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)

Diploid chromosome set of kissing bug Triatoma baratai (Hemiptera, Triatominae)

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

De novo transcriptome assembly for a non-model species, the blood-sucking bug Triatoma brasiliensis, a vector of Chagas disease

High throughput sequencing (HTS) provides new research opportunities for work on non-model organisms, such as differential expression studies between populations exposed to different environmental conditions. However, such transcriptomic studies first require the production of a reference assembly. The choice of sampling procedure, sequencing strategy and assembly workflow is crucial. To develop a reliable reference transcriptome for Triatoma brasiliensis, the major Chagas disease vector in Northeastern Brazil, different de novo assembly protocols were generated using various datasets and software. Both 454 and Illumina sequencing technologies were applied on RNA extracted from antennae and mouthparts from single or pooled individuals. The 454 library yielded 278 Mb. Fifteen Illumina libraries were constructed and yielded nearly 360 million RNA-seq single reads and 46 million RNA-seq paired-end reads for nearly 45 Gb. For the 454 reads, we used three assemblers, Newbler, CAP3 and/or MIRA and for the Illumina reads, the Trinity assembler. Ten assembly workflows were compared using these programs separately or in combination. To compare the assemblies obtained, quantitative and qualitative criteria were used, including contig length, N50, contig number and the percentage of chimeric contigs. Completeness of the assemblies was estimated using the CEGMA pipeline. The best assembly (57,657 contigs, completeness of 80 %, < 1 % chimeric contigs) was a hybrid assembly leading to recommend the use of (1) a single individual with large representation of biological tissues, (2) merging both long reads and short paired-end Illumina reads, (3) several assemblers in order to combine the specific advantages of each.

Interactions of Bacillus thuringiensis bioinsecticides and the predatory stink bug Podisus nigrispinus to control Plutella xylostella

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Retrieval of Trichostrongylus colubriformis infective larvae from grass contaminated in winter and in spring

The survival of infective larvae (L3) of Trichostrongylus colubriformis was evaluated on Brachiaria, Coast-cross and Aruana forage grasses. Feces of sheep parasitized exclusively by T. colubriformis were deposited in winter and spring on experimental plots whose grasses were cut at two heights: 5 cm and 30 cm. One, two, four, eight, 12 and 16 weeks after depositing the feces, fecal and forage samples were collected for the retrieval and quantification of L3. Retrieval of L3 from feces and forage was negligible in winter due to the dry weather, although a few larvae were retrieved in the last larval collections. However, L3 retrieval from fecal samples was greater in spring, especially two weeks after feces were deposited on 30 cm high grasses. At this time, the L3 retrieval rate from the three forage grasses differed significantly (P < 0.05), with Aruana grass showing the highest average L3 retrieval rate, followed by Coast-cross and Brachiaria. In conclusion, the winter drought proved very unfavorable for the presence of L3 in the environment, and the microclimate of Aruana pastureland was generally the most favorable for the retrieval of infective larvae.

Infestation of Caliothrips phaseoli (Thysanoptera: Thripidae) on bean cultivars grown in the winter, rainy, and dry seasons in Brazil

The present study aimed to identify common bean (Phaseolus vulgaris L.) cultivars less susceptible to Caliothrips phaseoli (Hood) in different growing seasons, to evaluate whether climatic conditions influence plant resistance to C. phaseoli infestation, and to investigate the preferred plant part for insect feeding. Eighteen common bean cultivars were evaluated in the winter season, and 19 cultivars were assessed in the rainy and dry seasons, under field conditions in the municipality of Jaboticabal, state of São Paulo, Brazil. Infestation of C. phaseoli nymphs in the upper and lower parts of the beans plants was recorded at weekly intervals from 25 days after plant emergence (DAE) to 60 DAE. In the winter season, the cultivars 'IAC Galante,' 'IAC Centauro,' 'IAC Carioca Eté,' and 'IAC Formoso' had significantly lower number of thrips than the cultivar 'IAC Diplomata.' In the rainy season, the cultivars 'IAC Harmonia' and 'IPR Siriri' had the lowest thrips infestation, differing from the cultivars 'BRS Pontal' and 'IAC Una.' The bean cultivars were equally susceptible to C. phaseoli in the dry season. The results suggest that C. phaseoli nymphs prefer to infest leaves of the lower part of bean plants, like most generalist herbivorous insects. In the winter and dry seasons, the highest thrips infestation was observed at 60 DAE, while in the rainy season, it was recorded from 32 to 46 DAE. Overall, C. phaseoli infestation on bean cultivars was not influenced by either temperature, relative humidity, or rainfall.

