The tricot approach: an agile framework for decentralized on-farm testing supported by citizen science. A retrospective

Matching crop varieties to their target use context and user preferences is a challenge faced by many plant breeding programs serving smallholder agriculture. Numerous participatory approaches proposed by CGIAR and other research teams over the last four decades have attempted to capture farmers' priorities/preferences and crop variety field performance in representative growing environments through experimental trials with higher external validity. Yet none have overcome the challenges of scalability, data validity and reliability, and difficulties in capturing socio-economic and environmental heterogeneity. Building on the strengths of these attempts, we developed a new data-generation approach, called triadic comparison of technology options (tricot). Tricot is a decentralized experimental approach supported by crowdsourced citizen science. In this article, we review the development, validation, and evolution of the tricot approach, through our own research results and reviewing the literature in which tricot approaches have been successfully applied. The first results indicated that tricot-aggregated farmer-led assessments contained information with adequate validity and that reliability could be achieved with a large sample. Costs were lower than current participatory approaches. Scaling the tricot approach into a large on-farm testing network successfully registered specific climatic effects of crop variety performance in representative growing environments. Tricot's recent application in plant breeding networks in relation to decision-making has (i) advanced plant breeding lines recognizing socio-economic heterogeneity, and (ii) identified consumers' preferences and market demands, generating alternative breeding design priorities. We review lessons learned from tricot applications that have enabled a large scaling effort, which should lead to stronger decision-making in crop improvement and increased use of improved varieties in smallholder agriculture.

Genetic gains in early maturing maize hybrids developed by the International Maize and Wheat Improvement Center in Southern Africa during 2000-2018

Genetic gain estimation in a breeding program provides an opportunity to monitor breeding efficiency and genetic progress over a specific period. The present study was conducted to (i) assess the genetic gains in grain yield of the early maturing maize hybrids developed by the International Maize and Wheat Improvement Center (CIMMYT) Southern African breeding program during the period 2000-2018 and (ii) identify key agronomic traits contributing to the yield gains under various management conditions. Seventy-two early maturing hybrids developed by CIMMYT and three commercial checks were assessed under stress and non-stress conditions across 68 environments in seven eastern and southern African countries through the regional on-station trials. Genetic gain was estimated as the slope of the regression of grain yield and other traits against the year of first testing of the hybrid in the regional trial. The results showed highly significant (p< 0.01) annual grain yield gains of 118, 63, 46, and 61 kg ha-1 year-1 under optimum, low N, managed drought, and random stress conditions, respectively. The gains in grain yield realized in this study under both stress and non-stress conditions were associated with improvements in certain agronomic traits and resistance to major maize diseases. The findings of this study clearly demonstrate the significant progress made in developing productive and multiple stress-tolerant maize hybrids together with other desirable agronomic attributes in CIMMYT's hybrid breeding program.

Satellite imagery for high-throughput phenotyping in breeding plots

Advances in breeding efforts to increase the rate of genetic gains and enhance crop resilience to climate change have been limited by the procedure and costs of phenotyping methods. The recent rapid development of sensors, image-processing technology, and data-analysis has provided opportunities for multiple scales phenotyping methods and systems, including satellite imagery. Among these platforms, satellite imagery may represent one of the ultimate approaches to remotely monitor trials and nurseries planted in multiple locations while standardizing protocols and reducing costs. However, the deployment of satellite-based phenotyping in breeding trials has largely been limited by low spatial resolution of satellite images. The advent of a new generation of high-resolution satellites may finally overcome these limitations. The SkySat constellation started offering multispectral images at a 0.5 m resolution since 2020. In this communication we present a case study on the use of time series SkySat images to estimate NDVI from wheat and maize breeding plots encompassing different sizes and spacing. We evaluated the reliability of the calculated NDVI and tested its capacity to detect seasonal changes and genotypic differences. We discuss the advantages, limitations, and perspectives of this approach for high-throughput phenotyping in breeding programs.

