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Identification of Reference Genes for Quantitative Gene Expression Studies in Three Tissues of Japanese Quail
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Oxythermal window drastically constraints the survival and development of European sturgeon early life phases
No full textExpression of the Arabidopsis thaliana immune receptor EFR in Medicago truncatula reduces infection by a root pathogenic bacterium, but not nitrogen-fixing rhizobial symbiosis
No full textInterfamily transfer of plant pattern recognition receptors (PRRs) represents a promising biotechnological approach to engineer broad-spectrum, and potentially durable, disease resistance in crops. It is however unclear whether new recognition specificities to given pathogen-associated molecular patterns (PAMPs) affect the interaction of the recipient plant with beneficial microbes. To test this in a direct reductionist approach, we transferred the Brassicaceae-specific PRR ELONGATION FACTOR-THERMO UNSTABLE RECEPTOR (EFR), conferring recognition of the bacterial EF-Tu protein, from Arabidopsis thaliana to the legume Medicago truncatula. Constitutive EFR expression led to EFR accumulation and activation of immune responses upon treatment with the EF-Tu-derived elf18 peptide in leaves and roots. The interaction of M. truncatula with the bacterial symbiont Sinorhizobium meliloti is characterized by the formation of root nodules that fix atmospheric nitrogen. Although nodule numbers were slightly reduced at an early stage of the infection in EFR-Medicago when compared to control lines, nodulation was similar in all lines at later stages. Furthermore, nodule colonization by rhizobia, and nitrogen fixation were not compromised by EFR expression. Importantly, the M. truncatula lines expressing EFR were substantially more resistant to the root bacterial pathogen Ralstonia solanacearum. Our data suggest that the transfer of EFR to M. truncatula does not impede root nodule symbiosis, but has a positive impact on disease resistance against a bacterial pathogen. In addition, our results indicate that Rhizobium can either avoid PAMP recognition during the infection process, or is able to actively suppress immune signaling
Testing hopkins' bioclimatic law with PhenoCam data
No full textPremise of the Study We investigated the spatial and temporal patterns of vegetation phenology with phenometrics derived from PhenoCam imagery. Specifically, we evaluated the Bioclimatic Law proposed by Hopkins, which relates phenological transitions to latitude, longitude, and elevation.[br/]
Methods “Green‐up” and “green‐down” dates—representing the start and end of the annual cycles of vegetation activity—were estimated from measures of canopy greenness calculated from digital repeat photography. We used data from 65 deciduous broadleaf (DB) forest sites, 18 evergreen needleleaf (EN) forest sites, and 21 grassland (GR) sites.[br/]
Results DB green‐up dates were well correlated with mean annual temperature and varied along spatial gradients consistent with the Bioclimatic Law. Interannual variation in DB phenology was most strongly associated with temperature anomalies during a relatively narrow window of time. EN phenology was not well correlated with either climatic factors or spatial gradients, but similar to DB phenology, interannual variation was most closely associated with temperature anomalies. For GR sites, mean annual precipitation explained most of the spatial variation in the duration of vegetation activity, whereas both temperature and precipitation anomalies explained interannual variation in phenology.[br/]
Discussion PhenoCam data provide an objective and consistent means by which spatial and temporal patterns in vegetation phenology can be investigated
Complete Genome Sequence of Bradyrhizobium sp. Strain ORS3257, an Efficient Nitrogen-Fixing Bacterium Isolated from Cowpea in Senegal
No full textHere, we report the complete genome sequence of Bradyrhizobium sp. strain ORS3257, which forms efficient symbioses with cowpea, peanut, or groundnut. These genomic data will be useful to identify genes associated with symbiotic performance and host compatibility on several legumes, including Aeschynomene species, with which a Nod-independent type III secretion system (T3SS)-dependent symbiosis can be established
Effect of feed restriction and refeeding on performance and metabolism of European and Caribbean growing pigs in a tropical climate