Comparing de novo and reference-based transcriptome assembly strategies by applying them to the blood-sucking bug Rhodnius prolixus

High Throughput Sequencing capabilities have made the process of assembling a transcriptome easier, whether or not there is a reference genome. But the quality of a transcriptome assembly must be good enough to capture the most comprehensive catalog of transcripts and their variations, and to carry out further experiments on transcriptomics. There is currently no consensus on which of the many sequencing technologies and assembly tools are the most effective. Many non-model organisms lack a reference genome to guide the transcriptome assembly. One question, therefore, is whether or not a reference-based genome assembly gives better results than de novo assembly. The blood-sucking insect Rhodnius prolixus-a vector for Chagas disease-has a reference genome. It is therefore a good model on which to compare reference-based and de novo transcriptome assemblies. In this study, we compared de novo and reference-based genome assembly strategies using three datasets (454, Illumina, 454 combined with Illumina) and various assembly software. We developed criteria to compare the resulting assemblies: the size distribution and number of transcripts, the proportion of potentially chimeric transcripts, how complete the assembly was (completeness evaluated both through CEGMA software and R. prolixus proteome fraction retrieved). Moreover, we looked for the presence of two chemosensory gene families (Odorant-Binding Proteins and Chemosensory Proteins) to validate the assembly quality. The reference-based assemblies after genome annotation were clearly better than those generated using de novo strategies alone. Reference-based strategies revealed new transcripts, including new isoforms unpredicted by automatic genome annotation. However, a combination of both de novo and reference-based strategies gave the best result, and allowed us to assemble fragmented transcripts.

Towards biological control strategies for the bronze bug, Thaumastocoris peregrinus, on eucalyptus plantations in South America

The bronze bug is an invasive Australian pest that has reached eucalypt production areas worldwide in <10 years. The fi rst record in South America was in 2005 in Argentina. Collaboration in the region towards a unifi ed strategy for the management of the bronze bug started soon after the dispersal of the pest into Brazil and Uruguay was confi rmed. Here, we present the main achievements of this collaboration in four main topics: 1) biology of the pest, 2) monitoring, 3) biological control, and 4) cooperative networks. Two mass rearing procedures have been implemented in the region with relative success, allowing basic biological studies on the pest. Continuous monitoring in the region for >5 years has provided a reasonable knowledge on seasonal patterns of T. peregrinus. Biological control strategies developed include the use of local natural enemies of T. peregrinus, the development of biopesticides, and the introduction of Cleruchoides noackae, an egg parasitoid of T. peregrinus from Australia. We review the main achievements in each country. Finally, a regional network of institutions, researchers, and students has strengthened in the region, providing a solid background for future collaboration.

Biological control of the bronze bug, Thaumastocoris peregrinus, in eucalyptus plantations in Brazil

The bronze bug Thaumastocoris peregrinus (Hemiptera: Thaumastocoridae) was detected in Brazil in 2008 and infested >180 000 ha of eucalyptus plantations in 2011. The bronze bug can cause a reduction of 10–15% in wood productivity after 2 years of heavy infestation. Although there is not an effective control method known, biological control is the main control strategy studied. An exotic egg parasitoid, Cleruchoides noackae (Hymenoptera: Mymaridae), was imported from Australia in 2012, reared in a laboratory and released in three Brazilian regions. Parasitoids were recovered at release points after 20–30 d. In 2013, preliminary evaluations demonstrated parasitoid establishment in these areas, and the parasitoid was recovered in adjacent areas after 1 year of release. Bioassays confi rmed egg parasitism of 15–20% by C. noackae. Other native natural enemies were studied. We found green lacewing Chrysoperla externa and predatory bugs Supputius cincticeps and Atopozelus opsimus preying on nymphs and/or adults of T. peregrinus. Another promising possibility is entomopathogenic fungi. Commercial formulations of Beauveria bassiana were tested with success in lab and fi eld conditions. Fusarium proliferatum and Paecilomyces cateniannulatus caused mortality of T. peregrinus in natural epizooties. After 5 years of research, it is possible to develop an integrated pest management system (IPM) for eucalyptus plantations based on biocontrol strategy for bronze bug.

