Multiple-trait genomic evaluation for milk yield and milk quality traits using genomic and phenotypic data in buffalo in Brazil.

The objective of this study was to compare the multi-trait model using pedigree information and a model using genomic information in addition to pedigree information. We used data from 5896 lactations of 2021 buffalo cows, of which 384 were genotyped using the Illumina Infinium(®) bovine HD BeadChip, considering seven traits related to milk yield (MY305), fat (FY305), protein (PY305), and lactose (LY305), percentages of fat (%F) and protein (%P), and somatic cell score (SCS). We carried out two analyses, one using phenotype and pedigree information (matrix A) and the other using the relationship matrix based on pedigree and genomics information (a single step, matrix H). The (co)variance components were estimated using multiple-trait analysis by the Bayesian inference method. The model included the fixed effects of contemporary groups (herd-year and calving season), and the age of cow at calving as (co)variables (quadratic and linear effect). The additive genetic, permanent environmental, and residual effects were included as random effects in the model. The estimates of heritability using matrix A were 0.25, 0.22, 0.26, 0.25, 0.37, 0.42, and 0.17, while using matrix H the heritability values were 0.25, 0.24, 0.26, 0.26, 0.38, 0.47, and 0.18 for MY305, FY305, PY305, LY305, %F, %P, and SCS, respectively. The estimates of breeding values in the two analyses were similar for the traits studied, but the accuracies were greater when using matrix H (higher than 8% in the traits studied). Therefore, the use of genomic information in the analyses improved the accuracy.

Additive genetic relationships between heifer pregnancy and scrotal circumference in Nellore cattle.

To estimate heritability (h2) for yearling heifer pregnancy and to estimate the genetic correlation between heifer pregnancy and scrotal circumference, 18,145 records of Nellore heifers exposed to breeding at an age of approximately 14 mo and 25,466 records of contemporary young bulls were analyzed. Heifer pregnancy was considered as a categorical trait, with the value 1 (success) assigned to heifers that were pregnant after rectal palpation approximately 60 d after the end of a 90-d breeding season and the value 0 (failure) otherwise. A single-trait animal model for heifer pregnancy and a two-trait animal model including heifer pregnancy and scrotal circumference were used. Contemporary groups were defined in two ways: including (CG2) or not including (CG1) weaning management of the heifer. Heritability estimates obtained by Method R in single-trait analyses were 0.68 +/- 0.09 and 0.61 +/- 0.10 using CG1 and CG2 definitions, respectively. Heritability estimates for two-trait analyses were 0.69 +/- 0.09 (CG1) and 0.63 +/- 0.08 (CG2) for heifer pregnancy and 0.57 +/- 0.03 (both CG) for scrotal circumference. The genetic correlation estimates between the two traits were 0.20 +/- 0.12 (CG1) and 0.20 +/- 0.13 (CG2). Based on the results of this study, EPD for heifer pregnancy can be used to select bulls for the production of precocious daughters and will be more effective than selecting on scrotal circumference EPD in Nellore cattle. However, scrotal circumference can be incorporated in a two-trait analysis to increase the accuracy of prediction for heifer pregnancy EPD for young bulls. Using contemporary group without heifer weaning management gave higher h2 and, for two-trait analysis, converged more quickly.

Prospection of genomic regions divergently selected in racing line of Quarter Horses in relation to cutting line.

Selection of Quarter Horses for different purposes has led to the formation of lines, including racing and cutting horses. The objective of this study was to identify genomic regions divergently selected in racing line of Quarter Horses in relation to cutting line applying relative extended haplotype homozygosity (REHH) analysis, an extension of extended haplotype homozygosity (EHH) analysis, and the fixation index (F ST) statistic. A total of 188 horses of both sexes, born between 1985 and 2009 and registered at the Brazilian Association of Quarter Horse Breeders, including 120 of the racing line and 68 of the cutting line, were genotyped using single nucleotide polymorphism arrays. On the basis of 27 genomic regions identified as selection signatures by REHH and F ST statistics, functional annotations of genes were made in order to identify those that could have been important during formation of the racing line and that could be used subsequently for the development of selection tools. Genes involved in muscle growth (n=8), skeletal growth (n=10), muscle energy metabolism (n=15), cardiovascular system (n=14) and nervous system (n=23) were identified, including the FKTN, INSR, GYS1, CLCN1, MYLK, SYK, ANG, CNTFR and HTR2B.

Comparison of a genetic group and unknown paternity models for growth traits in Nellore cattle.

