like most reproduction traits are influenced by the animal's genetics and its environment. For some traits, when the environment has a large effect and it interacts with the genetics of the animals, selection might be less successful. Therefore, it is important to investigate genotype by environment interactions and their effect on reproduction traits used for selection. In this study, SC was measured at four different ages in Brahman cattle. We found weak evidence of genotype by environment effect on SC measured at 12 and 18 mo. In short, SC measured at these ages can be a good indicator of sexual precocity. No changes in sire rankings were observed when SC was measured at those ages, meaning that selecting the best sire is more straightforward than if the environment was playing a bigger role.

Methodology for the identification of relevant loci for milk traits in dairy cattle, using machine learning algorithms.

Machine learning methods were considered efficient in identifying single nucleotide polymorphisms (SNP) underlying a trait of interest. This study aimed to construct predictive models using machine learning algorithms, to identify loci that best explain the variance in milk traits of dairy cattle. Further objectives involved validating the results by comparison with reported relevant regions and retrieving the pathways overrepresented by the genes flanking relevant SNPs. Regression models using XGBoost (XGB), LightGBM (LGB), and Random Forest (RF) algorithms were trained using estimated breeding values for milk production (EBVM), milk fat content (EBVF) and milk protein content (EBVP) as phenotypes and genotypes on 40417 SNPs as predictor variables. To evaluate their efficiency, metrics for actual vs. predicted values were determined in validation folds (XGB and LGB) and out-of-bag data (RF). Less than 4500 relevant SNPs were retrieved for each trait. Among the genes flanking them, signaling and transmembrane transporter activities were overrepresented. The models trained:•Predicted breeding values for animals not included in the dataset.•Were efficient in identifying a subset of SNPs explaining phenotypic variation. The results obtained using XGB and LGB algorithms agreed with previous results. Therefore, the method proposed could be applied for future association studies on milk traits.

Increasing cassava root yield: Additive-dominant genetic models for selection of parents and clones.

Genomic selection has been promising in situations where phenotypic assessments are expensive, laborious, and/or inefficient. This work evaluated the efficiency of genomic prediction methods combined with genetic models in clone and parent selection with the goal of increasing fresh root yield, dry root yield, as well as dry matter content in cassava roots. The bias and predictive ability of the combinations of prediction methods Genomic Best Linear Unbiased Prediction (G-BLUP), Bayes B, Bayes Cπ, and Reproducing Kernel Hilbert Spaces with additive and additive-dominant genetic models were estimated. Fresh and dry root yield exhibited predominantly dominant heritability, while dry matter content exhibited predominantly additive heritability. The combination of prediction methods and genetic models did not show significant differences in the predictive ability for dry matter content. On the other hand, the prediction methods with additive-dominant genetic models had significantly higher predictive ability than the additive genetic models for fresh and dry root yield, allowing higher genetic gains in clone selection. However, higher predictive ability for genotypic values did not result in differences in breeding value predictions between additive and additive-dominant genetic models. G-BLUP with the classical additive-dominant genetic model had the best predictive ability and bias estimates for fresh and dry root yield. For dry matter content, the highest predictive ability was obtained by G-BLUP with the additive genetic model. Dry matter content exhibited the highest heritability, predictive ability, and bias estimates compared with other traits. The prediction methods showed similar selection gains with approximately 67% of the phenotypic selection gain. By shortening the breeding cycle time by 40%, genomic selection may overcome phenotypic selection by 10%, 13%, and 18% for fresh root yield, dry root yield, and dry matter content, respectively, with a selection proportion of 15%. The most suitable genetic model for each trait allows for genomic selection optimization in cassava with high selection gains, thereby accelerating the release of new varieties.

Selection indexes using principal component analysis for reproductive, beef and milk traits in Simmental cattle.

