Accuracy of genomic breeding values and predictive ability for postweaning liveweight and age at first calving in a Nellore cattle population with missing sire information.

The multiple sire system (MSS) is a common mating scheme in extensive beef production systems. However, MSS does not allow paternity identification and lead to inaccurate genetic predictions. The objective of this study was to investigate the implementation of single-step genomic BLUP (ssGBLUP) in different scenarios of uncertain paternity in the evaluation for 450-day adjusted liveweight (W450) and age at first calving (AFC) in a Nellore cattle population. To estimate the variance components using BLUP and ssGBLUP, the relationship matrix (A) with different proportions of animals with missing sires (MS) (scenarios 0, 25, 50, 75, and 100% of MS) was created. The genotyped animals with MS were randomly chosen, and ten replicates were performed for each scenario and trait. Five groups of animals were evaluated in each scenario: PHE, all animals with phenotypic records in the population; SIR, proven sires; GEN, genotyped animals; YNG, young animals without phenotypes and progeny; and YNGEN, young genotyped animals. The additive genetic variance decreased for both traits as the proportion of MS increased in the population when using the regular REML. When using the ssGBLUP, accuracies ranged from 0.13 to 0.47 for W450 and from 0.10 to 0.25 for AFC. For both traits, the prediction ability of the direct genomic value (DGV) decreased as the percentage of MS increased. These results emphasize that indirect prediction via DGV of young animals is more accurate when the SNP effects are derived from ssGBLUP with a reference population with known sires. The ssGBLUP could be applied in situations of uncertain paternity, especially when selecting young animals. This methodology is shown to be accurate, mainly in scenarios with a high percentage of MS.

Impact of including information from bulls and their daughters in the training population of multiple-step genomic evaluations in dairy cattle: A simulation study.

The objective of this study was to investigate the impact of accounting for parent average (PA) and genotyped daughters' average (GDA) on the estimation of deregressed estimated breeding values (dEBVs) used as pseudo-phenotypes in multiple-step genomic evaluations. Genomic estimated breeding values (GEBVs) were predicted, in eight different simulated scenarios, using dEBVs calculated based on four methods. These methods included PA and GDA in the dEBV (VR) or only GDA (VRpa) and excluded both PA and GDA from the dEBV with either all information or only information from PA and GDA (JA and NEW, respectively). In general, VR and NEW showed the lowest and highest GEBV reliabilities across scenarios, respectively. Among all deregression methods, VRpa and NEW provided the most consistent bias estimates across the majority of scenarios, and they significantly yielded the least biased GEBVs. Our results indicate that removing PA and GDA information from dEBVs used in multiple-step genomic evaluations can increase the reliability of GEBVs, when both bulls and their daughters are included in the training population.

Application of single step genomic BLUP under different uncertain paternity scenarios using simulated data.

The objective of this study was to investigate the application of BLUP and single step genomic BLUP (ssGBLUP) models in different scenarios of paternity uncertainty with different strategies of scaling the G matrix to match the A22 matrix, using simulated data for beef cattle. Genotypes, pedigree, and phenotypes for age at first calving (AFC) and weight at 550 days (W550) were simulated using heritabilities based on real data (0.12 for AFC and 0.34 for W550). Paternity uncertainty scenarios using 0, 25, 50, 75, and 100% of multiple sires (MS) were studied. The simulated genome had a total length of 2,333 cM, containing 735,293 biallelic markers and 7,000 QTLs randomly distributed over the 29 BTA. It was assumed that QTLs explained 100% of the genetic variance. For QTL, the amount of alleles per loci randomly ranged from two to four. The BLUP model that considers phenotypic and pedigree data, and the ssGBLUP model that combines phenotypic, pedigree and genomic information were used for genetic evaluations. Four ways of scaling the mean of the genomic matrix (G) to match to the mean of the pedigree relationship matrix among genotyped animals (A22) were tested. Accuracy, bias, and inflation were investigated for five groups of animals: ALL = all animals; BULL = only bulls; GEN = genotyped animals; FEM = females; and YOUNG = young males. With the BLUP model, the accuracies of genetic evaluations decreased for both traits as the proportion of unknown sires in the population increased. The EBV accuracy reduction was higher for GEN and YOUNG groups. By analyzing the scenarios for YOUNG (from 0 to 100% of MS), the decrease was 87.8 and 86% for AFC and W550, respectively. When applying the ssGBLUP model, the accuracies of genetic evaluation also decreased as the MS in the pedigree for both traits increased. However, the accuracy reduction was less than those observed for BLUP model. Using the same comparison (scenario 0 to 100% of MS), the accuracies reductions were 38 and 44.6% for AFC and W550, respectively. There were no differences between the strategies for scaling the G matrix for ALL, BULL, and FEM groups under the different scenarios with missing pedigree. These results pointed out that the uninformative part of the A22 matrix and genotyped animals with paternity uncertainty did not influence the scaling of G matrix. On the basis of the results, it is important to have a G matrix in the same scale of the A22 matrix, especially for the evaluation of young animals in situations with missing pedigree information. In these situations, the ssGBLUP model is an appropriate alternative to obtain a more reliable and less biased estimate of breeding values, especially for young animals with few or no phenotypic records. For accurate and unbiased genomic predictions with ssGBLUP, it is necessary to assure that the G matrix is compatible with the A22 matrix, even in situations with paternity uncertainty.

