Brachypodium as a model system for grass research

The combination of a tractable experimental system, molecular tools, facile genetics and comprehensive genomics resources places Brachypodium distachyon in a unique position to promote and accelerate biological investigations in cereal and grass crops. Brachypodium has a proven track-record as a bridge into Triticeae cereal crops by helping to navigate and assemble their large and complex genomes. Brachypodium’s compact genome already provides a useful reference for map-based cloning and comparative genomics. In this review, I argue that Brachypodium will also fulfill a more generic role as a functional genomics model. In this context, Brachypodium will play a pivotal role in multi-system approaches to underpin tomorrow’s grass research landscape.     

Effects of <Emphasis Type="Italic">Inga densiflora</Emphasis> on the microclimate of coffee (<Emphasis Type="Italic">Coffea arabica</Emphasis> L.) and overall biomass under optimal growing conditions in Costa Rica

The advantages of associating shade trees in coffee agroforestry systems (AFS) are generally thought to be restricted mostly to poor soil and sub-optimal ecological conditions for coffee cultivation whereas their role in optimal conditions remains controversial. Thus, the objective of this study was to investigate, under the optimal coffee cultivation conditions of the Central Valley of Costa Rica, the impact of Inga densiflora, a very common shade tree in Central America, on the microclimate, yield and vegetative development of shaded coffee in comparison to coffee monoculture (MC). Maximum temperature of shaded coffee leaves was reduced by up to 5°C relative to coffee leaf temperature in MC. The minimum air temperature at night was 0.5°C higher in AFS than air temperature in MC demonstrating the buffering effects of shade trees. As judged by the lower relative extractable water (REW) in the deep soil layers during the dry season, water use in AFS was higher than in MC. Nevertheless, competition for water between coffee and associated trees was assumed to be limited as REW in the 0–150 cm soil layer was always higher than 0.3 in shaded coffee compared to 0.4 in monoculture. Coffee production was quite similar in both systems during the establishment of shade trees, however a yield decrease of 30% was observed in AFS compared to MC with a decrease in radiation transmittance to less than 40% during the latter years in the absence of an adequate shade tree pruning. As a result of the high contribution (60%) of shade trees to overall biomass, permanent aerial biomass accumulation in AFS amounted to two times the biomass accumulated in MC after 7 years. Thus provided an adequate pruning, Inga-shaded plantations appeared more advantageous than MC in optimal conditions, especially considering the fact that coffee AFS provides high quality coffee, farmers’ revenue diversification and environmental benefits.     

SIMBA,a model for designing sustainable banana-based cropping systems

Banana monocultures (Musa spp., AAA, Cavendish sub-group cv. Grande Naine) can have a detrimental impact on the environment. In these agro-systems, pesticide treatments can lead to surface and groundwater pollution, as is the case in the tropical insular conditions of the French West Indies. Using models to design alternative cropping systems is of growing interest but most of the research work has been concentrated on annual crops and most often in temperate climate. A specific model called SIMBA was built to assess environmental risks under a large range of cropping techniques and to help design more sustainable cropping systems. SIMBA simulates banana-cropping systems at field level over several cropping cycles. It includes sub-models that simulate soil structure, water balance, root nematode populations, yield, and economic outputs with a sound balance between representing the major phenomena well and keeping the model simple to reduce the parameterization costs in a large range of conditions. Agro-environmental indicators generated by the model make it possible to assess the major potential environmental impacts. The model has been developed and calibrated in Guadeloupe and Martinique and is used to draw up practical recommendations for farmers and for virtual experiments of agro-technological innovations or field management strategies. The structure of SIMBA is presented and a methodology is proposed for designing sustainable banana-based cropping systems using the model. SIMBA has been evaluated in a broad range of cropping systems in Guadeloupe by comparing model estimates to data collected in field experiments and surveys. Simulations lead to trends in rotation-based cropping systems characterized by systems that can be considered as intensive for profit evaluation, and combinations of frequent replanting, low nematicide application, no ploughing, and low fertilization level, for environmental evaluation. Simulations performed to optimize the replanting decision rule showed that relatively frequent replanting is good for profit while low frequency replantations (over four banana cycles) give a better environmental evaluation.     

