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The objective of the present study was to evaluate the effects of different selection practices on the environmental sensitivity of reproductive and growth traits in males and females of three Nellore selection lines [control (NeC), selection (NeS), and traditional (NeT) lines]. Moreover, genetic trends for the intercept and slope were estimated for each line, and the possible reranking of sires was examined. A total of 8,757 records of selection weight (SW), 3,331 records of scrotal circumference (SC), and 2,311 records of days to first calving (DFC) from Nellore cattle born between 1981 and 2017 were analyzed. (Co)variance components and genetic parameters of all traits were estimated using a reaction norm model with Gibbs sampler. In all cattle lines, the mean heritability of the studied traits ranged from 0.39 to 0.75 for SW in both males and females, from 0.46 to 0.68 for SC, and from 0.06 to 0.57 for DFC along with the environmental descriptor. In all cattle lines, the genetic correlation coefficients between the intercept and slope ranged from 0.03 to 0.81 for SW, from -0.14 to 0.39 for SC, and from -0.87 to -0.42 for DFC. Genetic trends for the slope and proportion of plastic genotypes indicated that the NeS line was more responsive to environmental changes, whereas the NeC and NeT lines tended to respond more modestly. Reranking of sires was observed for all traits, specifically in the NeC and NeT lines, because of the weak correlation between the opposite extreme environments. In the NeS line, reranking of sires was observed for DFC alone. Our results indicate that the effects of genotype-environment interaction are important and should be considered in genetic evaluations of Nellore cattle. Moreover, different selection practices affected the environmental sensitivity of the Nellore selection lines tested in this study.

Abstract Background While autozygosity as a consequence of selection is well understood, there is limited information on the ability of different methods to measure true inbreeding. In the present study, a gene dropping simulation was performed and inbreeding estimates based on runs of homozygosity (ROH), pedigree, and the genomic relationship matrix were compared to true inbreeding. Inbreeding based on ROH was estimated using SNP1101, PLINK, and BCFtools software with different threshold parameters. The effects of different selection methods on ROH patterns were also compared. Furthermore, inbreeding coefficients were estimated in a sample of genotyped North American Holstein animals born from 1990 to 2016 using 50 k chip data and ROH patterns were assessed before and after genomic selection. Results Using ROH with a minimum window size of 20 to 50 using SNP1101 provided the closest estimates to true inbreeding in simulation study. Pedigree inbreeding tended to underestimate true inbreeding, and results for genomic inbreeding varied depending on assumptions about base allele frequencies. Using an ROH approach also made it possible to assess the effect of population structure and selection on distribution of runs of autozygosity across the genome. In the simulation, the longest individual ROH and the largest average length of ROH were observed when selection was based on best linear unbiased prediction (BLUP), whereas genomic selection showed the largest number of small ROH compared to BLUP estimated breeding values (BLUP-EBV). In North American Holsteins, the average number of ROH segments of 1 Mb or more per individual increased from 57 in 1990 to 82 in 2016. The rate of increase in the last 5 years was almost double that of previous 5 year periods. Genomic selection results in less autozygosity per generation, but more per year given the reduced generation interval. Conclusions This study shows that existing software based on the measurement of ROH can accurately identify autozygosity across the genome, provided appropriate threshold parameters are used. Our results show how different selection strategies affect the distribution of ROH, and how the distribution of ROH has changed in the North American dairy cattle population over the last 25 years.

