Although genome-wide association studies (GWAS) have provided valuable insights into the decoding of the relationships between sequence variation and complex phenotypes, they have explained little heritability. Regional heritability mapping (RHM) provides heritability estimates for genomic segments containing both common and rare allelic effects that individually contribute too little variance to be detected by GWAS. We carried out GWAS and RHM for seven growth, wood and disease resistance traits in a breeding population of 768 Eucalyptus hybrid trees using EuCHIP60K. Total genomic heritabilities accounted for large proportions (64-89%) of pedigree-based trait heritabilities, providing additional evidence that complex traits in eucalypts are controlled by many sequence variants across the frequency spectrum, each with small contributions to the phenotypic variance. RHM detected 26 quantitative trait loci (QTLs) encompassing 2191 single nucleotide polymorphisms (SNPs), whereas GWAS detected 13 single SNP-trait associations. RHM and GWAS QTLs individually explained 5-15% and 4-6% of the genomic heritability, respectively. RHM was superior to GWAS in capturing larger proportions of genomic heritability. Equated to previously mapped QTLs, our results highlighted genomic regions for further examination towards gene discovery. RHM-QTLs bearing a combination of common and rare variants could be useful enhancements to incorporate prior knowledge of the underlying genetic architecture in genomic prediction models.

Grazing supplementation: availability and quality x supplementation levels x performance ABSTRACT -The objective was to evaluate the results of supplementation in the dry season of the year and the possible interference of the forage availability and quality and level of supplementation on performance. The total DM and green dry matter pasture availability deferred for use in the dry season has an average of all experiments of 6,431 kg ha -1 and 2,173 kg ha -1 . The Brachiaria under grazing in the dry season have high levels of NDF, with an average of 74.50%, high levels of ADF, with an average of 44.19%, low levels of CP, with average of 5.59% and low levels of IVDM/O, with an average of 51.36%. In this sense, the diet taken by the animal usually presents higher crude protein and lower levels of NDF. On consumption in grazing, note that the intake reduction is limited by until the level of supplementation of 0.3% of body weight (BW) per day and when the consumption of supplement increases to levels above 0.3% of BW, the consumption of grass is low and that this decrease may be even greater when the supply of supplement is 0.8% of the BW. Supplementation of cattle provided larger gains than those receiving only mineral in the dry season. Must be guaranteed at least 4,500 kg DM total.ha -1 , 1,200 kg.ha -1 of green dry matter, offering 10 to 12% of the BW offorage DM and 6% of DM potentially digestible to ensure selectivity and earnings satisfactory individual without compromising the gain per area. A supplementation in the dry season in Brachiaria is biologically feasible for positive effect on weight gain, but the economic viability of the system is location dependent. Supplementation levels above 0.8% of the BW should be investigated as alternatives that may avoid possible negative effects on the rumen environment to reduce the expectations of gain, as the fractionation of supplementation.

Precision animal agriculture is poised to rise to prominence in the livestock enterprise in the domains of management, production, welfare, sustainability, health surveillance, and environmental footprint. Considerable progress has been made in the use of tools to routinely monitor and collect information from animals and farms in a less laborious manner than before. These efforts have enabled the animal sciences to embark on information technology-driven discoveries to improve animal agriculture. However, the growing amount and complexity of data generated by fully automated, high-throughput data recording or phenotyping platforms, including digital images, sensor and sound data, unmanned systems, and information obtained from real-time noninvasive computer vision, pose challenges to the successful implementation of precision animal agriculture. The emerging fields of machine learning and data mining are expected to be instrumental in helping meet the daunting challenges facing global agriculture. Yet, their impact and potential in “big data” analysis have not been adequately appreciated in the animal science community, where this recognition has remained only fragmentary. To address such knowledge gaps, this article outlines a framework for machine learning and data mining and offers a glimpse into how they can be applied to solve pressing problems in animal sciences.

BackgroundA complete approach for genome-wide selection (GWS) involves reliable statistical genetics models and methods. Reports on this topic are common for additive genetic models but not for additive-dominance models. The objective of this paper was (i) to compare the performance of 10 additive-dominance predictive models (including current models and proposed modifications), fitted using Bayesian, Lasso and Ridge regression approaches; and (ii) to decompose genomic heritability and accuracy in terms of three quantitative genetic information sources, namely, linkage disequilibrium (LD), co-segregation (CS) and pedigree relationships or family structure (PR). The simulation study considered two broad sense heritability levels (0.30 and 0.50, associated with narrow sense heritabilities of 0.20 and 0.35, respectively) and two genetic architectures for traits (the first consisting of small gene effects and the second consisting of a mixed inheritance model with five major genes).ResultsG-REML/G-BLUP and a modified Bayesian/Lasso (called BayesA*B* or t-BLASSO) method performed best in the prediction of genomic breeding as well as the total genotypic values of individuals in all four scenarios (two heritabilities x two genetic architectures). The BayesA*B*-type method showed a better ability to recover the dominance variance/additive variance ratio. Decomposition of genomic heritability and accuracy revealed the following descending importance order of information: LD, CS and PR not captured by markers, the last two being very close.ConclusionsAmongst the 10 models/methods evaluated, the G-BLUP, BAYESA*B* (−2,8) and BAYESA*B* (4,6) methods presented the best results and were found to be adequate for accurately predicting genomic breeding and total genotypic values as well as for estimating additive and dominance in additive-dominance genomic models.

