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.

Climatic groups in Ibero-America viticulture compared to worldwide wine producer regions.

The wine production is an important activity in many Ibero-American countries. The wine producer regions of these countries configure a large use of different climate types and viticultural climates. In a vitivinicultural zoning project of CYTED (Ibero-American Program for Science, Technology and Development), a viticultural climatic characterization was done in this macro viticultural region. The project have assembled a climatic database that characterizes the viticultural regions, including relevant variables for viticulture: air temperature (mean, maximum, and minimum), precipitation, relative humidity, solar radiation, number of sunshine hours, wind speed, and evapotranspiration. Using indices of the Geoviticulture MCC System (HI, CI and DI), more than 70 viticultural regions in different countries (Argentina, Bolivia, Brazil, Chile, Cuba, Spain, Mexico, Peru, Portugal and Uruguay) were characterized according to its viticultural climatic. The results, which will be integrated to the worldwide database of the MCC System, showed that the Ibero-American viticulture is placed in a wide range of climatic groups of the wine producing regions around the world. This article presents the climatic groups found in Ibero-America, identifying also some new climatic groups not yet found in other regions of the world. This work also identifies some climatic groups not found in Ibero-America viticulture. The research has also highlighted viticultural areas characterized by climates with ?intra-annual climatic variability?, with the potential to produce more than one growing cycle per year. The results allow to conclude that the wide variability and climatic diversity present in Ibero-America may be one of the reasons to explain the diversity in terms of wine types, sensorial characteristics, typicity and uniqueness of wines produced on this macro-region.

Mineralogical changes caused by grape production in a regosol from subtropical Brazilian climate.

Purpose Inadequate soil use and management practices promote commonly negative impacts on the soil constituents and their properties, with consequences to ecosystems. As the soil mineralogy can be permanently altered due to soil use, this approach can be used as a tool to monitor the anthropogenic pressure. The objective of the present study was to assess the mineralogical alterations of a Brazilian regosol used for grape production for 40 years in comparison with a soil under natural vegetation (forest), aiming to discuss anthropogenic pressure on soils. Material and methods Soil samples were collected at depths of 0?0.20 and 0.20?0.40 m from vineyard production and natural vegetation sites. Physical and chemical parameters were analysed by classic approaches. Mineralogical analyses were carried out on <2 mm, silt and clay fractions. Clay minerals were estimated by the relative percentage of peak surface area of the X-ray patterns. Results and discussion Grape production reduced the organic matter content by 28% and the clay content by 23% resulting in a decreasing cation exchange capacity. A similar clay fraction was observed in both soils, containing kaolinite, illite/mica and vermiculite with hydroxy-Al polymers interlayered. Neither gibbsite nor chlorite was found. However, in the soil under native vegetation, the proportion of illite (79 %) was higher than vermiculite (21 %). Whereas, in the soil used for grape production during 40 years, the formation of vermiculite was promoted. Conclusions Grape production alters the proportions of soil constituents of the regosol, reducing clay fraction and organic matter contents, as well as promoting changes in the soil clay minerals with the formation of vermiculite to the detriment of illite, which suggests weathering acceleration and susceptibility to anthropogenic pressure. Recommendations and perspectives Ecosystems in tropical and subtropical climates can be more easily and permanently altered due to anthropogenic pressure, mainly as a consequence of a great magnitude of phenomena such as temperature amplitude and rainfall that occurs in these regions. This is more worrying when soils are located on steep grades with a high anthropogenic pressure, like regosols in Southern Brazil. Thus, this study suggests that changes in soil mineralogy can be used as an important tool to assess anthropogenic pressure in ecosystems and that soil quality maintenance should be a priority in sensible landscapes to maintain the ecosystem quality.

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.

Genesis and classification of soils from subtropical mountain regions of Southern Brazil.

Soils formed in high mountainous regions in southern Brazil are characterized by great accumulation of organic matter (OM) in the surface horizons and variation in the degree of development. We hypothesized that soil properties and genesis are influenced by the interaction of parent materials and climate factors, which differ depending on the location along the altitudinal gradient. The goal of this study was to characterize and classify the soil, evaluate soil distribution, and determine the interactive effects of soil-forming factors in the subtropical mountain regions in Santa Catarina state. Soil samples were collected in areas known for wine production, for a total of 38 modal profiles. Based on morphological, physical, and chemical properties, soils were evaluated for pedogenesis and classified according to the Brazilian System of Soil Classification, with equivalent classes in the World Reference Basis (WRB). The results indicated that pedogenesis was strongly influenced by the parent material, weather, and relief. In the areas where basic effusive rocks (basalt) were observed, there was formation of extensive areas of clayey soils with reddish color and higher iron oxide contents. There was a predominance of Nitossolos Vermelhos and Háplicos (Nitisols), Latossolos Vermelhos (Ferralsols), and Cambissolos Háplicos (Cambisols), highlighting the pedogenetic processes of eluviation, illuviation of clay, and latosolization in conditions of year-long, large-volume, well-distributed rainfall and stability of land forms. In areas with acid effusive rocks (rhyodacites), medial or clayey soils were observed with lower iron oxide content, invariably acidic, and with low base content. For these soils, relief promoted substantial removal of material, resulting in intense rejuvenation, with a predominance of Cambissolos Háplicos (Cambisols) and lesser occurrence of Nitossolos Brunos (Nitisols) and Neossolos Litólicos (Leptosols). Soils formed from sedimentary rocks also tended to be more acidic, but with higher sand content, and the soils identified were Cambissolos Háplicos and Húmicos (Cambisols). Cluster analysis separated the soil profiles into three groups: the first and largest was formed by profiles originating from sedimentary rocks and rhyodacites; the second, smaller group was formed by four profiles in the Água Doce region (acidic rocks); and the third was formed by profiles derived from basalt. Discriminant analysis was effective in grouping soil classes. Thus, the study highlighted the importance of geology in the formation of soils in this landscape associated with climate and relief.