Beat the stress: breeding for climate resilience in maize for the tropical rainfed environments

Intensive public sector breeding efforts and public-private partnerships have led to the increase in genetic gains, and deployment of elite climate-resilient maize cultivars for the stress-prone environments in the tropics. Maize (Zea mays L.) plays a critical role in ensuring food and nutritional security, and livelihoods of millions of resource-constrained smallholders. However, maize yields in the tropical rainfed environments are now increasingly vulnerable to various climate-induced stresses, especially drought, heat, waterlogging, salinity, cold, diseases, and insect pests, which often come in combinations to severely impact maize crops. The International Maize and Wheat Improvement Center (CIMMYT), in partnership with several public and private sector institutions, has been intensively engaged over the last four decades in breeding elite tropical maize germplasm with tolerance to key abiotic and biotic stresses, using an extensive managed stress screening network and on-farm testing system. This has led to the successful development and deployment of an array of elite stress-tolerant maize cultivars across sub-Saharan Africa, Asia, and Latin America. Further increasing genetic gains in the tropical maize breeding programs demands judicious integration of doubled haploidy, high-throughput and precise phenotyping, genomics-assisted breeding, breeding data management, and more effective decision support tools. Multi-institutional efforts, especially public-private alliances, are key to ensure that the improved maize varieties effectively reach the climate-vulnerable farming communities in the tropics, including accelerated replacement of old/obsolete varieties.

Transpiration difference under high evaporative demand in chickpea (Cicer arietinum L.) may be explained by differences in the water transport pathway in the root cylinder

Terminal drought substantially reduces chickpea yield. Reducing water use at vegetative stage by reducing transpiration under high vapor pressure deficit (VPD), i.e. under dry/hot conditions, contributes to drought adaptation. We hypothesized that this trait could relate to differences in a genotype's dependence on root water transport pathways and hydraulics. Transpiration rate responses in conservative and profligate chickpea genotypes were evaluated under increasing VPD in the presence/absence of apoplastic and cell-to-cell transport inhibitors. Conservative genotypes ICC 4958 and ICC 8058 restricted transpiration under high VPD compared to the profligate genotypes ICC 14799 and ICC 867. Profligate genotypes were more affected by aquaporin inhibition of the cell-to-cell pathway than conservative genotypes, as measured by the root hydraulic conductance and transpiration under high VPD. Aquaporin inhibitor treatment also led to a larger reduction in root hydraulic conductivity in profligate than in conservative genotypes. In contrast, blockage of the apoplastic pathway in roots decreased transpiration more in conservative than in profligate genotypes. Interestingly, conservative genotypes had high early vigour, whereas profligate genotypes had low early vigour. In conclusion, profligate genotypes depend more on the cell-to-cell pathway, which might explain their higher root hydraulic conductivity, whereas water-saving by restricting transpiration led to higher dependence on the apoplastic pathway. This opens the possibility to screen for conservative or profligate chickpea phenotypes using inhibitors, itself opening to the search of the genetic basis of these differences.

Nitrogen rate impacts on tropical maize nitrogen use efficiency and soil nitrogen depletion in eastern and southern Africa

Sub-Saharan Africa is facing food security challenges due, in part, to decades of soil nitrogen (N) depletion. Applying N fertilizer could increase crop yields and replenish soil N pools. From 2010 to 2015, field experiments conducted in Embu and Kiboko, Kenya and Harare, Zimbabwe investigated yield and N uptake response of six maize (Zea mays L.) hybrids to four N fertilizer rates (0 to 160 kg N ha^-1) in continuous maize production systems. The N recovery efficiency (NRE), cumulative N balance, and soil N content in the upper 0.9 m of soil following the final harvest were determined at each N rate. Plant and soil responses to N fertilizer applications did not differ amongst hybrids. Across locations and N rates, NRE ranged from 0.4 to 1.8 kg kg^-1. Higher NRE values in Kiboko and Harare occurred at lower post-harvest soil inorganic N levels. The excessively high NRE value of 1.8 kg kg^-1 at 40 kg N ha^-1 in Harare suggested that maize hybrids deplete soil inorganic N most at low N rates. Still, negative cumulative N balances indicated that inorganic soil N depletion occurred at all N rates in Embu and Harare (up to - 193 and - 167 kg N ha^-1, respectively) and at the 40 kg N ha^-1 rate in Kiboko (- 72 kg N ha^-1). Overall, maize N uptake exceeded fertilizer N applied and so, while yields increased, soil N pools were not replenished, especially at low total soil N levels (< 10,000 kg N ha^-1 in top 0.9 m).