The aim of this study was to evaluate the level of introgression of breeds in the Canchim (CA: 62.5% Charolais-37.5% Zebu) and MA genetic group (MA: 65.6% Charolais-34.4% Zebu) cattle using genomic information on Charolais (CH), Nelore (NE), and Indubrasil (IB) breeds. The number of animals used was 395 (CA and MA), 763 (NE), 338 (CH), and 37 (IB). The Bovine50SNP BeadChip from Illumina panel was used to estimate the levels of introgression of breeds considering the Maximum likelihood, Bayesian, and Single Regression method. After genotype quality control, 32,308 SNPs were considered in the analysis. Furthermore, three thresholds to prune out SNPs in linkage disequilibrium higher than 0.10, 0.05, and 0.01 were considered, resulting in 15,286, 7,652, and 1,582 SNPs, respectively. For k = 2, the proportion of taurine and indicine varied from the expected proportion based on pedigree for all methods studied. For k = 3, the Regression method was able to differentiate the animals in three main clusters assigned to each purebred breed, showing more reasonable according to its biological viewpoint. Analyzing the data considering k = 2 seems to be more appropriate for Canchim-MA animals due to its biological interpretation. The usage of 32,308 SNPs in the analyses resulted in similar findings between the estimated and expected breed proportions. Using the Regression approach, a contribution of Indubrasil was observed in Canchim-MA when k = 3 was considered. Genetic parameter estimation could account for this breed composition information as a source of variation in order to improve the accuracy of genetic models. Our findings may help assemble appropriate reference populations for genomic prediction for Canchim-MA in order to improve prediction accuracy. Using the information on the level of introgression in each individual could also be useful in breeding or crossing design to improve individual heterosis in crossbred cattle.

The aim of this study was to compare iterative and direct solvers for estimation of marker effects in genomic selection. One iterative and two direct methods were used: Gauss-Seidel with Residual Update, Cholesky Decomposition and Gentleman-Givens rotations. For resembling different scenarios with respect to number of markers and of genotyped animals, a simulated data set divided into 25 subsets was used. Number of markers ranged from 1,200 to 5,925 and number of animals ranged from 1,200 to 5,865. Methods were also applied to real data comprising 3081 individuals genotyped for 45181 SNPs. Results from simulated data showed that the iterative solver was substantially faster than direct methods for larger numbers of markers. Use of a direct solver may allow for computing (co)variances of SNP effects. When applied to real data, performance of the iterative method varied substantially, depending on the level of ill-conditioning of the coefficient matrix. From results with real data, Gentleman-Givens rotations would be the method of choice in this particular application as it provided an exact solution within a fairly reasonable time frame (less than two hours). It would indeed be the preferred method whenever computer resources allow its use.

Apolipoprotein B (APOB) and Adiponectin Receptor 1 (ADIPOR1) are related to the regulation of feed intake, fat metabolism and protein deposition and are candidate genes for genomic studies in birds. In this study, associations of two single nucleotide polymorphisms (SNPs) g.102A>T (APOB) and g.729C>T (ADIPOR1) with carcass, bone integrity and performance traits in broilers were investigated. Genotyping was performed on a paternal line of 1,454 broilers. The SNP detection was carried out by PCR-RFLP technique using the restriction enzymes HhaI for the SNP g.729C>T and MslI for the SNP g.102A>T. The association analyses of the two SNPs with 85 traits were performed using the restricted maximum likelihood (REML) and Generalized Quasi-Likelihood Score (GQLS) methods. For REML the model included the random additive genetic effect of animal and fixed effects of sex, hatch and SNP genotypes. In the GQLS method, a logistic regression was used to associate the genotypes with phenotypes adjusted for fixed effects of sex and hatch. The SNP g.729C>T in the ADIPOR1 gene was associated with thickness of the femur and breast skin yield. Thus, the ADIPOR1 gene seems implicated in the metabolism and/or fat deposition and bone integrity in broilers.

