Genome-wide association study for birth weight in Nellore cattle points to previously described orthologous genes affecting human and bovine height

Background: Birth weight (BW) is an economically important trait in beef cattle, and is associated with growth- and stature-related traits and calving difficulty. One region of the cattle genome, located on Bos primigenius taurus chromosome 14 (BTA14), has been previously shown to be associated with stature by multiple independent studies, and contains orthologous genes affecting human height. A genome-wide association study (GWAS) for BW in Brazilian Nellore cattle (Bos primigenius indicus) was performed using estimated breeding values (EBVs) of 654 progeny-tested bulls genotyped for over 777,000 single nucleotide polymorphisms (SNPs).Results: The most significant SNP (rs133012258, PGC = 1.34 × 10-9), located at BTA14:25376827, explained 4.62% of the variance in BW EBVs. The surrounding 1 Mb region presented high identity with human, pig and mouse autosomes 8, 4 and 4, respectively, and contains the orthologous height genes PLAG1, CHCHD7, MOS, RPS20, LYN, RDHE2 (SDR16C5) and PENK. The region also overlapped 28 quantitative trait loci (QTLs) previously reported in literature by linkage mapping studies in cattle, including QTLs for birth weight, mature height, carcass weight, stature, pre-weaning average daily gain, calving ease, and gestation length.Conclusions: This study presents the first GWAS applying a high-density SNP panel to identify putative chromosome regions affecting birth weight in Nellore cattle. These results suggest that the QTLs on BTA14 associated with body size in taurine cattle (Bos primigenius taurus) also affect birth weight and size in zebu cattle (Bos primigenius indicus). © 2013 Utsunomiya et al.; licensee BioMed Central Ltd.

Metrics to support the evaluation of association rule clustering

Many topics related to association mining have received attention in the research community, especially the ones focused on the discovery of interesting knowledge. A promising approach, related to this topic, is the application of clustering in the pre-processing step to aid the user to find the relevant associative patterns of the domain. In this paper, we propose nine metrics to support the evaluation of this kind of approach. The metrics are important since they provide criteria to: (a) analyze the methodologies, (b) identify their positive and negative aspects, (c) carry out comparisons among them and, therefore, (d) help the users to select the most suitable solution for their problems. Some experiments were done in order to present how the metrics can be used and their usefulness. © 2013 Springer-Verlag GmbH.

Ajuste de modelos não lineares e estimativas de parâmetros genéticos para produção de ovos de uma linhagem de poedeiras White Leghorn

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Abordagem multivariada na seleção de progênies de soja superiores e portadoras do gene RR

Pós-graduação em Agronomia (Genética e Melhoramento de Plantas) - FCAV

Divergência genética entre clones de eucalipto por caracteres biométricos e fisiológicos sob deficiência hídrica

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Influence of spray mixture volume and flight height on herbicide deposition in aerial applications on pastures

The objective of the present study was to analyze the influence of spray mixture volume and flight height on herbicide deposition in aerial applications on pastures. The experimental plots were arranged in a pasture area in the district of Porto Esperidião (Mato Grosso, Brazil). In all of the treatments, the applications contained the herbicides aminopyralid and fluroxypyr (Dominum) at the dose of 2.5 L c.p. ha-1, including the adjuvant mineral oil (Joint Oil) at the dose of 1.0 L and a tracer to determine the deposition by high-performance liquid chromatography (HPLC) (rhodamine at a concentration of 0.6%). The experiment consisted of nine treatments that comprised the combinations of three spray volumes (20, 30 and 50 L ha-1) and three flight heights (10, 30 and 40 m). The results showed that, on average, there was a tendency for larger deposits for the smallest flight heights, with a significant difference between the heights of 10 and 40 m. There was no significant difference among the deposits obtained with the different spray mixture volumes.

Initial height of pasture deferred and utilized in winter and tillering dynamics of signal grass during the following spring

Tillering dynamics during regrowth in the spring (September to December 2009) on signal grass (Brachiaria decumbens cv. Basilisk) pastures deferred in the beginning of April 2009 is evaluated. Four pasture heights were evaluated at the beginning of deferment (10, 20, 30 and 40 cm). The experimental design consisted of completely randomized blocks with two replications. Rise in pasture height at the beginning of deferment decreased the appearance rate, increased the mortality rate and reduced the survival rate, the balance between appearance and mortality and the stability index of the tiller population at the beginning of the spring. Pastures deferred at initial height of 30 and 40 cm presented relatively stable tiller appearance rate between the beginning and end of spring. However, these pastures presented greater mortality rate, lower survival rate, lower balance between appearance and mortality and lower stability index of the tiller population at the beginning of spring when compared to rates at the end of spring. Pastures managed with shorter initial heights (10 and 20 cm) provided more tissue renewal in the subsequent growth season after their utilization in the winter.