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Resumo -O objetivo deste trabalho foi propor uma abordagem bayesiana do método de Eberhart & Russell para avaliar a adaptabilidade e da estabilidade fenotípica de genótipos de alfafa (Medicago sativa), bem como avaliar a eficiência da utilização de distribuições a priori informativas e pouco informativas. Foram utilizados dados de um experimento em blocos ao acaso, no qual se avaliou a produção de massa de matéria seca de 92 genótipos. A metodologia bayesiana proposta foi implementada no programa livre R por meio da função MCMCregress do pacote MCMCpack. Para representar as distribuições a priori pouco informativas, utilizaram-se distribuições de probabilidade com grande variância; e, para representar distribuições a priori informativas, adotou-se o conceito de meta-análise, que se caracteriza pela utilização de informações provenientes de trabalhos anteriores. A comparação entre as distribuições a priori foi realizada por meio do fator de Bayes, com a função BayesFactor do pacote MCMCpack, que indicou a priori informativa como a mais adequada nas condições deste estudo.Termos para indexação: Medicago sativa, fator de Bayes, priori informativa, interação genótipo x ambiente, MCMC. Bayesian approach for the evaluation of adaptability and stability of alfalfa genotypesAbstract -The objective of this work was to propose a Bayesian approach for the Eberhart & Russell method to evaluate the phenotypic adaptability and stability of alfafa (Medicago sativa) genotypes, as well as to evaluate the efficiency of the use of prior informative and noninformative distributions. Data from a randomized block design experiment evaluating the forage dry weight of 92 genotypes were used. The Bayesian methodology proposed was implemented in the free software R by the MCMCregress function of the MCMCpack package. To represent the noninformative prior distributions, a probability distribution with high variance was used; and, to represent the informative prior, a meta-analysis concept was adopted, characterized by the use of information provided by previous studies. The comparison between the prior distributions was done using the Bayes Factor, with the BayesFactor function of the MCMCpack package, which indicated that an informative prior is more appropriate under the conditions of this study.

Identifying maize inbred lines that are more efficient in nitrogen (N) use is an important strategy and a necessity in the context of environmental and economic impacts attributed to the excessive N fertilization. N-uptake efficiency (NUpE) and N-utilization efficiency (NUtE) are components of N-use efficiency (NUE). Despite the most maize breeding data have a multi-trait structure, they are often analyzed under a single-trait framework. We aimed to estimate the genetic parameters for NUpE and NUtE in contrasting N levels, in order to identify superior maize inbred lines, and to propose a Bayesian multi-trait multi-environment (MTME) model. Sixty-four tropical maize inbred lines were evaluated in two experiments: at high (HN) and low N (LN) levels. The MTME model was compared to single-trait multi-environment (STME) models. Based on deviance information criteria (DIC), both multi- and single-trait models revealed genotypes x environments (G x E) interaction. In the MTME model, NUpE was found to be weakly heritable with posterior modes of heritability of 0.016 and 0.023 under HN and LN, respectively. NUtE at HN was found to be highly heritable (0.490), whereas under LN condition it was moderately heritable (0.215). We adopted the MTME model, since combined analysis often presents more accurate breeding values than single models. Superior inbred lines for NUpE and NUtE were identified and this information can be used to plan crosses to obtain maize hybrids that have superior nitrogen use efficiency.

Understanding the genetic architecture of beef cattle growth cannot be limited simply to the genome-wide association study (GWAS) for body weight at any specific ages, but should be extended to a more general purpose by considering the whole growth trajectory over time using a growth curve approach. For such an approach, the parameters that are used to describe growth curves were treated as phenotypes under a GWAS model. Data from 1,255 Brahman cattle that were weighed at birth, 6, 12, 15, 18, and 24 months of age were analyzed. Parameter estimates, such as mature weight (A) and maturity rate (K) from nonlinear models are utilized as substitutes for the original body weights for the GWAS analysis. We chose the best nonlinear model to describe the weight-age data, and the estimated parameters were used as phenotypes in a multi-trait GWAS. Our aims were to identify and characterize associated SNP markers to indicate SNP-derived candidate genes and annotate their function as related to growth processes in beef cattle. The Brody model presented the best goodness of fit, and the heritability values for the parameter estimates for mature weight (A) and maturity rate (K) were 0.23 and 0.32, respectively, proving that these traits can be a feasible alternative when the objective is to change the shape of growth curves within genetic improvement programs. The genetic correlation between A and K was -0.84, indicating that animals with lower mature body weights reached that weight at younger ages. One hundred and sixty seven (167) and two hundred and sixty two (262) significant SNPs were associated with A and K, respectively. The annotated genes closest to the most significant SNPs for A had direct biological functions related to muscle development (RAB28), myogenic induction (BTG1), fetal growth (IL2), and body weights (APEX2); K genes were functionally associated with body weight, body height, average daily gain (TMEM18), and skeletal muscle development (SMN1). Candidate genes emerging from this GWAS may inform the search for causative mutations that could underpin genomic breeding for improved growth rates.