Correction to: High-throughput method for ear phenotyping and kernel weight estimation in maize using ear digital imaging

[This corrects the article DOI: 10.1186/s13007-018-0317-4.].

Identification of donors for low-nitrogen stress with maize lethal necrosis (MLN) tolerance for maize breeding in sub-Saharan Africa

After drought, a major challenge to smallholder farmers in sub-Saharan Africa is low-fertility soils with poor nitrogen (N)-supplying capacity. Many challenges in this region need to be overcome to create a viable fertilizer market. An intermediate solution is the development of maize varieties with an enhanced ability to take up or utilize N in severely depleted soils, and to more efficiently use the small amounts of N that farmers can supply to their crops. Over 400 elite inbred lines from seven maize breeding programs were screened to identify new sources of tolerance to low-N stress and maize lethal necrosis (MLN) for introgression into Africa-adapted elite germplasm. Lines with high levels of tolerance to both stresses were identified. Lines previously considered to be tolerant to low-N stress ranked in the bottom 10% under low-N confirming the need to replace these lines with new donors identified in this study. The lines that performed best under low-N yielded about 0. 5 Mg ha-1 (20%) more in testcross combinations than some widely used commercial parent lines such as CML442 and CML395. This is the first large scale study to identify maize inbred lines with tolerance to low-N stress and MLN in eastern and southern Africa.

Translating High-Throughput Phenotyping into Genetic Gain

Inability to efficiently implement high-throughput field phenotyping is increasingly perceived as a key component that limits genetic gain in breeding programs. Field phenotyping must be integrated into a wider context than just choosing the correct selection traits, deployment tools, evaluation platforms, or basic data-management methods. Phenotyping means more than conducting such activities in a resource-efficient manner; it also requires appropriate trial management and spatial variability handling, definition of key constraining conditions prevalent in the target population of environments, and the development of more comprehensive data management, including crop modeling. This review will provide a wide perspective on how field phenotyping is best implemented. It will also outline how to bridge the gap between breeders and 'phenotypers' in an effective manner.

High-Throughput Phenotyping of Canopy Cover and Senescence in Maize Field Trials Using Aerial Digital Canopy Imaging

In the crop breeding process, the use of data collection methods that allow reliable assessment of crop adaptation traits, faster and cheaper than those currently in use, can significantly improve resource use efficiency by reducing selection cost and can contribute to increased genetic gain through improved selection efficiency. Current methods to estimate crop growth (ground canopy cover) and leaf senescence are essentially manual and/or by visual scoring, and are therefore often subjective, time consuming, and expensive. Aerial sensing technologies offer radically new perspectives for assessing these traits at low cost, faster, and in a more objective manner. We report the use of an unmanned aerial vehicle (UAV) equipped with an RGB camera for crop cover and canopy senescence assessment in maize field trials. Aerial-imaging-derived data showed a moderately high heritability for both traits with a significant genetic correlation with grain yield. In addition, in some cases, the correlation between the visual assessment (prone to subjectivity) of crop senescence and the senescence index, calculated from aerial imaging data, was significant. We concluded that the UAV-based aerial sensing platforms have great potential for monitoring the dynamics of crop canopy characteristics like crop vigor through ground canopy cover and canopy senescence in breeding trial plots. This is anticipated to assist in improving selection efficiency through higher accuracy and precision, as well as reduced time and cost of data collection.

High-throughput method for ear phenotyping and kernel weight estimation in maize using ear digital imaging

BACKGROUND

Grain yield, ear and kernel attributes can assist to understand the performance of maize plant under different environmental conditions and can be used in the variety development process to address farmer's preferences. These parameters are however still laborious and expensive to measure.

