Michael Dingkuhn

Genome-wide association mapping of root traits in a japonica rice panel.

Rice is a crop prone to drought stress in upland and rainfed lowland ecosystems. A deep root system is recognized as the best drought avoidance mechanism. Genome-wide association mapping offers higher resolution for locating quantitative trait loci (QTLs) than QTL mapping in biparental populations. We performed an association mapping study for root traits using a panel of 167 japonica accessions, mostly of tropical origin. The panel was genotyped at an average density of one marker per 22.5 kb using genotyping by sequencing technology. The linkage disequilibrium in the panel was high (r2>0.6, on average, for 20 kb mean distances between markers). The plants were grown in transparent 50 cm × 20 cm × 2 cm Plexiglas nailboard sandwiches filled with 1.5 mm glass beads through which a nutrient solution was circulated. Root system architecture and biomass traits were measured in 30-day-old plants. The panel showed a moderate to high diversity in the various traits, particularly for deep (below 30 cm depth) root mass and the number of deep roots. Association analyses were conducted using a mixed model involving both population structure and kinship to control for false positives. Nineteen associations were significant at P<1e-05, and 78 were significant at P<1e-04. The greatest numbers of significant associations were detected for deep root mass and the number of deep roots, whereas no significant associations were found for total root biomass or deep root proportion. Because several QTLs for different traits were co-localized, 51 unique loci were detected; several co-localized with meta-QTLs for root traits, but none co-localized with rice genes known to be involved in root growth. Several likely candidate genes were found in close proximity to these loci. Additional work is necessary to assess whether these markers are relevant in other backgrounds and whether the genes identified are robust candidates.

From GCM grid cell to agricultural plot: scale issues affecting modelling of climate impact

General circulation models (GCM) are increasingly capable of making relevant predictions of seasonal and long-term climate variability, thus improving prospects of predicting impact on crop yields. This is particularly important for semi-arid West Africa where climate variability and drought threaten food security. Translating GCM outputs into attainable crop yields is difficult because GCM grid boxes are of larger scale than the processes governing yield, involving partitioning of rain among runoff, evaporation, transpiration, drainage and storage at plot scale. This study analyses the bias introduced to crop simulation when climatic data is aggregated spatially or in time, resulting in loss of relevant variation. A detailed case study was conducted using historical weather data for Senegal, applied to the crop model SARRA-H (version for millet). The study was then extended to a 10°N–17° N climatic gradient and a 31 year climate sequence to evaluate yield sensitivity to the variability of solar radiation and rainfall. Finally, a down-scaling model called LGO (Lebel–Guillot–Onibon), generating local rain patterns from grid cell means, was used to restore the variability lost by aggregation. Results indicate that forcing the crop model with spatially aggregated rainfall causes yield overestimations of 10–50% in dry latitudes, but nearly none in humid zones, due to a biased fraction of rainfall available for crop transpiration. Aggregation of solar radiation data caused significant bias in wetter zones where radiation was limiting yield. Where climatic gradients are steep, these two situations can occur within the same GCM grid cell. Disaggregation of grid cell means into a pattern of virtual synoptic stations having high-resolution rainfall distribution removed much of the bias caused by aggregation and gave realistic simulations of yield. It is concluded that coupling of GCM outputs with plot level crop models can cause large systematic errors due to scale incompatibility. These errors can be avoided by transforming GCM outputs, especially rainfall, to simulate the variability found at plot level.

EcoMeristem, a model of morphogenesis and competition among sinks in rice. 1. Concept, validation and sensitivity analysis