O objetivo deste trabalho foi avaliar o efeito de duas cargas animais (CA280= 280 e CA360= 360 kg PV/ha) em campo nativo e de duas composições raciais (½ Nelore ½ Hereford e ¼ Nelore ¾ Hereford) na produção de leite de vacas primíparas e no desenvolvimento de seus bezerros. A carga animal não afetou significativamente a produção de leite das vacas (CA280 = 6,16 e CA360 = 5,88 kg leite/vaca/dia). A composição racial das vacas influenciou significativamente a produção de leite, tendo as vacas ½ Nelore ½ Hereford maior produção diária que as ¼ Nelore ¾ Hereford (6,21 vs 5,84 kg leite/vaca/dia, respectivamente). A carga animal não influenciou significativamente o peso e o ganho médio diário (GMD) dos bezerros até a desmama. Bezerros filhos de vacas ½ Nelore ½ Hereford tiveram GMD do nascimento à desmama e pesos à desmama significativamente maiores que filhos de vacas ¼ Nelore ¾ Hereford (0,799 vs 0,727 kg/dia e 211,51 vs 193.12 kg, respectivamente). O sexo dos bezerros não influenciou significativamente a produção de leite das vacas e o GMD e o peso à desmama dos bezerros. Portanto, o desempenho dos bezerros não diferiu significativamente entre as cargas animais e foi melhor para bezerros filhos de vacas ½ Nelore ½ Hereford do que de vacas ¼ Nelore ¾ Hereford.The aim of the experiment was to evaluate the effect of two stocking rates (CA280= 280 kg and CA360= 360 kg of live weight/ha) on natural pasture and of two breed compositions (½ Nelore ½ Hereford and ¼ Nelore ¾ Hereford) on milk production of primiparous beef cows and on growth of their calves. The stocking rate did not affect milk production (CA280 = 6.16 and CA360 = 5.88 kg/cow/day). Breed composition of cows significantly affected milk production, with ½ Nelore ½ Hereford cows showing higher daily yield production than ¼ Nelore ¾ Hereford cows (6.21 vs. 5.84 kg, respectively). The stocking rate did not affect daily live weight gain (ADG) and live weight of the calves at weaning. Calves born from ½ Nelore ½ Hereford cows had significantly higher ADG and live weight at weaning than calves born from ¼ Nelore ¾ Hereford (0.799 vs. 0.727 kg/day and 211.51 vs. 193.12 kg, respectively). Calves sex did not affect cow milk production and ADG and live weight of calves at weaning. Therefore, the calves performance did not significantly differ between stocking rates and was better for calves born from ½ Nelore ½ Hereford cows than from ¼ Nelore ¾ Hereford cows.

Os efeitos no desenvolvimento de bezerros submetidos a: a) três tratamentos, consitindo de cargas animais pós-parto (CA) de 240 kg de peso vivo (PV)/ha (tratamento 1, T1), de 320 kg de PV/ha (T2), ambas em campo nativo, e de 400 kg de PV/ha em pastagem melhorada de azevém (Lolium multiflorum L.) por 80 dias pós-parto e, posteriormente, em CA igual à do T2 em campo nativo (T3); b) duas idades de desmame, consistindo de desmame aos 100 (DP) ou 180 (DC) dias de idade, foram avaliados utilizando 92 bezerros filhos de vacas primíparas Hereford e Braford. O sexo dos bezerros influenciou significativamente o peso ao nascer, não sendo observado efeito da raça da vaca. Os tratamentos e a raça da vaca não influenciaram o ganho médio diário (GMD) dos bezerros do nascimento ao desmame precoce. Bezerros filhos de vacas Braford tiveram maiores pesos no DP (PDP) que os filhos de vacas Hereford, enquanto os tratamentos não influenciaram o PDP. Os bezerros filhos de vacas Braford no T2 tiveram GMD até os 180 dias (GMD180) e PV aos 180 dias (PAJ180) superiores aos bezerros filhos de vacas Braford no T1 e Hereford no T2. Os bezerros do DP tiveram GMD180 e PAJ180 significativamente inferiores aos bezerros do DC. Entretanto, não se verificaram efeitos de tratamentos e idade de desmame sobre o GMD até os 365 dias e o peso ajustado aos 365 dias de idade. Portanto, os três manejos pós-parto das vacas e as duas idades de desmame dos bezerros avaliados não influenciaram o desenvolvimento dos bezerros a um ano de idade.The effects on the performance of calves submitted to: a) three treatments, consisted of post-partum stocking rates (CA) of 240 kg of live weight (LW)/ha (treatment 1, T1), of 320 kg of LW/ha (T2), both on natural pastures, and of 400 kg of LW/ha on improved pasture of Italian ryegrass (Lolium multiflorum L.) during the first 80 days post-partum, and after on natural pasture at the same stocking rate as T2 afterwards (T3); b) two weaning ages, consisted of weaning at 100 (EW) and at 180 (CW) days of age, were evaluated using 92 beef calves from Hereford and Braford primiparous cows. The sex of the calves affected significantly the birth weight, and no effect was observed for the breed of cow. The treatments and breed of cow did not affect the average daily gain (ADG) of the calves from birth to early weaning (GEW). Calves born from Braford cows had higher LW at EW (WEW) than calves born from Hereford cows, while the WEW was not affected by the treatments. Calves born from Braford cows on T2 had ADG up to 180 days (ADG180) and LW at 180 days (LW180) greater than calves born from Braford cows on T1 and Hereford cows on T2. Calves from CW had greater LW180 and ADG180 than calves from EW. However, treatments and weaning ages did not affect the LW at 365 days and the ADG up to 365 days of age. The three cows post-partum management schemes and the two calves weaning ages evaluated did not affect the calves performance up to one year of age.