RESULTS

A low-cost ear digital imaging method was developed that provides estimates of ear and kernel attributes i.e., ear number and size, kernel number and size as well as kernel weight from photos of ears harvested from field trial plots. The image processing method uses a script that runs in a batch mode on ImageJ; an open source software. Kernel weight was estimated using the total kernel number derived from the number of kernels visible on the image and the average kernel size. Data showed a good agreement in terms of accuracy and precision between ground truth measurements and data generated through image processing. Broad-sense heritability of the estimated parameters was in the range or higher than that for measured grain weight. Limitation of the method for kernel weight estimation is discussed.

CONCLUSION

The method developed in this work provides an opportunity to significantly reduce the cost of selection in the breeding process, especially for resource constrained crop improvement programs and can be used to learn more about the genetic bases of grain yield determinants.

Higher flower and seed number leads to higher yield under water stress conditions imposed during reproduction in chickpea

The reproductive phase of chickpea (Cicer arietinum L.) is more sensitive to water deficits than the vegetative phase. The characteristics that confer drought tolerance to genotypes at the reproductive stage are not well understood; especially which characteristics are responsible for differences in seed yield under water stress. In two consecutive years, 10 genotypes with contrasting yields under terminal drought stress in the field were exposed to a gradual, but similar, water stress in the glasshouse. Flower number, flower+pod+seed abortion percentage, pod number, pod weight, seed number, seed yield, 100-seed weight (seed size), stem+leaf weight and harvest index (HI) were recorded in well watered plants (WW) and in water-stressed plants (WS) when the level of deficit was mild (phase I), and when the stress was severe (phase II). The WS treatment reduced seed yield, seed and pod number, but not flower+pod+seed abortion percentage or 100-seed weight. Although there were significant differences in total seed yield among the genotypes, the ranking of the seed yield in the glasshouse differed from the ranking in the field, indicating large genotype×environment interaction. Genetic variation for seed yield and seed yield components was observed in the WW treatment, which also showed differences across years, as well as in the WS treatment in both the years, so that the relative seed yield and relative yield components (ratio of values under WS to those under WW) were used as measures of drought tolerance. Relative total seed yield was positively associated with relative total flower number (R2=0.23 in year 2) and relative total seed number (R2=0.83, R2=0.79 in years 1 and 2 respectively). In phase I (mild stress), relative yield of seed produced in that phase was found to be associated with the flower number in both the years (R2=0.69, R2=0.76 respectively). Therefore, the controlled drought imposition that was used, where daily water loss from the soil was made equal for all plants, revealed genotypic differences in the sensitivity of the reproductive process to drought. Under these conditions, the seed yield differences in chickpea were largely related to the capacity to produce a large number of flowers and to set seeds, especially in the early phase of drought stress when the degree of water deficit was mild.

Unmanned aerial platform-based multi-spectral imaging for field phenotyping of maize

BACKGROUND

Recent developments in unmanned aerial platforms (UAP) have provided research opportunities in assessing land allocation and crop physiological traits, including response to abiotic and biotic stresses. UAP-based remote sensing can be used to rapidly and cost-effectively phenotype large numbers of plots and field trials in a dynamic way using time series. This is anticipated to have tremendous implications for progress in crop genetic improvement.

RESULTS

We present the use of a UAP equipped with sensors for multispectral imaging in spatial field variability assessment and phenotyping for low-nitrogen (low-N) stress tolerance in maize. Multispectral aerial images were used to (1) characterize experimental fields for spatial soil-nitrogen variability and (2) derive indices for crop performance under low-N stress. Overall, results showed that the aerial platform enables to effectively characterize spatial field variation and assess crop performance under low-N stress. The Normalized Difference Vegetation Index (NDVI) data derived from spectral imaging presented a strong correlation with ground-measured NDVI, crop senescence index and grain yield.

CONCLUSION

This work suggests that the aerial sensing platform designed for phenotyping studies has the potential to effectively assist in crop genetic improvement against abiotic stresses like low-N provided that sensors have enough resolution for plot level data collection. Limitations and future potential uses are also discussed.