Because of rapid advances in functional genomics there is an increasing demand for models simulating complex traits, such as the physiological and environmental controls of plant morphology. This paper describes, validates and explores the behaviour of the structural-functional model EcoMeristem, developed for cereals in the context of the Generation Challenge Program (GCP; CGIAR). EcoMeristem constructs the plant on the basis of an organogenetic body plan, driven by intrinsic (genetic) behavioural norms of meristems. These norms consist of phenological-topological rules for organ initiation and pre-dimensioning (sink creation) and rules enabling feedbacks of the plants resource status on the organogenetic processes. Plant resource status is expressed by a state variable called Internal Competition Index (Ic) calculated daily as the ratio of assimilate source (supply) over the sum of active sinks (demand). Ic constitutes an internal signal analogous to sugar signalling. Ic affects potential phytomer size, tiller initiation, leaf senescence, and carbohydrate storage and mobilisation. The model was calibrated and tested on IR64 rice grown in controlled environments, and validated with field observations for the same cultivar (Philippines). Observed distributions and dynamics of soluble sugars and starch in plant organs supported the model concepts of internal competition and the role of reserves as a buffer for Ic fluctuations. Model sensitivity analyses suggested that plant growth and development depend not only on assimilate supply, but also on organogenesis-based demand. If true, this conclusion has important consequences for crop improvement strategies.

Assessing climate change impacts on sorghum and millet yields in the Sudanian and Sahelian savannas of West Africa

Sub-Saharan West Africa is a vulnerable region where a better quantification and understanding of the impact of climate change on crop yields is urgently needed. Here, we have applied the process-based crop model SARRA-H calibrated and validated over multi-year field trials and surveys at eight contrasting sites in terms of climate and agricultural practices in Senegal, Mali, Burkina Faso and Niger. The model gives a reasonable correlation with observed yields of sorghum and millet under a range of cultivars and traditional crop management practices. We applied the model to more than 7000 simulations of yields of sorghum and millet for 35 stations across West Africa and under very different future climate conditions. We took into account 35 possible climate scenarios by combining precipitation anomalies from 20% to 20% and temperature anomalies fromC0 toC6 C. We found that most of the 35 scenarios (31/35) showed a negative impact on yields, up to 41% forC6 C= 20% rainfall. Moreover, the potential future climate impacts on yields are very different from those recorded in the recent past. This is because of the increasingly adverse role of higher temperatures in reducing crop yields, irrespective of rainfall changes. When warming exceedsC2 C, negative impacts caused by temperature rise cannot be counteracted by any rainfall change. The probability of a yield reduction appears to be greater in the Sudanian region (southern Senegal, Mali, Burkina Faso, northern Togo and Benin), because of an exacerbated sensitivity to temperature changes compared to the Sahelian region (Niger, Mali, northern parts of Senegal and Burkina Faso), where crop yields are more sensitive to rainfall change. Finally, our simulations show that the photoperiod-sensitive traditional cultivars of millet and sorghum used by local farmers for centuries seem more resilient to future climate conditions than modern cultivars bred for their high yield potential ( 28% versus 40% for theC4 C= 20% scenario). Photoperiod-sensitive cultivars counteract the effect of temperature increase on shortening cultivar duration and thus would likely avoid the need to shift to cultivars with a greater thermal time requirement. However, given the large difference in mean yields of the modern versus traditional varieties, the modern varieties would still yield more under optimal fertility conditions in a warmer world, even if they are more affected by climate change.

Relationships between ripening-phase productivity and crop duration, canopy photosynthesis and senescence in transplanted and direct-seeded lowland rice

Abstract A field experiment was conducted to analyze the effect of crop duration on growth and the yield-formation process in tropical lowland rice. Three semidwarf rices (IR58, IR64, and IR29723-143-3-2-1) of different growth durations were either transplanted or broadcast-seeded, and grown under different nitrogen fertilizer regimes. Dry-matter accumulation and N concentration of various plant organs, leaf-area index ( L ), tissue death, tiller number, plant height, and canopy photosynthesis were recorded periodically. Crop duration increased plant biomass but did not significantly affect grain-yield. Plant N uptake was not affected by crop duration. Direct seeding gave grain yields superior to those of transplanted rice using short-duration IR58, but equal or lower grain-yield using the medium- and long-duration varieties. Growth and development were delayed, and tillering and foliage growth were reduced in transplanted rice due to transplant shock. Tiller production and abortion were a function of relative growth rate. Tissue death occurred during the reproductive phase and depended on L and foliage N concentration. IR58 had the highest L (up to 11.6) and IR64 the lowest. Direct-seeded rice had higher L and dry-matter during vegetative and reproductive growth, but lower foliage N concentration, than had transplanted rice. Growth during ripening was negatively affected by high biomass and L at flowering but enhanced by high foliage N concentration. It is concluded that grain-yield is impeded by high biomass at flowering in direct-seeded rice, particularly in long-duration varieties. High biomass at flowering, however, may enable further yield improvement if N partitioning and foliage expansion patterns are modified.