Selection indexes in dual-purpose cattle should include beef, milk and reproductive traits. The principal component analysis is a multivariate technique that allows researchers to explore relationships between explanatory variables and traits of interest. The objective of this study was to construct selection indexes for tropical dual-purpose Simmental cattle based on principal components. The evaluated traits were weight at 8 months of age; age at first calving; cumulative first-lactation milk yield at 60, 150, 210 and 305 days; and first calving interval. The selection indexes were estimated as the sum of the products of the estimated breeding values for the seven traits times their respective eigenvectors for the first three principal components. The three selection indexes from principal components analysis generated favourable expected genetic progress for all the traits. However, a selection index with a high expected genetic progress for all traits could not be obtained. The principal component analysis allows breeders to have a selection index that simultaneously improves milk, beef and reproductive traits in dual-purpose Simmental cattle. Because a selection index yielding high expected genetic progress for all traits could not be achieved, the decision to use a specific selection index will depend on the specific conditions of the market, the local needs and the farmer preference.

Additive genetic variance and covariance between relatives in synthetic wheat crosses with variable parental ploidy levels.

Cultivated bread wheat (Triticum aestivum L.) is an allohexaploid species resulting from the natural hybridization and chromosome doubling of allotetraploid durum wheat (T. turgidum) and a diploid goatgrass Aegilops tauschii Coss (Ae. tauschii). Synthetic hexaploid wheat (SHW) was developed through the interspecific hybridization of Ae. tauschii and T. turgidum, and then crossed to T. aestivum to produce synthetic hexaploid wheat derivatives (SHWDs). Owing to this founding variability, one may infer that the genetic variances of native wild populations vs improved wheat may vary due to their differential origin and evolutionary history. In this study, we partitioned the additive variance of SHW and SHWD with respect to their breed origin by fitting a hierarchical Bayesian model with heterogeneous covariance structure for breeding values to estimate variance components for each breed category, and segregation variance. Two data sets were used to test the proposed hierarchical Bayesian model, one from a multi-year multi-location field trial of SHWD and the other comprising the two species of SHW. For the SHWD, the Bayesian estimates of additive variances of grain yield from each breed category were similar for T. turgidum and Ae. tauschii, but smaller for T. aestivum. Segregation variances between Ae. tauschii-T. aestivum and T. turgidum-T. aestivum populations explained a sizable proportion of the phenotypic variance. Bayesian additive variance components and the Best Linear Unbiased Predictors (BLUPs) estimated by two well-known software programs were similar for multi-breed origin and for the sum of the breeding values by origin for both data sets. Our results support the suitability of models with heterogeneous additive genetic variances to predict breeding values in wheat crosses with variable ploidy levels.

Applying the Metafounders Approach for Genomic Evaluation in a Multibreed Beef Cattle Population.

Pedigree information is incomplete by nature and commonly not well-established because many of the genetic ties are not known a priori or can be wrong. The genomic era brought new opportunities to assess relationships between individuals. However, when pedigree and genomic information are used simultaneously, which is the case of single-step genomic BLUP (ssGBLUP), defining the genetic base is still a challenge. One alternative to overcome this challenge is to use metafounders, which are pseudo-individuals that describe the genetic relationship between the base population individuals. The purpose of this study was to evaluate the impact of metafounders on the estimation of breeding values for tick resistance under ssGBLUP for a multibreed population composed by Hereford, Braford, and Zebu animals. Three different scenarios were studied: pedigree-based model (BLUP), ssGBLUP, and ssGBLUP with metafounders (ssGBLUPm). In ssGBLUPm, a total of four different metafounders based on breed of origin (i.e., Hereford, Braford, Zebu, and unknown) were included for the animals with missing parents. The relationship coefficient between metafounders was in average 0.54 (ranging from 0.34 to 0.96) suggesting an overlap between ancestor populations. The estimates of metafounder relationships indicate that Hereford and Zebu breeds have a possible common ancestral relationship. Inbreeding coefficients calculated following the metafounder approach had less negative values, suggesting that ancestral populations were large enough and that gametes inherited from the historical population were not identical. Variance components were estimated based on ssGBLUPm, ssGBLUP, and BLUP, but the values from ssGBLUPm were scaled to provide a fair comparison with estimates from the other two models. In general, additive, residual, and phenotypic variance components in the Hereford population were smaller than in Braford across different models. The addition of genomic information increased heritability for Hereford, possibly because of improved genetic relationships. As expected, genomic models had greater predictive ability, with an additional gain for ssGBLUPm over ssGBLUP. The increase in predictive ability was greater for Herefords. Our results show the potential of using metafounders to increase accuracy of GEBV, and therefore, the rate of genetic gain in beef cattle populations with partial levels of missing pedigree information.