Water: the most important 'molecular' component of water stress tolerance research

Water deficit is the main yield-limiting factor across the Asian and African semiarid tropics and a basic consideration when developing crop cultivars for water-limited conditions is to ensure that crop water demand matches season water supply. Conventional breeding has contributed to the development of varieties that are better adapted to water stress, such as early maturing cultivars that match water supply and demand and then escape terminal water stress. However, an optimisation of this match is possible. Also, further progress in breeding varieties that cope with water stress is hampered by the typically large genotype×environment interactions in most field studies. Therefore, a more comprehensive approach is required to revitalise the development of materials that are adapted to water stress. In the past two decades, transgenic and candidate gene approaches have been proposed for improving crop productivity under water stress, but have had limited real success. The major drawback of these approaches has been their failure to consider realistic water limitations and their link to yield when designing biotechnological experiments. Although the genes are many, the plant traits contributing to crop adaptation to water limitation are few and revolve around the critical need to match water supply and demand. We focus here on the genetic aspects of this, although we acknowledge that crop management options also have a role to play. These traits are related in part to increased, better or more conservative uses of soil water. However, the traits themselves are highly dynamic during crop development: they interact with each other and with the environment. Hence, success in breeding cultivars that are more resilient under water stress requires an understanding of plant traits affecting yield under water deficit as well as an understanding of their mutual and environmental interactions. Given that the phenotypic evaluation of germplasm/breeding material is limited by the number of locations and years of testing, crop simulation modelling then becomes a powerful tool for navigating the complexity of biological systems, for predicting the effects on yield and for determining the probability of success of specific traits or trait combinations across water stress scenarios.

A phytase gene is overexpressed in root nodules cortex of Phaseolus vulgaris-rhizobia symbiosis under phosphorus deficiency

Phosphorus is an essential nutrient for rhizobial symbioses to convert N2 into NH4 usable for N nutrition in legumes and N cycle in ecosystems. This N2 fixation process occurs in nodules with a high energy cost. Phytate is the major storage form of P and accounts for more than 50 % of the total P in seeds of cereals and legumes. The phytases, a group of enzymes widely distributed in plant and microorganisms, are able to hydrolyze a variety of inositol phosphates. Recently, phytase activity was discovered in nodules. However, the gene expression localization and its role in N2-fixing nodules are still unknown. In this work, two recombinant inbred lines (RILs) of common bean (Phaseolus vulgaris L.), selected as contrasting for N2 fixation under P deficiency, namely RILs 115 (P-efficient) and 147 (P-inefficient) were inoculated with Rhizobium tropici CIAT 899, and grown under hydroaeroponic conditions with sufficient versus deficient P supply. With in situ RT-PCR methodology, we found that phytase transcripts were particularly abundant in the nodule cortex and infected zone of both RILs. Under P deficiency, phytase transcripts were significantly more abundant for RIL115 than for RIL147, and more in the outer cortex than in the infected zone. Additionally, the high expression of phytase among nodule tissues for the P-deficient RIL115 was associated with an increase in phytase (33 %) and phosphatase (49 %) activities and efficiency in use of the rhizobial symbiosis (34 %). It is argued that phytase activity in nodules would contribute to the adaptation of the rhizobia-legume symbiosis to low-P environments.

Restriction of transpiration rate under high vapour pressure deficit and non-limiting water conditions is important for terminal drought tolerance in cowpea

