Evolution of the mechanical properties of a tropical soil stabilized with lime and ash of rice rind

The ash of rice rind is a pozzolanic material that reacts with the calcium hydroxide (Ca (OH)2) forming bonding composites, when finely worn out and in water presence. Considering this behavior, the objective of the present work was to evaluate the potential use of this residue in the enrichment of the content of pozzolanic materials of a tropical soil stabilized with a commercial hydrated lime. The laboratory testing program incorporated unconfined compression strength tests performed on the soil and on its mixtures with contents of 8% of lime enriched with 5 and 10% of ash of rice rind in relation to the soil dry mass. The results of the testing program supported that the use of the residue was effective in increasing the degree of reactivity of the soil that was also directly related with the increase in the ash content and the period of cure of the mixtures.

Impact of changes in the European Union import regimes for sugar, banana and rice on selected CARICOM countries

Includes bibliography

Development and validation of a Xanthomonas axonopodis pv. citri DNA microarray platform (XACarray) generated from the shotgun libraries previously used in the sequencing of this bacterial genome

Background. From shotgun libraries used for the genomic sequencing of the phytopathogenic bacterium Xanthomonas axonopodis pv. citri (XAC), clones that were representative of the largest possible number of coding sequences (CDSs) were selected to create a DNA microarray platform on glass slides (XACarray). The creation of the XACarray allowed for the establishment of a tool that is capable of providing data for the analysis of global genome expression in this organism. Findings. The inserts from the selected clones were amplified by PCR with the universal oligonucleotide primers M13R and M13F. The obtained products were purified and fixed in duplicate on glass slides specific for use in DNA microarrays. The number of spots on the microarray totaled 6,144 and included 768 positive controls and 624 negative controls per slide. Validation of the platform was performed through hybridization of total DNA probes from XAC labeled with different fluorophores, Cy3 and Cy5. In this validation assay, 86% of all PCR products fixed on the glass slides were confirmed to present a hybridization signal greater than twice the standard deviation of the deviation of the global median signal-to-noise ration. Conclusions. Our validation of the XACArray platform using DNA-DNA hybridization revealed that it can be used to evaluate the expression of 2,365 individual CDSs from all major functional categories, which corresponds to 52.7% of the annotated CDSs of the XAC genome. As a proof of concept, we used this platform in a previously work to verify the absence of genomic regions that could not be detected by sequencing in related strains of Xanthomonas. © 2010 Moreira et al; licensee BioMed Central Ltd.

Monoclonal Antibody Production and Immunolocalization of a Salinity Stress-Related Protein in Rice (Oryza sativa)

Among various physiological responses to salt stress, the synthesis of a lectin-related protein of 14.5 kDa was observed in rice plants (Oryza sativa L.) under the treatment of 170 mmol/L NaCl. In order to better understand the role of the SALT protein in the physiological processes involving salinity, it was immunolocalized in mesophilic cells of leaf sheath and blade of a rice variety IAC-4440 following monoclonal antibodies produced by hybridome culture technique. This variety turned out to be an excellent model for that purpose, since it accumulates SALT protein even in absence of salt treatment and it has been classified as moderately sensitive to salinity and a superior grain producer. This feature was relevant for this work since it allowed the use of plants without the deleterious effects caused by salinity. Immunocytochemistry assays revealed that the SALT protein is located in the stroma of chloroplasts under non-stressing condition. Since the chloroplast is the main target affected by salinity and considering that the SALT protein does not present any apparent signal peptide for organelle localization, its lectin-like activity seems to play an important role in the establishment of stable complexes, either to other proteins or to oligosaccharides that are translocated to the chloroplast. © 2011 China National Rice Research Institute.

Characterization and genome organization of a repetitive element associated with the nucleolus organizer region in leporinuselongatus (anostomidae: Characiformes)

Chromosome mapping and studies of the genomic organization of repetitive DNA sequences provide valuable insights that enhance our evolutionary and structural understanding of these sequences, as well as identifying chromosomal rearrangements and sex determination. This study investigated the occurrence and organization of repetitive DNA sequences in Leporinus elongatus using restriction enzyme digestion and the mapping of sequences by chromosomal fluorescence in situ hybridization (FISH). A 378-bp fragment with a 54.2% GC content was isolated after digestion with the SmaI restriction enzyme. BLASTN search found no similarity with previously described sequences, so this repetitive sequence was named LeSmaI. FISH experiments were conducted using L. elongatus and other Anostomidae species, i.e. L. macrocephalus,L. obtusidens, L. striatus, L. lacustris, L. friderici, Schizodon borellii, S. isognathus, and Abramites hypselonotus which detected signals that were unique to male and female L. elongatus individuals. Double-FISH using LeSmaI and 18S rDNA showed that LeSmaI was located in a nucleolus organizer region (NOR) in the male and female metaphases of L. elongatus. This report also discusses the role of repetitive DNA associated with NORs in the diversification of Anostomidae species karyotypes. Copyright © 2012 S. Karger AG, Basel.

Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds

Intense selective pressures applied over short evolutionary time have resulted in homogeneity within, but substantial variation among, horse breeds. Utilizing this population structure, 744 individuals from 33 breeds, and a 54,000 SNP genotyping array, breed-specific targets of selection were identified using an FST-based statistic calculated in 500-kb windows across the genome. A 5.5-Mb region of ECA18, in which the myostatin (MSTN) gene was centered, contained the highest signature of selection in both the Paint and Quarter Horse. Gene sequencing and histological analysis of gluteal muscle biopsies showed a promoter variant and intronic SNP of MSTN were each significantly associated with higher Type 2B and lower Type 1 muscle fiber proportions in the Quarter Horse, demonstrating a functional consequence of selection at this locus. Signatures of selection on ECA23 in all gaited breeds in the sample led to the identification of a shared, 186-kb haplotype including two doublesex related mab transcription factor genes (DMRT2 and 3). The recent identification of a DMRT3 mutation within this haplotype, which appears necessary for the ability to perform alternative gaits, provides further evidence for selection at this locus. Finally, putative loci for the determination of size were identified in the draft breeds and the Miniature horse on ECA11, as well as when signatures of selection surrounding candidate genes at other loci were examined. This work provides further evidence of the importance of MSTN in racing breeds, provides strong evidence for selection upon gait and size, and illustrates the potential for population-based techniques to find genomic regions driving important phenotypes in the modern horse. © 2013 Petersen et al.

Upland rice growth and mineral nutrition as affected by cultivars and sulfur availability

A better understanding of the differential growth of upland rice (Oryza sativa L.) cultivars with increasing soil S availability could help improve rice yield under upland conditions. The objective of this study was to evaluate root and shoot growth and nutrition of upland traditional and modern rice cultivars as affected by S availability. The experimental design was completely randomized in a 3 (rates of S) × 3 (cultivars) factorial with four replications. Low availability of S in the soil reduces root and shoot development and the efficiency of N, P, and S uptake, as well as the concentration and content of these nutrients in rice cultivars. At 0 mg dm-3 of S, rice cultivars prioritize root growth over shoots, and the traditional cultivar does so with greater intensity. Our results suggested that more development of traditional cultivars under low S availability facilitates its adaptation in soils under this condition. On the other hand, the intermediate and modern cultivars are more responsive to S fertilization. Moreover, S fertilization allows significant increases in upland rice growth and must be considered in cropping systems aiming for high yields. © Soil Science Society of America.

Genetic Diversity in the Modern Horse Illustrated from Genome-Wide SNP Data

Horses were domesticated from the Eurasian steppes 5,000-6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. FST calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection. © 2013 Petersen et al.

Root distribution, nutrient uptake, and yield of two upland rice cultivars under two water regimes

Upland rice (Oryza sativa L.) cultivation has been increasing in global importance due to the decreasing water availability for flood- irrigated rice. The use of sprinkler irrigation to supplement rainfall and the identification of cultivars more adapted to lower water availability could be effective alternatives for producing upland rice without yield losses while using less water. The objective of this field study was to evaluate the root distribution, plant nutrition, and grain yield of two drought tolerant upland rice cultivars under two water regimes in the Cerrado Region of Brazil during two growing seasons. The main plots were two water regimes (rainfed and sprinkler-irrigation plus rainfall). Subplots were two upland rice cultivars Carajás and IAC 201. Low water availability reduced root growth by 7% and grain yields were from 2644 to 4002 kg ha-1 on average for rainfed and sprinkler irrigation treatments, respectively. Carajás had a significantly better root distribution, nutrient uptake, and higher grain yield (3732 kg ha-1) compared with IAC 201 (2914 kg ha-1) averaged over two growing seasons and water regimes. There were no treatment interactions. Our results suggest that, even when cultivars with a higher tolerance to less water availability are used, using sprinkler irrigation to augment limited rainfall during dry periods may be a viable method to increase upland rice grain yields. © 2013 by the American Society of Agronomy.

The no-tillage system and cover crops-Alternatives to increase upland rice yields

Upland rice (Oryza sativa L.) cultivation has been increasing in importance in Asia while water availability for irrigation has been decreasing because of rapid growth in industry and urban centers. Therefore, the development of technologies that increase upland rice yields under aerobic conditions, thereby saving water, would be an effective strategy to avoid a decrease in global rice grain production. The use of the no-tillage system (NTS) and cover crops that maintain soil moisture would prove advantageous in the move toward sustainable agriculture. However, upland rice develops better in plowed soil, and it has been reported that this crop does not perform well under the NTS. Therefore, the aim of this study was to investigate the effect of cover crops on upland rice grain yield and yield components sowed in a NTS. A field experiment was conducted during two growing seasons (2008-2009 and 2009-2010), and treatments consisted of growing rice under five cover crops in a NTS and two control treatments under the conventional tillage system (plowing once and disking twice). Treatments were carried out in a randomized block design with three replications. Our findings are as follows: On average, Brachiaria brizantha (12.32Mgha-1), Brachiaria ruziziensis (11.08Mgha-1) and Panicum maximum (11.62Mgha-1) had outstanding biomass production; however, these grasses provided the worst upland rice yields (2.30, 2.04, and 2.67Mgha-1, respectively) and are not recommended as cover crops before upland rice. Millet and fallow exhibited the fastest straw degradation (half-lives of 52 and 54 days, respectively), and millet exhibited the fastest nitrogen release (N half-life of 28 days). The use of a NTS was promising when millet was used as a cover crop; this allowed the highest upland rice yield (3.94Mgha-1) and did not statistically differ from plowed fallow (3.52Mgha-1). © 2012 Elsevier B.V.