Decay of interspecific avian flock networks along a disturbance gradient in Amazonia

Our understanding of how anthropogenic habitat change shapes species interactions is in its infancy. This is in large part because analytical approaches such as network theory have only recently been applied to characterize complex community dynamics. Network models are a powerful tool for quantifying how ecological interactions are affected by habitat modification because they provide metrics that quantify community structure and function. Here, we examine how large-scale habitat alteration has affected ecological interactions among mixed-species flocking birds in Amazonian rainforest. These flocks provide a model system for investigating how habitat heterogeneity influences non-trophic interactions and the subsequent social structure of forest-dependent mixed-species bird flocks. We analyse 21 flock interaction networks throughout a mosaic of primary forest, fragments of varying sizes and secondary forest (SF) at the Biological Dynamics of Forest Fragments Project in central Amazonian Brazil. Habitat type had a strong effect on network structure at the levels of both species and flock. Frequency of associations among species, as summarized by weighted degree, declined with increasing levels of forest fragmentation and SF. At the flock level, clustering coefficients and overall attendance positively correlated with mean vegetation height, indicating a strong effect of habitat structure on flock cohesion and stability. Prior research has shown that trophic interactions are often resilient to large-scale changes in habitat structure because species are ecologically redundant. By contrast, our results suggest that behavioural interactions and the structure of non-trophic networks are highly sensitive to environmental change. Thus, a more nuanced, system-by-system approach may be needed when thinking about the resiliency of ecological networks.

Chemometric optimization of solid-liquid extraction with low-temperature partition (SLE-LTP) for determination of persistent organic pollutants in Caiman yacare eggs

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Optimizing row spacing and plant population arrangement for a new short-height castor genotype in fall-winter

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Static Video Summarization through Optimum-Path Forest Clustering

This paper introduces the Optimum-Path Forest (OPF) classifier for static video summarization, being its results comparable to the ones obtained by some state-of-the-art video summarization techniques. The experimental section has been conducted using several image descriptors in two public datasets, followed by an analysis of OPF robustness regarding one ad-hoc parameter. Future works are guided to improve OPF effectiveness on each distinct video category.

Pseudechis guttatus venom proteome: Insights into evolution and toxin clustering

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Automatic visual dictionary generation through optimum-path forest clusteringautomatic visual dictionary generation through optimum-path forest clustering

Image categorization by means of bag of visual words has received increasing attention by the image processing and vision communities in the last years. In these approaches, each image is represented by invariant points of interest which are mapped to a Hilbert Space representing a visual dictionary which aims at comprising the most discriminative features in a set of images. Notwithstanding, the main problem of such approaches is to find a compact and representative dictionary. Finding such representative dictionary automatically with no user intervention is an even more difficult task. In this paper, we propose a method to automatically find such dictionary by employing a recent developed graph-based clustering algorithm called Optimum-Path Forest, which does not make any assumption about the visual dictionary's size and is more efficient and effective than the state-of-the-art techniques used for dictionary generation.

Abordagem multivariada na análise de diversidade genética em cruzamentos para alto teor de óleo em soja

The soybean crop is considered a high expression around the world. In plant breeding programs, knowledge of genetic diversity is extremely important and in this context, are frequently used multivariate analyzes. Thus, the aim of the present study was to evaluate the genetic divergence between soybean crosses through multivariate techniques. In total, 16 crosses were evaluated, which were in the F2 generation of inbreeding. The evaluated characteristics were plant height at maturity, height of the first pod, number of branches per plant, number of pods per plant, number of nodes per plant, hundred seed weight, grain yield and oil content. For the analyzes was used Euclidean distance, methods of hierarchical clustering UPGMA and Ward and principal component analysis. Genetic distances estimated using Euclidean distance ranged from 1.24 to 8.13, with the smallest distance observed between crosses C1 and C4, and the greatest distance between the C2 crosses and C6. The methods UPGMA clustering and Ward met crossings in five different groups. The principal component analysis explained 86.2% of the variance contained in the original eight variables with three main components. The APM characters, NV, NR, NN, PG% and oil were the main contributors to genetic divergence among traits. Multivariate techniques were crucial to the analysis of genetic diversity, and the methods of Ward and UPGMA clustering and principal components have consistent results in this way, the simultaneous use of these tools in genetic analysis of crosses is indicated