No full textReduction in feed intake is a common physiological response of growing pigs facing stressful environmental conditions. The present experiment aims to study (1) the effects of a short-term feed restriction and refeeding on pig performance and metabolism and (2) the differential response between two breeds, Large White (LW), which has been selected for high performance, and Creole (CR), which is adapted to tropical conditions. A trial of 36 castrated male pigs (18 LW and 18 CR) was carried out. For each breed, half of the animals were restrictively fed at 50% of the standard feed allowance for 6 days and then fed normally for the next 14 days. Growth performance, thermoregulatory responses, plasma hormones and metabolites were measured. Results showed that, for all traits, the difference in response between the two breeds was small and rarely significant, which may be due to the short duration of the feed restriction. Irrespective of breed, feed restriction induced a reduction of growth rate and feed efficiency that was rapidly compensated for upon refeeding. Feed restriction also reduced skin temperature, rectal temperature and respiratory rate, as well as blood urea and cholesterol, which are of interest as potential biomarkers for feed restriction
Phenological asynchrony between the fruit fly Anastrepha fraterculus and early maturing peach cultivars could contribute to pesticide use reduction
No full textPhenological asynchrony between fruit crops and pests consists of a discrepancy between the period of fruit susceptibility and that of high pest abundance in the orchards. Therefore, it may be used for reducing pesticide applications. We assayed the potential phenological asynchrony between peach cultivars with different growing cycles and the Anastrepha fraterculus (Diptera: Tephritidae). To this end, we assessed fruit infestation by A. fraterculus at harvest for one growing season (2012-2013) in early, average and late maturing peach cultivars. Moreover, the fruit infestation was checked for non-cultivated native and non-cultivated wild exotic plant hosts around the peach orchards of the experimental area during 2013 and 2014. In addition, we monitored A. fraterculus abundance weekly during three consecutive growing seasons, S1 (2011-2012), S2 (2012-2013) and S3 (2013-2014), to assess phenological asynchrony between peach cultivars and A. fraterculus. In particular, we checked the influence of meteorological variables on A. fraterculus abundance, and tested if A. fraterculus abundance at the time when fruits are susceptible differed among cultivars. Eventually we discuss the possibility of sustainable management of peach in southern Brazil. This study constitutes a first assessment of the periods of crop vulnerability and pest presence in peach orchards in South of Brazil and provides necessary information for taking advantage of the phenological asynchrony phenomenon for this pest-crop association
Adjacency-constrained hierarchical clustering of a band similarity matrix with application to genomics
No full textWe focus on a modification of the classical hierarchical agglomerative clustering (HAC), where only adjacent clusters (according to the ordering of positions within a chromosome) can be merged. Adjacency-constrained HAC is implemented in the R package rioja. Our main contribution with respect to existing works is an efficient implementation of adjacency-constrained HAC in the case where the similarity between genomically distant objects can be considered as negligible. We propose an algorithm that is almost linear in time and space with respect to the number of objects to be clustered. It uses a sparse band strategy based on pre-computations of certain cumulative sums of similarities, combined with a min-heap approach to efficiently store and maintain a list of candidate merges. This algorithm is implemented in the R package adjclust, which is available at https://CRAN.R-project.org/package=adjclust. We provide applications to SNP and Hi-C datasets
Genetic characterization of worldwide Prunus domestica (plum) germplasm using sequence-based genotyping.
No full textPrunus domestica commonly known as European plum is a hexaploid fruit tree species cultivated around the world. Locally it is used for fresh consumption, in jams or jellies, and the production of spirits while commercially the fruit is primarily sold dried (prunes). Despite its agricultural importance and long history of cultivation, many questions remain about the origin of this species, the relationships among its many pomological types, and its underlying genetics. Here, we used a sequence-based genotyping approach to characterize worldwide plum germplasm including the potential progenitor Eurasian plum species. Analysis of 405 DNA samples established a set of four clades consistent with the pomological groups Greengages, Mirabelles, European plums, and d'Agen (French) prune plums. A number of cultivars from each clade were identified as likely clonal selections, particularly among the "French" type prune germplasm that is widely cultivated today. Overall, there was relatively low genetic diversity across all cultivated plums suggesting they have been largely inbred and/or derived from a limited number of founders. The results agree with P. domestica having originated as an interspecific hybrid of a diploid P. cerasifera and a tetraploid P. spinosa that itself may have been an interspecific hybrid of P. cerasifera and an unknown Eurasian plum species. The low genetic diversity and lack of true wild-types coupled with the known cultivation history of Eurasian plums imply that P. domestica may have been a product of inter-specific cross breeding and artificial selection by early agrarian Eurasian societies