The aim of the present study was to compare a model assuming unknown paternity and a model using genetic grouping to indicate the most adequate statistical procedure for the estimation of breeding values for animals with uncertain paternity. After data consistency, 62,212 Nellore animals, offspring of 581 bulls and 27,743 cows, were used in the analyses. The pedigree file contained 75,088 animals, including 22,810 (30.18%) offspring of multiple sires and 12,876 animals belonging to the base population with unknown parents. Three different approaches were adopted to deal with uncertain paternity of multiple-sire (MS) offspring. In the model of unknown paternity, the MS groups were ignored, and the sires of MS offspring were considered to be unknown and to belong to a single base population. In the genetic group approach, 2 definitions were used. In the first definition (GGa), "phantom parents" for animals with uncertain paternity were attributed, defining the genetic group as the MS group. In the other approach, GGb, phantom parents for animals with uncertain paternity were also attributed; however, MS offspring were clustered in genetic groups according to their year of birth, every 3 yr, on the basis of the average of male generation interval. Univariate analyses were performed under the Bayesian approach via Markov chain Monte Carlo methods. Models were compared by deviance information criteria and the conditional predictive ordinate. According to the choice criteria results, the genetic group model defined by the generation interval of males was more appropriate for predicting the genetic merit of animals with uncertain paternity. Therefore, the use of this model is recommended for the prediction of genetic merit and classification of offspring of multiple sires.

Reproductive tract development and puberty in two lines of Nellore heifers selected for postweaning weight.

The objective was to evaluate reproductive tract development (ovary and uterus) and onset of puberty in two lines of Nellore heifers (Bos indicus) selected for postweaning weight. A total of 123 heifers, including 46 from the control Nellore line (NeC) and 77 from the selection Nellore line (NeS) were used. Every 18 to 21 days from 12 to 24 months of age, average ovarian area (OVA), endometrial thickness (ETh), and diameter of the largest follicle in each ovary were evaluated (using transrectal ultrasonography), and body weight, hip height, and body condition score were measured. There were no differences between NeS and NeC heifers for ETh or OVA (P < 0.05). Genetic selection for higher postweaning weight had no negative influence on the onset of puberty, with 52% and 48% of NeC and NeS heifers, respectively, pubertal at 24 months of age (P = 0.49). Heifers that reached puberty at the end of the study were heavier (NeC, 296.9 vs. 276.7 kg; NeS, 343.5 vs. 327.9 kg; P < 0.01) and younger (NeC, 23.4 vs. 24.2 mo; NeS, 22.7 vs. 24.0 months; P < 0.01) than those that did not. Furthermore, heifers that were heavier at weaning reached puberty earlier. Pubertal heifers had a greater OVA (4.15 vs. 3.14 cm(2); P < 0.01) and ETh (12.15 vs. 9.93 mm; P < 0.01) than nonpubertal heifers. Taken together, OVA and ETh had positive effects (P < 0.01) on the onset of puberty and were suitable indicator traits of heifer sexual precocity in pasture management systems. However, selection for weight did not alter ovarian or endometrial development, or manifestation of puberty at 24 months of age. Among the growth traits studied, weaning weight and weight at puberty had significant positive effects on manifestation of first estrus.

Estimation of genetic parameters for body weights, scrotal circumference, and testicular volume measured at different ages in Nellore cattle.

Data from 129,575 Nellore cattle born between 1993 and 2006, belonging to the Jacarezinho cattle-raising farm, were used to estimate genetic parameters for scrotal circumference measured at 9 (SC9), 12 (SC12), and 18 (SC18) mo of age and testicular volume measured at the same ages (TV9, TV12, and TV18) and to determine their correlation with weaning weight (WW) and yearling weight (YW), to provide information for the definition of selection criteria in beef cattle. Estimates of (co)variance components were calculated by the REML method applying an animal model in single- and multiple-trait analysis. The following heritability estimates and their respective SE were obtained for WW, YW, SC9, SC12, SC18, TV9, TV12, and TV18: 0.33 +/- 0.02, 0.37 +/- 0.03, 0.29 +/- 0.03, 0.39 +/- 0.04, 0.42 +/- 0.03, 0.19 +/- 0.04, 0.26 +/- 0.05, and 0.39 +/- 0.04, respectively. The genetic correlation between WW and YW was positive and high (0.80 +/- 0.04), indicating that these traits are mainly determined by the same genes. Genetic correlations between the growth traits and scrotal circumference measures were positive and of low to moderate magnitude, ranging from 0.23 +/- 0.04 to 0.38 +/- 0.04. On the other hand, increased genetic associations were estimated between scrotal circumference and testicular volume at different ages (0.61 +/- 0.04 to 0.86 +/- 0.04). Selection for greater scrotal circumference in males should result in greater WW, YW, and testicular volume. In conclusion, in view of the difficulty in measuring testicular volume, there is no need to change the selection criterion from scrotal circumference to testicular volume in genetic breeding programs of Zebu breeds.