PB1908-27 Loss From Cornstalk Disease in Custer County, Nebraska, During the Winter of 1906-1907 (Distributed January 1908, Reprinted December 1930)

"Cornstalk disease" is the name given to the cause or causes of death of cattle allowed to run in fields of standing cornstalks from which the ears have been gathered. It is probable that "many different maladies have been included under this name." In Nebraska, however, there is such a similarity in the symptoms reported by the farmers that it seems probable that the great majority of the losses attributed to cornstalk disease are really due to some common cause. As to the exact nature of this cause nothing is known. However, various theories have been advanced, and methods of prevention or treatment based upon these theories have been described.

Long-term recovery patterns of arctic tundra after winter seismic exploration

In response to the increasing global demand for energy, oil exploration and development are expanding into frontier areas of the Arctic, where slow-growing tundra vegetation and the underlying permafrost soils are very sensitive to disturbance. The creation of vehicle trails on the tundra from seismic exploration for oil has accelerated in the past decade, and the cumulative impact represents a geographic footprint that covers a greater extent of Alaska’s North Slope tundra than all other direct human impacts combined. Seismic exploration for oil and gas was conducted on the coastal plain of the Arctic National Wildlife Refuge, Alaska, USA, in the winters of 1984 and 1985. This study documents recovery of vegetation and permafrost soils over a two-decade period after vehicle traffic on snow-covered tundra. Paired permanent vegetation plots (disturbed vs. reference) were monitored six times from 1984 to 2002. Data were collected on percent vegetative cover by plant species and on soil and ground ice characteristics. We developed Bayesian hierarchical models, with temporally and spatially autocorrelated errors, to analyze the effects of vegetation type and initial disturbance levels on recovery patterns of the different plant growth forms as well as soil thaw depth. Plant community composition was altered on the trails by species-specific responses to initial disturbance and subsequent changes in substrate. Long-term changes included increased cover of graminoids and decreased cover of evergreen shrubs and mosses. Trails with low levels of initial disturbance usually improved well over time, whereas those with medium to high levels of initial disturbance recovered slowly. Trails on ice-poor, gravel substrates of riparian areas recovered better than those on ice-rich loamy soils of the uplands, even after severe initial damage. Recovery to pre-disturbance communities was not possible where trail subsidence occurred due to thawing of ground ice. Previous studies of disturbance from winter seismic vehicles in the Arctic predicted short-term and mostly aesthetic impacts, but we found that severe impacts to tundra vegetation persisted for two decades after disturbance under some conditions. We recommend management approaches that should be used to prevent persistent tundra damage.

QUANTITATIVE TRAIT LOCI FOR AGRONOMIC AND END-USE QUALITY PERFORMANCE AND THE EFFECT OF SOILBORNE WHEAT MOSAIC VIRUS IN A HARD WINTER WHEAT POPULATION IN NEBRASKA

To better understand agronomic and end-use quality in wheat (Triticum aestivum L.) we developed a population containing 154 F6:8 recombinant inbred lines (RILs) from the cross TAM107-R7/Arlin. The parental lines and RILs were phenotyped at six environments in Nebraska and differed for resistance to Wheat soilborne mosaic virus (WSBMV), morphological, agronomic, and end-use quality traits. Additionally, a 2300 cM genome-wide linkage map was created for quantitative trait loci (QTL) analysis. Based on our results across multiple environments, the best RILs could be used for cultivar improvement. The population and marker data are publicly available for interested researchers for future research. The population was used to determine the effect of WSBMV on agronomic and end-use quality and for the mapping of a resistance locus. Results from two infected environments showed that all but two agronomic traits were significantly affected by the disease. Specifically, the disease reduced grain yield by 30% of susceptible RILs and they flowered 5 d later and were 11 cm shorter. End-use quality traits were not negatively affected but flour protein content was increased in susceptible RILs. The resistance locus SbmTmr1 mapped to 27.1 cM near marker wPt-5870 on chromosome 5DL using ELISA data. Finally, we investigated how WSBMV affected QTL detection in the population. QTLs were mapped at two WSBMV infected environments, four uninfected environments, and in the resistant and susceptible RIL subpopulations in the infected environments. Fifty-two significant (LOD≥3) QTLs were mapped in RILs at uninfected environments. Many of the QTLs were pleiotropic or closely linked at 6 chromosomal regions. Forty-seven QTLs were mapped in RILs at WSBMV infected environments. Comparisons between uninfected and infected environments identified 20 common QTLs and 21 environmentally specific QTLs. Finally, 24 QTLs were determined to be affected by WSBMV by comparing the subpopulations in QTL analyses within the same environment. The comparisons were statistically validated using marker by disease interactions. These results showed that QTLs can be affected by WSBMV and careful interpretation of QTL results is needed where biotic stresses are present. Finally, beneficial QTLs not affected by WSBMV or the environment are candidates for marker-assisted selection.