Environmental and genetic control of morphogenesis in crops: towards models simulating phenotypic plasticity

As molecular biologists are realising the importance of physiology in understanding functional genomics of quantitative traits, and as physiologists are realising the formidable prospects for improving their phenotypic models with information on the underlying gene networks, researchers worldwide are working on linked physiological-genetic models. These efforts are in their early methodological stage despite, or because of, the availability of many different types of models, the problem being to bring together the different ways that scientists see the plant. This paper describes some current efforts to adapt phenotype models to the objective of simulating gene-phene processes at the plant or crop scale. Particular emphasis is given to the models capacity to simulate genotype x environment interaction and the resulting phenotypic plasticity, assuming that this permits the defining of model parameters that are closer to specific gene action. Three different types of approaches are presented: (1) a generic, mathematical-architectural model called GREENLAB that simulates resource-modulated morphogenesis; (2) an ecophysiological model of peach tree fruit development and filling, parameterised for a mapping population to evaluate the potential of plugging quantitative trait locus (QTL) effects into the model; and (3) the new model Ecomeristem that constructs plant architecture and its phenotypic plasticity from meristem behaviour, the principal hypothesis being that resource limitations and stresses feed back on the meristems. This latter choice is based on the fact that gene expression happens to a large extent in the meristems. The model is evaluated on the basis of preliminary studies on vegetative-stage rice. The different modelling concepts are critically discussed with respect to their ability to simulate phenotypic plasticity and to operate with parameters that approximate specific gene action, particularly in the area of morphogenesis.

Regulation of tillering in sorghum: Environmental effects

BACKGROUND AND AIMSnTillering has a significant effect on canopy development and, hence, on resource capture, crop growth and grain yield in sorghum. However, the physiological basis of tillering and its regulation by environmental effects are not fully understood. The objective of this study was to understand and quantify the environmental effects on tillering in sorghum using a carbohydrate supply-demand framework.nnnMETHODSnA series of five experiments with a wide range of radiation and temperature conditions was conducted and details of the tillering responses of a single representative hybrid were monitored. The concept of internal plant competition for carbohydrate was developed for analysis of these responses.nnnKEY RESULTSnTiller appearance was highly synchronized with main shoot leaf appearance, with a consistent hierarchy for tillering across environments. The main environmental effect was on the frequency of tiller appearance, in particular of the lower-rank tillers. This explained some of the observed environmental differences in the onset of tillering. A generalized index of internal plant competition, which took account of plant assimilate supply and demand (S/D(index)) during the critical period for tillering, explained most of the variation in maximum tiller number observed across the five experiments.nnnCONCLUSIONSnThis result was consistent with the hypothesis that internal plant competition for assimilates regulates tillering in sorghum. Hence, the framework outlined has a predictive value that could provide the basis for dynamic simulation of tillering in crop growth models.

Variability of Phyllochron, Plastochron and Rate of Increase in Height in Photoperiod-sensitive Sorghum Varieties