Drought stress is a major constraint on cowpea productivity, since the crop is grown under warm conditions on sandy soils having low water-holding capacity. For enhanced performance of crops facing terminal drought stress, like cowpea, water-saving strategies are crucial. In this work, the growth and transpiration rate (TR) of 40 cowpea genotypes with contrasting response to terminal drought were measured under well-watered conditions across different vapour pressure deficits (VPD) to investigate whether tolerant and sensitive genotypes differ in their control of leaf water loss. A method is presented to indirectly assess TR through canopy temperature (CT) and the index of canopy conductance (Ig). Overall, plants developed larger leaf area under low than under high VPD, and there was a consistent trend of lower plant biomass in tolerant genotypes. Substantial differences were recorded among genotypes in TR response to VPD, with tolerant genotypes having significantly lower TR than sensitive ones, especially at times with the highest VPD. Genotypes differed in TR response to increasing VPD, with some tolerant genotypes exhibiting a clear VPD breakpoint at about 2.25 kPa, above which there was very little increase in TR. In contrast, sensitive genotypes presented a linear increase in TR as VPD increased, and the same pattern was found in some tolerant lines, but with a smaller slope. CT, estimated with thermal imagery, correlated well with TR and Ig and could therefore be used as proxy for TR. These results indicate that control of water loss discriminated between tolerant and sensitive genotypes and may, therefore, be a reliable indicator of terminal drought stress tolerance. The water-saving characteristics of some genotypes are hypothesised to leave more soil water for pod filling, which is crucial for terminal drought adaptation.

Integrated genomics, physiology and breeding approaches for improving drought tolerance in crops

Drought is one of the most serious production constraint for world agriculture and is projected to worsen with anticipated climate change. Inter-disciplinary scientists have been trying to understand and dissect the mechanisms of plant tolerance to drought stress using a variety of approaches; however, success has been limited. Modern genomics and genetic approaches coupled with advances in precise phenotyping and breeding methodologies are expected to more effectively unravel the genes and metabolic pathways that confer drought tolerance in crops. This article discusses the most recent advances in plant physiology for precision phenotyping of drought response, a vital step before implementing the genetic and molecular-physiological strategies to unravel the complex multilayered drought tolerance mechanism and further exploration using molecular breeding approaches for crop improvement. Emphasis has been given to molecular dissection of drought tolerance by QTL or gene discovery through linkage and association mapping, QTL cloning, candidate gene identification, transcriptomics and functional genomics. Molecular breeding approaches such as marker-assisted backcrossing, marker-assisted recurrent selection and genome-wide selection have been suggested to be integrated in crop improvement strategies to develop drought-tolerant cultivars that will enhance food security in the context of a changing and more variable climate.

Lower soil moisture threshold for transpiration decline under water deficit correlates with lower canopy conductance and higher transpiration efficiency in drought-tolerant cowpea

As water availability is critical for reproduction, terminal drought tolerance may involve water-saving traits. Experiments were undertaken under different vapour pressure deficit (VPD) and water regimes (water stress (WS) and well watered (WW)) to test genotypic differences and trait relationships in the fraction of transpirable soil water (FTSW) at which transpiration declines, canopy conductance (proxied by transpiration rate (TR, g H2Ocm-2h-1)), canopy temperature depression (CTD, °C), transpiration efficiency (TE, gkg-1) and growth parameters, using 15 contrasting cowpea (Vigna unguiculata (L.) Walp.) genotypes. Under WW conditions at the vegetative and early podding stages, plant mass and leaf area were larger under low VPD, and was generally lower in tolerant than in sensitive genotypes. Several tolerant lines had lower TR under WW conditions and restricted TR more than sensitive lines under high VPD. Under WS conditions, transpiration declined at a lower FTSW in tolerant than in sensitive lines. Tolerant lines also maintained higher TR and CTD under severe stress. TE was higher in tolerant genotypes under WS conditions. Significant relationships were found between TR, and TE, CTD and FTSW under different water regimes. In summary, traits that condition how genotypes manage limited water resources discriminated between tolerant and sensitive lines. Arguably, a lower canopy conductance limits plant growth and plant water use, and allows tolerant lines to behave like unstressed plants until the soil is drier and to maintain a higher TR under severe stress, as lower TR at high VPD leads to higher TE.