EXPERIMENTAL TREE TRIMMING TO CONTROL AN URBAN WINTER BLACKBIRD ROOST

Every fall millions of blackbirds come down the Mississippi Flyway to return to their winter roosts in Arkansas, Louisiana, and East Texas. When these roosts are located in urban areas, public pressure makes the more common chemical means of control impractical. A less destructive and more permanent method of control was sought. At Rice University, in Houston, Texas, there has been a blackbird roost of various sizes and durations since 1956. For the past two years we have had the opportunity both to study roosting blackbird biology and experiment with habitat alteration as a control method. This particular report concentrates on the results and interpretation of the tree- trimming program initiated in August 1974. The birds involved are primarily Brown-headed Cowbirds (Molothrus ater), along with Starlings (sturnus vulgaris), Common and Great-tailed Grackles (Quiscalus quiscula and Cassidix mexicanus), Red-winged Blackbirds (Agelaius phoenicus) and Robins (Turdus migratorius). The campus comprises 121 ha and was planted with live oaks (Quercus virginiana) in 1912. These trees retain their foliage throughout the winter and now form a closed canopy over some 5-6 ha. In the 60s and early 70s most of the birds that came to Houston for the winter roosted in a 64-ha woodlot 10 km north of campus. In January 1970, the U.S. Fish and Wildlife Roosting Survey reported one million birds at this site we call the North Loop. Fifteen- thousand birds were estimated at Rice.

Variability of the subtropical shelf front off eastern South America: Winter 2003 and summer 2004

Hydrographic data collected during surveys carried out in austral winter 2003 and summer 2004 are used to analyze the distributions of temperature (T) and salinity (S) over the continental shelf and slope of eastern South America between 27 degrees S and 39 degrees S. The water mass structure and the characteristics of the transition between subantarctic and subtropical shelf water (STSW), referred to as the subtropical shelf front (STSF), as revealed by the vertical structure of temperature and salinity are discussed. During both surveys, the front intensifies downward and extends southwestward from the near coastal zone at 33 degrees S to the shelf break at 36 degrees S. In austral winter subantarctic shelf water (SASW), derived from the northern Patagonia shelf, forms a vertically coherent cold wedge of low salinity waters that locally separate the outer shelf STSW from the fresher inner shelf Plata Plume Water (PPW) derived from the Rio de la Plata. Winter T-S diagrams and cross-shelf T and S distributions indicate that mixtures of PPW and tropical water only occur beyond the northernmost extent of pure SASW, and form STSW and an inverted thermocline characteristic of this region. In summer 2004, dilution of Tropical water (TW) occurs at two distinct levels: a warm near surface layer, associated to PPW-TW mixtures, similar to but significantly warmer than winter STSW, and a colder (T similar to 16 degrees C) salinity minimum layer at 40-50 m depth, created by SASW-STSW mixtures across the STSF. In winter, the salinity distribution controls the density structure creating a cross-shore density gradient, which prevents isopycnal mixing across the STSF. Temperature stratification in summer induces a sharp pycnocline providing cross-shelf isopycnal connections across the STSF. Cooling and freshening of the upper layer observed at stations collected along the western edge of the Brazil Current suggest offshore export of shelf waters. Low T and S filaments, evident along the shelf break in the winter data, suggest that submesoscale eddies may enhance the property exchange across the shelf break. These observations suggest that as the subsurface shelf waters converge at the STSF, they flow southward along the front and are expelled offshore, primarily along the front axis. (C) 2008 Elsevier Ltd. All rights reserved.