BACKGROUND AND AIMSnWest African sorghum (Sorghum bicolor) varieties are generally highly photoperiod-sensitive, which is a necessary adaptation to the variable onset date of the rainy season and the variable dates of sowing in the savannah zone. Depending on sowing date, plants can produce from 12 to >40 leaves on the main culm, with height varying from 1 m to more than 5 m. The present study aimed to better understand the complex phenology of these variables.nnnMETHODSnA 2-year series of monthly sowings of three West African sorghum varieties was conducted near Bamako, Mali. Drought stress was avoided by supplemental irrigation. Rate of initiation of primordia at the stem apex was recorded, together with rate of leaf emergence and increase in plant height.nnnKEY RESULTSnLeaf initiation and appearance rates (plastochron(-1) and phyllochron(-1)) were constant for a given sowing date in cases where less than 20 leaves were produced (generally observed with late sowing dates). In contrast, rates were bilinear for early sowing dates, for which plants produced more than 20 leaves. The secondary rates, which occurred from the 20th leaf onwards, were only half of the initial rate. Plastochron and phyllochron showed large variations among sowing dates, and were correlated with the rate of plant height increase. The initial plastochron and phyllochron were positively correlated with soil temperature and negatively correlated with both day length and day-to-day change of day length prevailing at plant emergence, but these factors explained only half of the variation observed.nnnCONCLUSIONSnAlthough they belong to different genetic groups and have different height and photoperiod sensitivity, the three varieties studied exhibited similar response patterns of development rates among phenological phases and seasons, with the local landrace showing the greatest variation due to its longer vegetative phase and longer stem internodes. The possible adaptive advantages in African savannah environments of bilinear development rates and the associated limitation in height increase are discussed.

EcoMeristem, a model of morphogenesis and competition among sinks in rice. 2. Simulating genotype responses to phosphorus deficiency

Phenotypic plasticity enables plants to adjust their morphology and phenology to variable environments. Although potentially important for crop breeding and management, the physiology and genetics of plasticity traits are poorly understood, and few models exist for their study. In the previous paper of this series, the structural-functional model EcoMeristem was described and field validated for vegetative-stage rice. This study applies the model to an experimental study on phosphorus deficiency effects on two morphologically contrasting rice cultivars, IR64 and Azucena, grown in controlled environments under hydroponics culture. Phosphorus deficiency caused severe biomass growth reductions in the shoot but not in the root, thus increasing the rootu2009/u2009shoot weight ratio. It also inhibited tiller formation and leaf elongation, prolonged the phyllochron, and increased carbohydrate reserve pools in the plant. Analysis aided by the model identified inhibition of leaf extension and tillering as primary effects of the stress. Physiological feedback probably led to longer phyllochron, greater reserve accumulation and root growth stimulation. The main effect of P deficiency appeared to be a reduction in demand for assimilates in the shoot while photosynthetic radiation use efficiency remained nearly constant, resulting in spill-over of excess assimilates into reserve compartments and root growth. The results are discussed in the light of future applications of EcoMeristem for phenotyping and genetic analyses of phenotypic plasticity.

Effect of late-season N fertilization on photosynthesis and yield of transplanted and direct-seeded tropical flooded rice. I. Growth dynamics

Abstract Wet direct-seeding is becoming an increasingly popular alternative to transplanting in Asian rice ( Oryza sativa L.) culture. Modern tropical rice cultivars, when direct-seeded, because of vegetative overgrowth and foliar N dilution during reproductive growth, often fall short of their biological yield potential. A field study using ‘IR72’ rice during the 1989 dry season in the Philippines evaluated the effect of late-season N top-dressing on canopy CO 2 exchange rate ( P n ), growth and yield of a transplanted (TP), hillwise dibbled (DS) and broadcast seeded (BS) crop. In BS the higher seeding rate and absence of transplant shock led to a higher tiller number and leaf area index ( L ) than in TP. Foliar N concentration decreased faster in BS because of more rapid growth. Late-season N top-dressing, broadcast or applied as foliar spray, increased foliar N concentration and P n , and led to greater spikelet number and grain-yield. Higher spikelet number was explained by reduced spikelet degeneration after top-dressing. Grain weight limited grain-yield when no N was applied, but was equal among N-fertilized treatments. Panicle number limited yield for TP, whereas grain number per panicle was more limiting for BS and DS. The P n during various reproductive growth stages was correlated with grain-yield, whereas dry-matter at maturity depended more on L . Harvest index ( hi ) gave best correlations with foliar N concentration. The P n depended on both L and foliar N concentration, but the latter became more limiting as plant development advanced. It is concluded that late-season foliar N application raised grain-yield by enhancing the assimilate source through increasing foliar N concentration at a stage when it was limiting, and by enhancing the sink through the reduction of spikelet degeneration. Considering that both foliar N concentration and filled spikelet number are commonly limiting factors for BS yields, late-season foliar top-dressing may be a means specifically improve BS rice culture.