Study of using marker assisted selection on a beef cattle breeding program by model comparison

A data set of a commercial Nellore beef cattle selection program was used to compare breeding models that assumed or not markers effects to estimate the breeding values, when a reduced number of animals have phenotypic, genotypic and pedigree information available. This herd complete data set was composed of 83,404 animals measured for weaning weight (WW), post-weaning gain (PWG), scrotal circumference (SC) and muscle score (MS), corresponding to 116,652 animals in the relationship matrix. Single trait analyses were performed by MTDFREML software to estimate fixed and random effects solutions using this complete data. The additive effects estimated were assumed as the reference breeding values for those animals. The individual observed phenotype of each trait was adjusted for fixed and random effects solutions, except for direct additive effects. The adjusted phenotype composed of the additive and residual parts of observed phenotype was used as dependent variable for models' comparison. Among all measured animals of this herd, only 3160 animals were genotyped for 106 SNP markers. Three models were compared in terms of changes on animals' rank, global fit and predictive ability. Model 1 included only polygenic effects, model 2 included only markers effects and model 3 included both polygenic and markers effects. Bayesian inference via Markov chain Monte Carlo methods performed by TM software was used to analyze the data for model comparison. Two different priors were adopted for markers effects in models 2 and 3, the first prior assumed was a uniform distribution (U) and, as a second prior, was assumed that markers effects were distributed as normal (N). Higher rank correlation coefficients were observed for models 3_U and 3_N, indicating a greater similarity of these models animals' rank and the rank based on the reference breeding values. Model 3_N presented a better global fit, as demonstrated by its low DIC. The best models in terms of predictive ability were models 1 and 3_N. Differences due prior assumed to markers effects in models 2 and 3 could be attributed to the better ability of normal prior in handle with collinear effects. The models 2_U and 2_N presented the worst performance, indicating that this small set of markers should not be used to genetically evaluate animals with no data, since its predictive ability is restricted. In conclusion, model 3_N presented a slight superiority when a reduce number of animals have phenotypic, genotypic and pedigree information. It could be attributed to the variation retained by markers and polygenic effects assumed together and the normal prior assumed to markers effects, that deals better with the collinearity between markers. (C) 2012 Elsevier B.V. All rights reserved.

Multitemporal assessment of the geomorphologic evolution of the Restinga of Marambaia, Rio de Janeiro, Brazil

The Restinga of Marambaia is an emerged sand bar located between the Sepetiba Bay and the South Atlantic Ocean, on the south-east coast of Brazil. The objective of this study was to observe the geomorphologic evolution of the coastal zone of the Restinga of Marambaia using multitemporal satellite images acquired by multisensors from 1975 to 2004. The images were digitally segmented by a region growth algorithm and submitted to an unsupervised classification procedure (ISOSEG) followed by a raster edit based on visual interpretation. The image time-series showed a general trend of decrease in the total sand bar area with values varying from 80.61km(2) in 1975 to 78.15km(2) in 2004. The total area calculation based on the 1975 and 1978 Landsat MSS data was shown to be super-estimated in relation to the Landsat TM, Landsat ETM+, and CBERS-2 CCD data. These differences can also be associated to the relatively poorer spatial resolution of the MSS data, nominally 79m, against the 20m of the CCD data and 30m of the TM and ETM+ data. For the estimates of the width in the central portion of the sand bar the variation was from 158m (1975) to 100m (2004). The formation of a spit in the northern region of the study area was visually observed. The area of the spit was estimated, with values varying from 0.82km(2) (1975) to 0.55km(2) (2004).

Estimation methods of non-additive effects for characteristics of weight and scrotal circumference in crossbred beef cattle

The objective of this study was to investigate, in a population of crossbred cattle, the obtainment of the non-additive genetic effects for the characteristics weight at 205 and 390 days and scrotal circumference, and to evaluate the consideration of these effects in the prediction of breeding values of sires using different estimation methodologies. In method 1, the data were pre-adjusted for the non-additive effects obtained by least squares means method in a model that considered the direct additive, maternal and non-additive fixed genetic effects, the direct and total maternal heterozygosities, and epistasis. In method 2, the non-additive effects were considered covariates in genetic model. Genetic values for adjusted and non-adjusted data were predicted considering additive direct and maternal effects, and for weight at 205 days, also the permanent environmental effect, as random effects in the model. The breeding values of the categories of sires considered for the weight characteristic at 205 days were organized in files, in order to verify alterations in the magnitude of the predictions and ranking of animals in the two methods of correction data for the non-additives effects. The non-additive effects were not similar in magnitude and direction in the two estimation methods used, nor for the characteristics evaluated. Pearson and Spearman correlations between breeding values were higher than 0.94, and the use of different methods does not imply changes in the selection of animals.