A conservative pattern of water use, rather than deep or profuse rooting, is critical for the terminal drought tolerance of chickpea

Chickpea is mostly grown on stored soil moisture, and deep/profuse rooting has been hypothesized for almost three decades to be critical for improving chickpea tolerance to terminal drought. However, temporal patterns of water use that leave water available for reproduction and grain filling could be equally critical. Therefore, variation in water use pattern and root depth/density were measured, and their relationships to yield tested under fully irrigated and terminal drought stress, using lysimeters that provided soil volumes equivalent to field conditions. Twenty chickpea genotypes having similar plant phenology but contrasting for a field-derived terminal drought-tolerance index based on yield were used. The pattern of water extraction clearly discriminated tolerant and sensitive genotypes. Tolerant genotypes had a lower water uptake and a lower index of stomatal conductance at the vegetative stage than sensitive ones, while tolerant genotypes extracted more water than sensitive genotypes after flowering. The magnitude of the variation in root growth components (depth, length density, RLD, dry weight, RDW) did not distinguish tolerant from sensitive genotypes. The seed yield was not significantly correlated with the root length density (RLD) in any soil layers, whereas seed yield was both negatively related to water uptake between 23-38 DAS, and positively related to water uptake between 48-61 DAS. Under these conditions of terminal drought, the most critical component of tolerance in chickpea was the conservative use of water early in the cropping cycle, explained partly by a lower canopy conductance, which resulted in more water available in the soil profile during reproduction leading to higher reproductive success.

Chickpea genotypes contrasting for seed yield under terminal drought stress in the field differ for traits related to the control of water use

Chickpea (Cicer arietinum L.) is often exposed to terminal drought, and deep, profuse rooting has been proposed as the main breeding target to improve terminal drought tolerance. This work tested whether plant water use at the vegetative stage and under non-limited water conditions could relate to the degree of sensitivity of chickpea to terminal drought. Transpiration response to a range of vapour pressure deficits under controlled and outdoor conditions was measured with canopy conductance using gravimetric measurements and thermal imagery in eight chickpea genotypes with comparable phenology and contrasting seed yield under terminal drought in the field. Additionally, the response of plant growth and transpiration to progressive soil moisture depletion was assayed in the same genotypes. Drought-tolerant genotypes had a lower canopy conductance under fully irrigated conditions at the vegetative stage; this trend was reversed at the early pod filling stage. While two sensitive genotypes had high early growth vigour and leaf development, there was a trend of lower growth in tolerant genotypes under progressive soil drying than in sensitive ones. Tolerant genotypes also exhibited a decline of transpiration in wetter soil compared to sensitive genotypes. Canopy conductance could be proxied by measuring leaf temperature with an infrared camera, although the relationship lost sensitivity at the pod filling stage. This work suggests that some traits contribute to water saving when water does not limit plant growth and development in drought-tolerant chickpea. It is hypothesised that this water would be available for the reproduction and grain filling stages.

The salt-responsive transcriptome of chickpea roots and nodules via deepSuperSAGE

BACKGROUND

The combination of high-throughput transcript profiling and next-generation sequencing technologies is a prerequisite for genome-wide comprehensive transcriptome analysis. Our recent innovation of deepSuperSAGE is based on an advanced SuperSAGE protocol and its combination with massively parallel pyrosequencing on Roche's 454 sequencing platform. As a demonstration of the power of this combination, we have chosen the salt stress transcriptomes of roots and nodules of the third most important legume crop chickpea (Cicer arietinum L.). While our report is more technology-oriented, it nevertheless addresses a major world-wide problem for crops generally: high salinity. Together with low temperatures and water stress, high salinity is responsible for crop losses of millions of tons of various legume (and other) crops. Continuously deteriorating environmental conditions will combine with salinity stress to further compromise crop yields. As a good example for such stress-exposed crop plants, we started to characterize salt stress responses of chickpeas on the transcriptome level.

RESULTS

We used deepSuperSAGE to detect early global transcriptome changes in salt-stressed chickpea. The salt stress responses of 86,919 transcripts representing 17,918 unique 26 bp deepSuperSAGE tags (UniTags) from roots of the salt-tolerant variety INRAT-93 two hours after treatment with 25 mM NaCl were characterized. Additionally, the expression of 57,281 transcripts representing 13,115 UniTags was monitored in nodules of the same plants. From a total of 144,200 analyzed 26 bp tags in roots and nodules together, 21,401 unique transcripts were identified. Of these, only 363 and 106 specific transcripts, respectively, were commonly up- or down-regulated (>3.0-fold) under salt stress in both organs, witnessing a differential organ-specific response to stress.Profiting from recent pioneer works on massive cDNA sequencing in chickpea, more than 9,400 UniTags were able to be linked to UniProt entries. Additionally, gene ontology (GO) categories over-representation analysis enabled to filter out enriched biological processes among the differentially expressed UniTags. Subsequently, the gathered information was further cross-checked with stress-related pathways. From several filtered pathways, here we focus exemplarily on transcripts associated with the generation and scavenging of reactive oxygen species (ROS), as well as on transcripts involved in Na+ homeostasis. Although both processes are already very well characterized in other plants, the information generated in the present work is of high value. Information on expression profiles and sequence similarity for several hundreds of transcripts of potential interest is now available.

