Genome-wide copy number variation (CNV) detection in Nelore cattle reveals highly frequent variants in genome regions harboring QTLs affecting production traits.

Background: Copy number variations (CNVs) have been shown to account for substantial portions of observed genomic variation and have been associated with qualitative and quantitative traits and the onset of disease in a number of species. Information from high-resolution studies to detect, characterize and estimate population-specific variant frequencies will facilitate the incorporation of CNVs in genomic studies to identify genes affecting traits of importance. Results: Genome-wide CNVs were detected in high-density single nucleotide polymorphism (SNP) genotyping data from 1,717 Nelore (Bos indicus) cattle, and in NGS data from eight key ancestral bulls. A total of 68,007 and 12,786 distinct CNVs were observed, respectively. Cross-comparisons of results obtained for the eight resequenced animals revealed that 92 % of the CNVs were observed in both datasets, while 62 % of all detected CNVs were observed to overlap with previously validated cattle copy number variant regions (CNVRs). Observed CNVs were used for obtaining breed-specific CNV frequencies and identification of CNVRs, which were subsequently used for gene annotation. A total of 688 of the detected CNVRs were observed to overlap with 286 non-redundant QTLs associated with important production traits in cattle. All of 34 CNVs previously reported to be associated with milk production traits in Holsteins were also observed in Nelore cattle. Comparisons of estimated frequencies of these CNVs in the two breeds revealed 14, 13, 6 and 14 regions in high (>20 %), low (<20 %) and divergent (NEL > HOL, NEL < HOL) frequencies, respectively. Conclusions: Obtained results significantly enriched the bovine CNV map and enabled the identification of variants that are potentially associated with traits under selection in Nelore cattle, particularly in genome regions harboring QTLs affecting production traits.

Wavelet analysis and hierarchical clustering of ofm phenotypic population's variations originated from southern america and europe and attempts of a first relation to molecular divergence.

In this work we compare Grapholita molesta Busck (Lepidoptera: Tortricidae) populations originated from Brazil, Chile, Spain, Italy and Greece using power spectral density and phylogenetic analysis to detect any similarities between the population macro- and the molecular micro-level. Log-transformed population data were normalized and AR(p) models were developed to generate for each case population time series of equal lengths. The time-frequency/scale properties of the population data were further analyzed using wavelet analysis to detect any population dynamics frequency changes and cluster the populations. Based on the power spectral of each population time series and the hierarchical clustering schemes, populations originated from Southern America (Brazil and Chile) exhibit similar rhythmic properties and are both closer related with populations originated from Greece. Populations from Spain and especially Italy, have higher distance by terms of periodic changes on their population dynamics. Moreover, the members within the same cluster share similar spectral information, therefore they are supposed to participate in the same temporally regulated population process. On the contrary, the phylogenetic approach revealed a less structured pattern that bears indications of panmixia, as the two clusters contain individuals from both Europe and South America. This preliminary outcome will be further assessed by incorporating more individuals and likely employed a second molecular marker.

Panicum maximum cv. Tanzânia: climate trends and regional pasture production in Brazil.

Projected change in forage production under a range of climate scenarios is important for the evaluation of the impacts of global climate change on pasture-based livestock production systems in Brazil. We evaluated the effects of regional climate trends on Panicum maximum cv. Tanzânia production, predicted by agro-meteorological model considering the sum of degree days and corrected by a water availa bility index. Data from Brazilian weather stations (1963?2009) were considered as the current climate (baseline), and future scenarios, based on contrasting scenarios interms of increased temperature and atmospheric CO2 concentrations (high and low increases), were determined for 2013?2040 (2025 scenario) and for 2043?2070 (2055 scenario). Predicted baseline scenarios indicated that there are regional and seasonal variations in P. maximum production related to variation intemperature and water availability during the year. Production was lower in the Northeast region and higher in the rainforest area. Total annual productionunder future climate scenarios was predicted toincrease by up to 20% for most of the Brazilian area, mainly due to temperature increase, according to each climate model and scenario evaluated. The highest increase in forage production is expected to be in the South, Southeast and Central-west areas of Brazil. In these regions, future climate scenarios will not lead to changes in the seasonal production, with largerincreases in productivity during the summer. Climate risk is expected to decrease, as the probability of occurrence of low forage productions will be lower. Due to the predicted increase in temperature and decrease in rainfall in the Northeast area, P. maximum production is expected to decrease, mainly when considering scenarios based on the PRECIS model for the 2055 scenario.