Using 3D architectural models to assess light availability and root bulkiness in coconut agroforestry systems

Using 3D architectural models to assess light availability and root bulkiness in agroforestry systems. In many parts of the humid tropics, coconut trees are frequently intercropped with food crops, or tree crops such as cocoa. The performance of such systems depends on planting patterns, but also on growing conditions for crops below the coconut canopy throughout the development of the coconut trees. We used a modelling approach providing indicators for assessing above-ground competition for light and below-ground competition for space, in order to optimize intercropping in coconut smallholdings. Light transmission and the number of coconut roots in the interrow were assessed in coconut smallholdings from 6 to 60 years old. The modelling of light transmission through coconut stands was based on three-dimensional virtual coconut trees and a numerical light model that computed the shade cast by coconut trees on underlying crops. Root colonization in the interrow was assessed with virtual 3D coconut root systems. Our results showed that intercropping with shade-tolerant species was not limited by light transmission from the 35th year after coconut tree planting. However, at that stage of coconut tree development, the density of primary roots in the interrow limited intercrop development, especially for root and tuber crops. Alteration of the planting pattern over time increased light transmission but did not significantly affect root density. This modelling approach, which involved little parameterization that was easily done, appeared to be an efficient tool for recommending coconut tree planting patterns and densities, as well as indicating intercrop potential depending on their location in the most sunlit areas with minimum root competition.

Growing Brassica juncea as a cover crop, then incorporating its residues provide complementary control of Rhizoctonia root rot of sugar beet

Biofumigation is increasingly viewed as a potentially useful technique for controlling soil-borne crop pathogens, but its efficacy has not systematically been demonstrated at field scale. We investigated the differences in efficacy observed in the field, by analysing the mechanisms by which a Brassica cover crop can act as a biofumigant crop in the prevention of soil-borne disease development. We hypothesised that the biofumigant crop might have a negative effect on soil-borne pathogens whilst growing, and that the pulverisation of this crop and the incorporation of its residues into the soil may enhance this effect. We tested this hypothesis by carrying out three field experiments in 2006, 2007 and 2008 in which Brassica juncea (brown mustard) was managed in different ways within a sugar beet–winter wheat rotation and analysing effects on sugar beet root rot caused by Rhizoctonia solani. Three treatments were studied: mustard pulled out at flowering (MP), mustard crushed at flowering and incorporated into the soil (MC) and bare soil (BS) as a control. We assessed the effect of each treatment on root rot incidence and severity at harvest. Over the 3 years of the experiment, disease incidence was significantly higher on BS plots than on the other plots and was significantly higher on MP plots than on MC plots. MC treatment gave a significantly lower mean conditional severity (severity calculated for diseased beets only) than the BS and MP treatments. Mustard residue incorporation was consistently effective at decreasing disease incidence from year to year (43, 44 and 47% efficacy, as determined by comparison with the disease incidence on BS plots, in 2006, 2007 and 2008, respectively), but the efficacy of growing mustard was variable (36, 16 and 39% efficacy in 2006, 2007 and 2008, respectively). These findings provide insight into the mechanisms by which biofumigant crops may affect soil-borne diseases. These findings have implications for the possible use of biofumigant crops as a biological method for controlling soil-borne diseases at the field scale.     

Light-dependent development of two competitive species (Rubus idaeus, Cytisus scoparius) colonizing gaps in temperate forest

Forest regeneration can be inhibited by competition for environmental resources (water, nutrients, light) between tree seedlings and some competitive species that are generally light-demanding species developing in gaps. The study’s aim was to quantify the development of two competitive species (Rubus idaeus and Cytisus scoparius) present in the chaîne des Puys, France, relatively to light in gaps inside Picea abies stands. On 29 transects linking the stand to the gap centre (223 points), light intensity was measured (0–80% of relative light) and floristic measurements (cover and height of the different species) were done. Development of both competitive species is positively connected to light, with a bell-shaped curve with a maximum of 40–50% for R. idaeus and a quite constant increase to 80% (maximum of light recorded in the experimentation) for C. scoparius. These results are discussed relatively to understorey vegetation management in order to favour forest regeneration.     

Can wood density be efficiently selected at early stage in maritime pine (Pinus pinaster Ait.)?

Growth and stem straightness are the two main selection criteria in the French maritime pine breeding programme. In this contribution, our objective was to study the possibility of selecting for wood density assessed at an early stage. We measured X-ray wood density, in three progeny tests, on more than 1 900 breast high increment cores. High relative expected genetic gain (from 3 to 9%) was found for wood density at mature stage. Juvenile and adult wood density estimations were well-correlated; the relative efficiency of early selection reached about 80% at 12 years old. As it would not be realistic to use the X-ray densitometer at an operational scale in a breeding programme, we tested the efficiency of using the Resistograph, an indirect method to assess wood density on live trees. High correlation between the Resistograph and density data (R ² = 0.93 on familial data) was found, suggesting that wood density through Resistograph assessment could be soon integrated as a new selection criterion in our breeding programme.     