CONCLUSIONS

This report demonstrates, that the combination of the high-throughput transcriptome profiling technology SuperSAGE with one of the next-generation sequencing platforms allows deep insights into the first molecular reactions of a plant exposed to salinity. Cross validation with recent reports enriched the information about the salt stress dynamics of more than 9,000 chickpea ESTs, and enlarged their pool of alternative transcripts isoforms. As an example for the high resolution of the employed technology that we coin deepSuperSAGE, we demonstrate that ROS-scavenging and -generating pathways undergo strong global transcriptome changes in chickpea roots and nodules already 2 hours after onset of moderate salt stress (25 mM NaCl). Additionally, a set of more than 15 candidate transcripts are proposed to be potential components of the salt overly sensitive (SOS) pathway in chickpea. Newly identified transcript isoforms are potential targets for breeding novel cultivars with high salinity tolerance. We demonstrate that these targets can be integrated into breeding schemes by micro-arrays and RT-PCR assays downstream of the generation of 26 bp tags by SuperSAGE.

Effect of salinity on root-nodule conductance to the oxygen diffusion in the Cicer arietinum-Mesorhizobium ciceri symbiosis

Nodule conductance to O2 diffusion has been involved as a major factor of the inhibition of N2 fixation by soil salinity that severely reduces the production of grain legumes. In order to determine the effect of this constraint on the nodule conductance, oxygen uptake by the nodulated roots of Cicer arietinum was measured by recording the concentration of O2 as a function of pO2 in a gas-tight incubator. After germination and inoculation with the strain Mesorhizobium ciceri UPMCa7, the varieties Amdoun 1 and INRAT 93-1 were hydroponically grown in a glasshouse on 1L glass bottles filled with nutrient solution containing 25 mM NaCl. Salinity induced a marked decrease in shoot (30% versus 14%), root (43% versus 20%), and nodule biomass (100% versus 43%) for Amdoun 1 relative to INRAT 93-1. Although salinity completely prevented nodule formation in the sensitive variety Amdoun 1, nodule number and biomass were higher in the first than in the second variety in the absence of salt. This effect was associated with a significantly higher O2 uptake by nodulated root (510 versus 255 micromol O2 plant(-1)h(-1)) and nodule conductance (20 versus 5 microm s(-1)) in Amdoun 1 than in INRAT 93-1. Salinity did not significantly change the nodule conductance and nodule permeability for INRAT 93-1. Thus, the salt tolerance of this variety appears to be associated with stability in nodule conductance and the capacity to form nodules under salt constraint.

Phenotypic and molecular characterization of chickpea rhizobia isolated from different areas of Tunisia

Several phenotypic markers were used in this study to determine the biodiversity of rhizobial strains nodulating Cicer arietinum L. in various areas of Tunisia. They include symbiotic traits, the use of 21 biochemical substrates, and tolerance to salinity and pH. In addition, restriction fragment length polymorphisms (RFLPs) of PCR-amplified 16S rDNA were compared with those of reference strains. Numeric analysis of the phenotypic characteristics showed that the 48 strains studied fell into three distinct groups. This heterogeneity was highly supported by the RFLP analysis of 16S rRNA genes, and two ribotypes were identified. Chickpea rhizobia isolated from Tunisian soils are both phenotypically and genetically diverse. Results showed that 40 and 8 isolates were assigned, respectively, to Mesorhizobium ciceri and Mesorhizobium mediterraneum .