A investigação foi realizada para avaliar os efeitos de duas cargas animais (CA280= 280 kg PV/ha e CA360= 360 kg PV/ha) e de duas idades de desmama dos bezerros (DC = Desmama convencional aos sete meses de idade e DP= Desmama precoce aos três/quatro meses) no comportamento reprodutivo de vacas de corte primíparas de duas composições raciais (½ Nelore ½ Hereford e ¼ Nelore ¾ Hereford). Foram avaliados os ganhos de peso médios diários (GMD) do pós-parto à data da desmama convencional, durante o acasalamento, da desmama precoce à desmama convencional (GPC), a condição corporal (CC) ao início do acasalamento, ao final do acasalamento e na data da desmama convencional, a taxa de prenhez (TP) e o intervalo de partos (IEP). As vacas conduzidas na CA280 tiveram significativamente maiores GMD do que vacas na CA360 nos três períodos estudados. Vacas submetidas ao tratamento de desmama precoce tiveram GPC maiores que vacas submetidas à desmama convencional (0,539 vs. 0,257 kg/dia, respectivamente). Vacas da CA280 tiveram significativamente maiores condições corporais do início do acasalamento à data da desmama convencional do que vacas da CA360, sendo que vacas submetidas à desmama precoce apresentaram condição corporal na data da desmama convencional superior àquela das vacas da desmama convencional sob ambas cargas animais (4,33 vs. 3,68 para CA280 e 3,14 vs. 2,92 para CA360). A composição racial das vacas não influenciou significativamente o GMD e a condição corporal das vacas no período experimental. A TP da CA280 (67,56%) foi significativamente superior à da CA360 (22,56%), bem como o seu IEP foi significativamente inferior ao da CA360 (395,4 vs. 409,9 dias). Portanto, a carga animal menor permitiu que as vacas apresentassem maiores recuperações de peso e condição corporal no pós-parto, determinando melhores taxas de reconcepção e menores intervalos de partos.