Spatio-temporal distribution of <Emphasis Type="Italic">Erysiphe necator</Emphasis> genetic groups and their relationship with disease levels in vineyards

The discovery of genetically distinct Erysiphe necator groups (A or B), with high phenotypic similarities, raises important questions about their coexistence. For plant pathogens, niche partitioning, allowing the coexistence on the same host (i.e. the same resource), might result from separation in space and/or time. We used a landscape genetic approach to study the geographic distribution of genetic groups of E. necator (distinguished by a SNP in the β-tubulin gene) at the spatial scale of the Languedoc-Roussillon region (southern France) and to assess the temporal succession of groups along the course of the 2007 epidemic. Spatial distribution revealed a high heterogeneity between vineyards: from 100% B to 100% A, with 62% and 38% of vineyards showing a majority of A and B isolates, respectively. Temporal isolation seems to be the major mechanism in the coexistence of the two genetic groups: all isolates collected towards the end of the epidemic belonged to group B, whatever the initial frequency of genetic groups. Our results confirm that both A or B isolates can lead to flag-shoot symptoms, and showed that group A isolates tend to disappear during the course of the epidemic, whereas group B isolates may be active during the entire epidemic and involved in further production of cleistothecia, when recombination takes place. For the first time, the relationship between the frequency of genetic groups and disease levels on leaves and clusters at the end of the epidemic was evaluated. We showed a strong relationship between the disease severity and the genetic composition of E. necator populations: the damage was more important when the epidemic was initiated by B isolates.     

Importance of seed-borne fungi of sorghum and pearl millet in Burkina Faso and their control using plant extracts

Seed-borne fungi of sorghum and pearl millet in Burkina Faso were surveyed. A total of 188 seed samples from various locations, collected in 1989 (42) and 2002 (146), were tested, using the blotter, dry inspection and washing methods. Infection experiments were carried out with the major fungi recorded on each crop by the blotter test. Six essential oils of plants were investigated for their inhibitory activity against eight pathogenic fungi. Thirty four and 27 fungal species were found in seed samples of sorghum and pearl millet, respectively. Phoma sp. and Fusarium moniliforme infected 95 to 100% of the seed samples of both sorghum and pearl millet. Sphacelotheca sorghi and Tolyposporium ehrenbergii were encountered in respectively, 75 and 33% of seed samples of sorghum. T. penicillariae, Sclerospora graminicola and Claviceps fusiformis were present in 88, 41 and 32% of seed samples of pearl millet, respectively. Seeds inoculated with Acremonium strictum, Curvularia oryzae, F. equiseti, F. moniliforme and F. subglutinans and sown in sterilized soil, showed considerable mortality of the seedlings. Three essential oils inhibited in vitro the mycelial growth of all the fungi used by 85 to 100% and reduced significantly sorghum and pearl millet seed infection rates of Phoma sp., Fusarium sp., Curvularia sp., Colletotrichum graminicola and Exserohilum sp. Presence of many pathogenic fungi in considerable number of seed samples indicates the need of field surveys for these and other pathogens. Development of plant extracts for the control of seed-borne pathogens and public awareness on seed-borne diseases management measures for maintaining quality seed should be increased.     

Are ecological gradients in seasonal Q10 of soil respiration explained by climate or by vegetation seasonality?

Soil respiration (SR) is highly sensitive to future climate change, and particularly to global warming. However, considerable uncertainties remain associated with the temperature sensitivity of SR and its controlling processes. Using 384 field measurement data from 114 published papers and one book, this study quantifies the variation in the seasonal Q₁₀ values of soil respiration, the multiplier by which respiration rates increase for a 10 °C increase in temperature, and its drivers across different sites. No significant correlation between Q₁₀ and mean annual temperature or mean annual precipitation is found when statistically controlling seasonal changes in vegetation activity, deduced from satellite vegetation greenness index observations (normalized difference vegetation index, or NDVI). In contrast, the seasonal amplitude of NDVI is significantly and positively correlated with the apparent Q₁₀ of SR. This result indicates that the variations of seasonal vegetation activity exert dominant control over the variations of the apparent Q₁₀ of SR across different sites, highlighting the ecological linkage between plant physiological processes and soil processes. It further implies that the seasonal variation of vegetation activity may thus dominate the apparent seasonal temperature sensitivity. We conclude that the apparent Q₁₀ value of SR estimated from field measurements is generally larger than the intrinsic temperature sensitivity of soil organic matter decomposition, and thus cautions should be taken when applying apparent Q₁₀ values directly in ecosystem models. Our regression analysis further shows that when the amplitude of NDVI variation approximates 0 (and thus when the seasonality in vegetation activity is marginal), the residual Q₁₀ of SR for soil temperature measured at 5 cm depth is about 1.5.