Invited review: Advances and applications of random regression models: From quantitative genetics to genomics.

An important goal in animal breeding is to improve longitudinal traits; that is, traits recorded multiple times during an individual's lifetime or physiological cycle. Longitudinal traits were first genetically evaluated based on accumulated phenotypic expression, phenotypic expression at specific time points, or repeatability models. Until now, the genetic evaluation of longitudinal traits has mainly focused on using random regression models (RRM). Random regression models enable fitting random genetic and environmental effects over time, which results in higher accuracy of estimated breeding values compared with other statistical approaches. In addition, RRM provide insights about temporal variation of biological processes and the physiological implications underlying the studied traits. Despite the fact that genomic information has substantially contributed to increase the rates of genetic progress for a variety of economically important traits in several livestock species, less attention has been given to longitudinal traits in recent years. However, including genomic information to evaluate longitudinal traits using RRM is a feasible alternative to yield more accurate selection and culling decisions, because selection of young animals may be based on the complete pattern of the production curve with higher accuracy compared with the use of traditional parent average (i.e., without genomic information). Moreover, RRM can be used to estimate SNP effects over time in genome-wide association studies. Thus, by analyzing marker associations over time, regions with higher effects at specific points in time are more likely to be identified. Despite the advances in applications of RRM in genetic evaluations, more research is needed to successfully combine RRM and genomic information. Future research should provide a better understanding of the temporal variation of biological processes and their physiological implications underlying the longitudinal traits.

Genetic Parameters and the Impact of Off-Types for Theobroma cacao L. in a Breeding Program in Brazil.

Breeding programs of cacao (Theobroma cacao L.) trees share the many challenges of breeding long-living perennial crops, and genetic progress is further constrained by both the limited understanding of the inheritance of complex traits and the prevalence of technical issues, such as mislabeled individuals (off-types). To better understand the genetic architecture of cacao, in this study, 13 years of phenotypic data collected from four progeny trials in Bahia, Brazil were analyzed jointly in a multisite analysis. Three separate analyses (multisite, single site with and without off-types) were performed to estimate genetic parameters from statistical models fitted on nine important agronomic traits (yield, seed index, pod index, % healthy pods, % pods infected with witches broom, % of pods other loss, vegetative brooms, diameter, and tree height). Genetic parameters were estimated along with variance components and heritabilities from the multisite analysis, and a trial was fingerprinted with low-density SNP markers to determine the impact of off-types on estimations. Heritabilities ranged from 0.37 to 0.64 for yield and its components and from 0.03 to 0.16 for disease resistance traits. A weighted index was used to make selections for clonal evaluation, and breeding values estimated for the parental selection and estimation of genetic gain. The impact of off-types to breeding progress in cacao was assessed for the first time. Even when present at <5% of the total population, off-types altered selections by 48%, and impacted heritability estimations for all nine of the traits analyzed, including a 41% difference in estimated heritability for yield. These results show that in a mixed model analysis, even a low level of pedigree error can significantly alter estimations of genetic parameters and selections in a breeding program.

Genomic predictions for economically important traits in Brazilian Braford and Hereford beef cattle using true and imputed genotypes.