Population genetic evidence that basidiospores play an important role in the disease cycle of rice-infecting populations of Rhizoctonia solani AG-1 IA in Iran

The fungus Rhizoctonia solani AG-1 IA causes sheath blight, one of the most important rice diseases worldwide. The first objective of this study was to analyse the genetic structure of R. solani AG-1 IA populations from three locations in the Iranian Caspian Sea rice agroecosystem. Three population samples of R. solani AG-1 IA isolates were obtained in 2006 from infected rice fields separated by 126-263km. Each field was sampled twice during the season: at the early booting stage and 45days later at the early mature grain stage. The genetic structure of these three populations was analysed using nine microsatellite loci. While the population genetic structure from Tonekabon and Amol indicated high gene flow, they were both differentiated from Rasht. The high gene flow between Tonekabon and Amol was probably due mainly to human-mediated movement of infested seeds. The second objective was to determine the importance of recombination. All three populations exhibited a mixed reproductive mode, including both sexual and asexual reproduction. No inbreeding was detected, suggesting that the pathogen is random mating. The third objective was to determine if genetic structure within a field changes over the course of a growing season. A decrease in the proportion of admixed genotypes from the early to the late season was detected. There was also a significant (P=0·002) increase in the proportion of loci under Hardy-Weinberg equilibrium. These two lines of evidence support the hypothesis that basidiospores can be a source of secondary inoculum. © 2012 BSPP.

Response of rice cultivars to nitrogen in upland conditions

Against the background of a growing world population, rice (Oryza sativa L.) consumption is expected to grow faster than its production. Therefore, an appropriate question would be: how to increase productivity in the shortterm? In this respect, it becomes important the implementation of modern agricultural production systems, such as upland rice with supplemental sprinkler irrigation. Additional information is needed to maximize the available resources, with special attention given to research on the use of nitrogen. This study aimed to evaluate the agronomic performance of commercial rice cultivars with different plant characteristics in upland conditions with supplemental sprinkler irrigation, when subjected to nitrogen in topdress application at the R1 stage (panicle differentiation). The experiment was arranged in a randomized block with split plot design, with 65 treatments, consisting of the combination of 13 cultivars in the plots, and five nitrogen levels in the subplots (0, 40, 80, 120 and 160 kg ha-1), with four replications. Genetic variability was detected among rice cultivars and the agronomic performance in response to the applied nitrogen. The topdressing application of nitrogen increases, in general, the production components and grain yield in rice. Cultivars BRS Primavera, Caiapó and IAC 202 stood out for grain yield, followed by Baldo, Carnaroli, BRS Curinga and IAC 500 with lower yields.

Elevated atmospheric CO2 concentration increases rice blast severity

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Study of whole genome linkage disequilibrium in Nellore cattle

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Detecting Loci under Recent Positive Selection in Dairy and Beef Cattle by Combining Different Genome-Wide Scan Methods

As the methodologies available for the detection of positive selection from genomic data vary in terms of assumptions and execution, weak correlations are expected among them. However, if there is any given signal that is consistently supported across different methodologies, it is strong evidence that the locus has been under past selection. In this paper, a straightforward frequentist approach based on the Stouffer Method to combine P-values across different tests for evidence of recent positive selection in common variations, as well as strategies for extracting biological information from the detected signals, were described and applied to high density single nucleotide polymorphism (SNP) data generated from dairy and beef cattle (taurine and indicine). The ancestral Bovinae allele state of over 440,000 SNP is also reported. Using this combination of methods, highly significant (P<3.17×10-7) population-specific sweeps pointing out to candidate genes and pathways that may be involved in beef and dairy production were identified. The most significant signal was found in the Cornichon homolog 3 gene (CNIH3) in Brown Swiss (P = 3.82×10-12), and may be involved in the regulation of pre-ovulatory luteinizing hormone surge. Other putative pathways under selection are the glucolysis/gluconeogenesis, transcription machinery and chemokine/cytokine activity in Angus; calpain-calpastatin system and ribosome biogenesis in Brown Swiss; and gangliosides deposition in milk fat globules in Gyr. The composite method, combined with the strategies applied to retrieve functional information, may be a useful tool for surveying genome-wide selective sweeps and providing insights in to the source of selection.