Trends of the genetic connectedness measures among Nelore beef cattle herds

Validity of comparisons between expected breeding values obtained from best linear unbiased prediction procedures in genetic evaluations is dependent on genetic connectedness among herds. Different cattle breeding programmes have their own particular features that distinguish their database structure and can affect connectedness. Thus, the evolution of these programmes can also alter the connectedness measures. This study analysed the evolution of the genetic connectedness measures among Brazilian Nelore cattle herds from 1999 to 2008, using the French Criterion of Admission to the group of Connected Herds (CACO) method, based on coefficients of determination (CD) of contrasts. Genetic connectedness levels were analysed by using simple and multiple regression analyses on herd descriptors to understand their relationship and their temporal trends from the 19992003 to the 20042008 period. The results showed a high level of genetic connectedness, with CACO estimates higher than 0.4 for the majority of them. Evaluation of the last 5-year period showed only a small increase in average CACO measures compared with the first 5 years, from 0.77 to 0.80. The percentage of herds with CACO estimates lower than 0.7 decreased from 27.5% in the first period to 16.2% in the last one. The connectedness measures were correlated with percentage of progeny from connecting sires, and the artificial insemination spread among Brazilian herds in recent years. But changes in connectedness levels were shown to be more complex, and their complete explanation cannot consider only herd descriptors. They involve more comprehensive changes in the relationship matrix, which can be only fully expressed by the CD of contrasts.

Estimate of corrected values and the effect of correction for measurement error in dietary data obtained by the Food Frequency Questionnaire for Adolescents (AFFQ)

The scope of this study was to estimate calibrated values for dietary data obtained by the Food Frequency Questionnaire for Adolescents (FFQA) and illustrate the effect of this approach on food consumption data. The adolescents were assessed on two occasions, with an average interval of twelve months. In 2004, 393 adolescents participated, and 289 were then reassessed in 2005. Dietary data obtained by the FFQA were calibrated using the regression coefficients estimated from the average of two 24-hour recalls (24HR) of the subsample. The calibrated values were similar to the the 24HR reference measurement in the subsample. In 2004 and 2005 a significant difference was observed between the average consumption levels of the FFQA before and after calibration for all nutrients. With the use of calibrated data the proportion of schoolchildren who had fiber intake below the recommended level increased. Therefore, it is seen that calibrated data can be used to obtain adjusted associations due to reclassification of subjects within the predetermined categories.

Genetic associations between flight speed and growth traits in Nellore cattle

The aim of the present study was to estimate genetic parameters for flight speed and its association with growth traits in Nellore beef cattle. The flight speed (FS) of 7,402 yearling animals was measured, using a device composed of a pair of photoelectric cells. Time interval data (s) were converted to speed (m/s) and faster animals were regarded as more reactive. The growth traits analyzed were weaning weight (WW), ADG from weaning to yearling age, and yearling scrotal circumference (SC). The (co)variance components were estimated using REML in a multitrait analysis applying an animal model. The model included random direct additive genetic and residual effects, fixed effects of contemporary groups, age of dam (classes), and age of animal as covariable. For WW, the model also included maternal genetic and permanent environmental random effects. The direct heritability estimate for FS was 0.26 +/- 0.05 and direct heritability estimates for WW, SC, and ADG were 0.30 +/- 0.01, 0.48 +/- 0.02, and 0.19 +/- 0.01, respectively. Estimates of the genetic correlation between FS and the growth traits were -0.12 +/- 0.07 (WW), -0.13 +/- 0.08 (ADG), and -0.11 +/- 0.07 (SC). Although the values were low, these correlations showed that animals with better temperaments (slower FS) tended to present better performance. It is possible to infer that long-term selection for weight and scrotal circumference can promote a positive genetic response in the temperament of animals. Nevertheless, to obtain faster genetic progress in temperament, it would be necessary to perform direct selection for such trait. Flight speed is an easily measured indicator of temperament and can be included as a selection criterion in breeding programs for Nellore cattle.

Correlations between yield and fruit quality characteristics of fresh market tomatoes

Genotypic, phenotypic and environmental correlations were estimated for all possible pairs among eleven characters of tomatoes. Fifteen treatments including five parents and ten hybrids of Instituto Agronômico (IAC) tomato breeding program were evaluated using a randomized complete block experimental design, with tree replications in Itatiba, São Paulo state, Brazil, during 2005/2006. The following traits were evaluated: fruit yield per plant (FP), fruit number per plant (FN), average fruit weight (FW), cluster number per plant (CN), fruit number per cluster (FC), number of locules per fruit (NL), fruit length (FL), fruit width (WI), fruit wall thickness (FT), total soluble solids (SS), and total titratable acidity (TA). The genotypic (rG), phenotypic (rF) and environmental correlations (rA) for two pairs of plant traits were estimated using the Genes© program. High similarity was found among the estimates of genotypic and phenotypic correlations. Positive and high phenotypic and genotypic correlations were observed between FP and the traits FN, FW and FT, and these associations contributed for yield increasing. FW and FT contributed to yield increase and should be considered together as primary yield components in tomato. Positive values of the genotypic and phenotypic correlations revealed that FP influenced FN with high direct effect and significant positive correlation. These traits may be included as the main selection criteria for tomato yield improvement.