BACKGROUND: Genomic selection (GS) has played an important role in cattle breeding programs. However, genotyping prices are still a challenge for implementation of GS in beef cattle and there is still a lack of information about the use of low-density Single Nucleotide Polymorphisms (SNP) chip panels for genomic predictions in breeds such as Brazilian Braford and Hereford. Therefore, this study investigated the effect of using imputed genotypes in the accuracy of genomic predictions for twenty economically important traits in Brazilian Braford and Hereford beef cattle. Various scenarios composed by different percentages of animals with imputed genotypes and different sizes of the training population were compared. De-regressed EBVs (estimated breeding values) were used as pseudo-phenotypes in a Genomic Best Linear Unbiased Prediction (GBLUP) model using two different mimicked panels derived from the 50 K (8 K and 15 K SNP panels), which were subsequently imputed to the 50 K panel. In addition, genomic prediction accuracies generated from a 777 K SNP (imputed from the 50 K SNP) were presented as another alternate scenario. RESULTS: The accuracy of genomic breeding values averaged over the twenty traits ranged from 0.38 to 0.40 across the different scenarios. The average losses in expected genomic estimated breeding values (GEBV) accuracy (accuracy obtained from the inverse of the mixed model equations) relative to the true 50 K genotypes ranged from -0.0007 to -0.0012 and from -0.0002 to -0.0005 when using the 50 K imputed from the 8 K or 15 K, respectively. When using the imputed 777 K panel the average losses in expected GEBV accuracy was -0.0021. The average gain in expected EBVs accuracy by including genomic information when compared to simple BLUP was between 0.02 and 0.03 across scenarios and traits. CONCLUSIONS: The percentage of animals with imputed genotypes in the training population did not significantly influence the validation accuracy. However, the size of the training population played a major role in the accuracies of genomic predictions in this population. The losses in the expected accuracies of GEBV due to imputation of genotypes were lower when using the 50 K SNP chip panel imputed from the 15 K compared to the one imputed from the 8 K SNP chip panel.

Genetic trends for live weight traits reflect breeding strategies in registered Charolais Farms in Mexico.

Genetic trends are commonly used to verify genetic improvement; however, there are few reports on beef cattle in Mexico. Data from 1998 to 2013 from four Charolais bull breeding farms were examined to verify the genetic responses to different breeding management and selection criteria. Analysis included the comparison of regression lines of breeding values for birth (BW), weaning (WW) and yearling weights (YW), and maternal weaning weight (MWW) on the year of birth of the animals. Results revealed differential genetic progress for BW and YW and indicated that the overall analysis may have diluted the perception of genetic progress from the farmer's point of view. The use of breeding values as a tool for selection is effective to achieve genetic progress, even in negatively correlated traits, such as birth weight and yearling weight.

Cluster analysis of breeding values for milk yield and lactation persistency in Guzerá cattle / Análises de agrupamento dos valores genéticos para produção de leite e persistência da lactação em bovinos da raça Guzerá

The aim of this study was to explore the pattern of genetic lactation curves of Guzerá cattle using cluster analysis. Test-day milk yields of 5,274 first-lactation Guzerá cows were recorded in a progeny test. A total of 34,193 monthly records were analyzed with a random regression animal model using Legendre polynomials to fit additive genetic and permanent environmental random effects and mean trends. Hierarchical and non-hierarchical cluster analyses were performed based on the EBVs for monthly test-day milk yield, peak yield, lactation persistency, and partial cumulative and 305-day yields. The heritability estimates for test-day milk yields ranged from 0.24 to 0.52. Cluster analysis identified animals in the population that belong to different groups according to milk production level and lactation persistency.(AU)

Objetivou-se neste estudo explorar o padrão das curvas de lactação genéticas de bovinos da raça Guzerá, empregando análises de agrupamento. Os 34.193 registros mensais de produção de leite foram provenientes de 5.274 vacas da raça Guzerá, participantes do teste de progênie. As análises foram realizadas com um modelo de regressão aleatória com polinômios de Legendre, composto pelos efeitos aleatórios genético aditivo, de ambiente permanente e o residual, e a curva média de lactação da população. Análise de agrupamento hierárquico e não hierárquico foram realizados com base nos VG para a produção acumulada até os 305 dias, pico e persistência da lactação, e períodos parciais da lactação. As estimativas de herdabilidade para produção de leite no dia do controle variaram entre 0,24 a 0,52. A análise de agrupamento identificou os animais da população que pertencem a diferentes grupos de acordo com o nível de produção de leite e persistência da lactação.(AU)