Toxicity of ß-(1→3, 1→6)-á´ -glucans produced by Diaporthe sp. endophytes on Metarhizium anisopliae (Metschnikoff) Sorokin assessed by conidia germination speed parameter / Toxicidade de ß- (1 → 3, 1 → 6) -á´ -glucanas produzidas por endófitos Diaporthe sp. sobre Metarhizium anisopliae (Metschnikoff) Sorokin avaliada pelo parâmetro de velocidade de germinação dos conídios

We have previously reported that ß-(1→3,1→6)-ᴅ-glucans produced by endophytes Diaporthe sp. G27-60 and G65-65 (GenBank accession codes JF766998 and JF767007, respectively) are promising anti-proliferation agents against human breast carcinoma (MCF-7) and hepatocellular carcinoma (HepG2-C3A) cells. However, the literature fails to describe the effects of Diaporthe exopolysaccharides (EPS) on eukaryotic healthy cells. The fungus Metarhiziumanisopliae has been employed as model-system to evaluate the toxicity of pharmaceutical and agricultural-interest substances, taking into account, among other parameters, the speed of conidia germination. Current study verified the effect of different concentrations of Diaporthe ß-glucans on the germination speed of M. anisopliae. Conidia were incubated with ß-glucans treatments (50, 200 and 400 µg/mL) at 28ºC, sampled during 24 h and analyzed by light microscopy. At the end of a 24-h incubation, the amount of germinated conidia reached ≈99% for controls and ranged between 97.7 and 98.6% for treatments. Bayesian analysis indicated that Diaporthe glucans had no toxicity on M. anisopliaeand the curve of germination occurred as expected for this fungal strain. Considering the validity of filamentous fungi as model-systems, results are important data on the toxicity of endophytic EPS on healthy cells and may be associated with our previous results obtained for these polymers against tumor cells.

Anteriormente, um estudo mostrou que ß-(1→3,1→6)-ᴅ-glucanas produzidas pelos endófitos Diaporthe sp. G27-60 e G65-65 (códigos de acesso no GenBank JF766998 e JF767007, respectivamente) são agentes promissores com ação antiproliferativa contra células HepG2-C3A (hepatoma humano) e MCF-7 (adenocarcinoma mamário humano). No entanto, os efeitos de exopolissacarídeos (EPS) produzidos por fungos do gênero Diaporthe em células eucarióticas sadias não estão descritos na literatura atual. O fungo Metarhiziumanisopliae tem sido utilizado como sistema-modelo para avaliar a toxicidade de substâncias de interesse farmacêutico e agronômico, considerando, entre outros parâmetros, a velocidade de germinação de conídios. O presente estudo teve como objetivo verificar os efeitos de diferentes concentrações de ß-glucanas produzidas por Diaporthe sp. sobre a velocidade de germinação de M. anisopliae. Os conídios foram incubados com os tratamentos de ß-glucanas (50, 200 e 400 µg/mL) a 28 ºC, com amostras coletadas ao longo de 24 h, e analisados por microscopia de luz. Ao final das 24 h de incubação, o total de conídios germinados nos controles foi de ≈99%, e variou entre 97,7 e 98,6% para os tratamentos. A análise bayesiana indicou que as glucanas de Diaporthe sp. não apresentaram toxicidade sobre M. anisopliae, e a curva de germinação atendeu ao esperado para essa linhagem fúngica. Considerando a validade dos fungos filamentosos como sistemas-modelo, esses resultados representam dados importantes sobre a toxicidade dos EPS de endófitos sobre células sadias e podem ser associados aos resultados anteriormente obtidos para esses polímeros em testes contra células tumorais.

Características morfogênicas do capim-Tanzânia fertilizado ou não com nitrogênio nas estações do ano / Morphogenic characteristics of Tanzania grass fertilized or not with nitrogen in the seasons of the year

O experimento foi conduzido na Fazenda Experimental de Iguatemi ­ UEM, entre Abril de 2008 a Setembro de 2009, com o objetivo de avaliar o efeito de crescentes doses de N sobre as características morfogênicas do Panicum maximum Jacq cv. Tanzânia nas estações do ano, sob pastejo intermitente. Utilizou-se um delineamento em blocos ao acaso com parcelas subdivididas no tempo, com quatro repetições sendo os tratamentos: N1 = zero, N2 = 150, N3 = 300 e N4 = 450 kg.ha-1 de nitrogênio e as estações do ano: outono, inverno, primavera e verão de 2008 e outono e inverno de 2009. No outono e inverno de 2009, os maiores comprimentos finais de lâminas foliares foram obtidos na maior dose de nitrogênio (450 kg). Tanto a taxa de aparecimento e alongamento de folhas responderam ao nitrogênio apresentando maiores taxas nas maiores doses de nitrogênio (300 e 450 kg) e no verão, seguida de primavera contribuindo com a queda do filocrono e da duração de vida das folhas. Em geral, houve efeito das doses de nitrogênio assim como das estações avaliadas para as todas as variáveis morfogênicas.

The experiment was conducted at the Experimental Farm of Iguatemi - UEM, from April 2008 to September 2009 in order to evaluate the effect of increasing doses of nitrogen on the morphogenesis of Panicum maximum cv. Tanzania in the seasons of the year under intermittent grazing. It was used a randomized block design with split plot with four replications and the treatments: N1 = zero, N2 = 150, N3 = 300 and N4 = 450 kg of N.ha-1 and the seasons: autumn, winter, spring and summer of 2008 and autumn and winter of 2009. In autumn and winter of 2009, the largest final lengths of leaf blade were obtained at the highest nitrogen dose (450 kg). In the fall and winter of 2009, the largest final leaf blade length was obtained at the highest dose of nitrogen (450 kg). Both the leaf appearance and elongation rate responded to nitrogen with higher rates at higher nitrogen doses (300 and 450 kg) and in summer, followed by spring contributing to the fall of phyllochron and life span of leaves. In general, there was effect of nitrogen doses as well as the stations evaluated for all variables analyzed.