Genetic associations of sexual precocity with growth traits and visual scores of conformation, finishing, and muscling in Nelore cattle.

The objective of this study was to determine the possible use of heifer pregnancy at 16 mo as a selection criterion and its possible genetic associations with hip height, yearling weight, and visual scores of conformation, finishing, and muscling. The data set contained records of 56,458 Nelore yearlings for the traits described above. Covariance components were estimated by bivariate animal models assuming a linear model for hip height, yearling weight and conformation, and finishing and muscling scores, and a nonlinear (threshold) model for heifer pregnancy. Variance components were estimated using Bayesian inference. Flat distributions were used for all (co)variance components and genetic correlations. The first 5,000 rounds were considered as the burn-in period and discarded. The heritability estimate of heifer pregnancy indicates that the trait can be used as a selection criterion. Long-term selection for heifer pregnancy will result in a reduction of animal height. However, selection for increasing yearling weight should be possible in this population of Nelore cattle without having major effects on fertility. Selection for increasing visual scores of conformation, finishing, and muscling will result in small or no response in heifer pregnancy at 16 mo.

Study of stayability in Nellore cows using a threshold model.

The objectives of the current study were to assess the feasibility of using stayability traits to improve fertility of Nellore cows and to examine the genetic relationship among the stayabilities at different ages. Stayability was defined as whether a cow calved every year up to the age of 5 (Stay5), 6 (Stay6), or 7 (Stay7) yr of age or more, given that she was provided the opportunity to breed. Data were analyzed based on a maximum a posteriori probit threshold model to predict breeding values on the liability scale, whereas the Gibbs sampler was used to estimate variance components. The EBV were obtained using all animals included in the pedigree or bulls with at least 10 daughters with stayability observations, and average genetic trends were obtained in the liability and transformed to the probability scale. Additional analyses were performed to study the genetic relationship among stayability traits, which were compared by contrasting results in terms of EBV and the average genetic superiority as a function of the selected proportion of sires. Heritability estimates and SD were 0.25 +/- 0.02, 0.22 +/- 0.03, and 0.28 +/- 0.03 for Stay5, Stay6, and Stay7, respectively. Average genetic trends, by year, were 0.51, 0.34, and 0.38% for Stay5, Stay6, and Stay7, respectively. Estimates of EBV SD, in the probability scale, for all animals included in the pedigree and for bulls with at least 10 daughters with stayability observations were 7.98 and 12.95, 6.93 and 11.38, and 8.24 and 14.30% for Stay5, Stay6, and Stay7, respectively. A reduction in the average genetic superiorities in Stay7 would be expected if the selection were based on Stay5 or Stay6. Nonetheless, the reduction in EPD, depending on selection intensity, is on average 0.74 and 1.55%, respectively. Regressions of the sires' EBV for Stay5 and Stay6 on the sires' EBV for Stay7 confirmed these results. The heritability and genetic trend estimates for all stayability traits indicate that it is possible to improve fertility with selection based on a threshold analysis of stayability. The SD of EBV for stayability traits show that there is adequate genetic variability among animals to justify inclusion of stayability as a selection criterion. The potential linear relationship among stayability traits indicates that selection for improved female traits would be more effective by having predictions on the Stay5 trait.

Valores econômicos para habilidade de permanência e probabilidade de prenhez aos 14 meses em bovinos de corte / Economic value for stayability and heifer pregnancy at 14 months in beef cattle herds

Estimaram-se os valores econômicos para as características reprodutivas de probabilidade de prenhez aos 14 meses (PP14) e habilidade de permanência (HP). Foram simulados dados de uma propriedade pecuária de corte, especializada na fase de cria para aplicação de modelagem bioeconômica. A PP 14 foi avaliada considerando taxas percentuais crescentes de prenhez de novilhas aos 14 meses de idade, e a HP foi avaliada a partir da diminuição da taxa de descarte de vacas. O valor econômico da PP 14 foi estimado em R$695,97 por unidade percentual de prenhez de novilhas aos 14 meses, avaliada para o sistema produtivo, enquanto o valor econômico da HP variou em função do custo de compra da novilha de reposição. Os valores, avaliados por unidade percentual de diminuição na taxa de descarte de vacas, foram de R$-2.l40,00, R$-140,00 e R$2.860,00 para o custo de compra da novilha de R$500,00, R$700,00 e R$1.000,00, respectivamente. Os valores econômicos negativos para HP indicaram que o valor de descarte da vaca superou o custo de compra da novilha. Quanto maior for o valor investido na reposição de novilhas maior será a importância econômica do HP.