O objetivo deste estudo foi investigar, por meio de dados simulados, o efeito da heterogeneidade de variância residual entre grupos de contemporâneos (GC) sobre as avaliações genéticas de bovinos de corte, e comparar o uso de uma avaliação genética ponderada (R¹Isigmae²) em relação à avaliação que pressupõe homogeneidade de variância (R=Isigmae²). A característica estudada foi ganho de peso pós-desmame corrigido para 345 dias, sendo esta simulada com variância fenotípica de 300 kg² e herdabilidade igual a 0,4. A estrutura de um conjunto real de dados foi utilizada para fornecer os GC e os pais referentes às observações de cada animal. Cinco níveis de heterogeneidade de variância residual foram considerados de forma que os componentes de variância fossem, na média, iguais aos da situação de homogeneidade de variância. Na medida em que níveis mais acentuados de heterogeneidade de variância residual foram considerados, os animais foram selecionados dos GC com maior variabilidade, especialmente com pressão de seleção intensa. Em relação à consistência de predição, os produtos e as vacas tiveram seus valores genéticos preditos mais afetados pela heterogeneidade de variância residual do que os touros. O fator de ponderação utilizado reduziu, mas não eliminou o efeito da heterogeneidade de variância. As avaliações genéticas ponderadas apresentaram resultados iguais ou superiores àqueles obtidos pelas avaliações que assumiram homogeneidade de variância. Mesmo quando não necessário, o uso de avaliações ponderadas produziu resultados não inferiores às avaliações que assumiram homogeneidade de variância.The objective of this study was to investigate, via simulated data, the effect of heterogeneity of residual variance among contemporary groups (CG) on genetic evaluation of beef cattle, and to compare a weighted genetic evaluation procedure (R¹Isigmae²) with one that assumes homogeneity of variances (R = Isigmae²). Different data sets of postweaning weight gain, adjusted to 345 days, were simulated with and without heterogeneity of residual variance, using a phenotypic variance of 300 kg² and a true heritability of 0.4. A real data set was used to provide the CG and parents related to each animal observation. Results showed that, when high levels of heterogeneity of residual variance were considered, animals were selected from CG with higher variability, especially with intense selection. With respect to prediction consistency, non parent animals and cows had their predicted breeding values more affected by heterogeneity of residual variance than sires. The weighed factor used reduced, but did not eliminate, the effect of heterogeneity of residual variance. The results of weighted genetic evaluations were similar or superior to those from evaluations that assumed homogeneity of variances. Even when the variances were homogeneous, the weighed genetic evaluations yielded results that were not inferior than those from the usual evaluations, which assumed homogeneity of variances.

O experimento foi conduzido na Estação Experimental Agronômica da Universidade Federal do Rio Grande do Sul, município de Eldorado do Sul, Brasil. O objetivo do estudo foi avaliar o efeito da data do desmame precoce (05/01/99) ou do convencional (26/03/99) sobre o desempenho reprodutivo de vacas de corte multíparas em duas estações de monta, 98/99, e a subseqüente, 99/00. Cinqüenta vacas tiveram seus bezerros desmamados em média aos 91 dias de vida, com peso mínimo de 70 kg (desmame precoce = DP), e 43 vacas desmamaram em média aos 170 dias, com peso médio de 131,2 kg (desmame convencional = DC). Os períodos de acasalamento ocorreram de 01/12/98 a 26/02/99, de 06/12/99 a 28/02/00. As vacas do DP apresentaram ganho médio diário (GMD) superior e melhor condição corporal (CC) que as do DC no primeiro acasalamento (0,828 kg x 0,549 kg; 2,4 x 2,0; P

Os objetivos deste trabalho foram a obtenção de fatores de correção para efeitos de idade do bezerro, idade da vaca e data juliana do nascimento sobre o ganho de peso do nascimento à desmama (GND) e sobre os escores visuais de conformação (C), precocidade (P) e musculatura (M) e a estimação dos efeitos das heteroses materna e individual nessas características. Foram utilizados dados dos Programas de Melhoramento Genético Natura e Conexão Delta G, totalizando 187.610 bezerros puros e cruzas, nascidos no período de 1989 a 1999 em vários estados do Brasil. Os modelos estatísticos utilizados nas análises consideraram os efeitos fixos de grupo contemporâneo, idade do bezerro (regressão quadrática), idade da vaca (regressão polinomial quadrática-quadrática com nó aos 7 anos), data juliana de nascimento (regressão polinomial quadrática-quadrática-quadrática com nós aos 165 e 260 dias para GND, 150 e 240 dias para C, 165 e 270 dias para P e 155 e 260 dias para M) e heterozigoses materna e individual (regressões lineares). Todos os efeitos considerados no modelo influenciaram de forma significativa o GND e os escores de C, P e M. Os valores estimados de heterose materna e individual foram, respectivamente, 8,9% e 9,9% para GND, 10,0% e 6,6% para C, 8,5% e 4,8 % para P e 10,9% e 5,0% para M.