Satoshi Tobita

Genetic Dissection of Drought and Heat Tolerance in Chickpea through Genome-Wide and Candidate Gene-Based Association Mapping Approaches

To understand the genetic basis of tolerance to drought and heat stresses in chickpea, a comprehensive association mapping approach has been undertaken. Phenotypic data were generated on the reference set (300 accessions, including 211 mini-core collection accessions) for drought tolerance related root traits, heat tolerance, yield and yield component traits from 1–7 seasons and 1–3 locations in India (Patancheru, Kanpur, Bangalore) and three locations in Africa (Nairobi, Egerton in Kenya and Debre Zeit in Ethiopia). Diversity Array Technology (DArT) markers equally distributed across chickpea genome were used to determine population structure and three sub-populations were identified using admixture model in STRUCTURE. The pairwise linkage disequilibrium (LD) estimated using the squared-allele frequency correlations (r2; when r2<0.20) was found to decay rapidly with the genetic distance of 5 cM. For establishing marker-trait associations (MTAs), both genome-wide and candidate gene-sequencing based association mapping approaches were conducted using 1,872 markers (1,072 DArTs, 651 single nucleotide polymorphisms [SNPs], 113 gene-based SNPs and 36 simple sequence repeats [SSRs]) and phenotyping data mentioned above employing mixed linear model (MLM) analysis with optimum compression with P3D method and kinship matrix. As a result, 312 significant MTAs were identified and a maximum number of MTAs (70) was identified for 100-seed weight. A total of 18 SNPs from 5 genes (ERECTA, 11 SNPs; ASR, 4 SNPs; DREB, 1 SNP; CAP2 promoter, 1 SNP and AMDH, 1SNP) were significantly associated with different traits. This study provides significant MTAs for drought and heat tolerance in chickpea that can be used, after validation, in molecular breeding for developing superior varieties with enhanced drought and heat tolerance.

Drought Tolerance Characteristics of Brazilian Soybean Cultivars

Abstract Drought is one of the major constraints for soybean production in Brazil. Seed yield of ten Brazilian soybean cultivarssheltered from rain (drought stress) for one month after the first flowering was examined over two growing seasons in the field in Londrina, Brazil. The drought tolerance on the basis of seed yield varied with the cultivar, and the yield ranking among cultivars was nearly the same across two years. In cultivars with higher drought tolerance, crop growth rate (CGR)during the drought stress period was higher than in other cultivars. They also maintained a larger leaf area during the stress period. Although reproductive development was retarded by the drought stress, it tended to be retarded less in drought-tolerant cultivars. The information obtained in this research may be useful for breeding drought-tolerant cultivars or selecting diverse germplasms of soybean cultivars.

Field evaluation of nitrogen fixation and use of nitrogen fertilizer by sorghum/pigeonpea intercropping on an Alfisol in the Indian semi-arid tropics

A field experiment was conducted to obtain the N balance sheet for sole crops and intercrops of sorghum [Sorghum bicolor (L.) Moench] and pigeonpeas [Cajanus cajan (L.) Millsp.]. Intercropping gave a significant advantage over sole cropping in terms of dry matter production and grain yield, as calculated on the basis of the land equivalent ratio and area-time equivalent ratio. The N fertilizer use efficiency and atmospheric N2 fixation by pigeonpea were estimated using 15N-labeling and natural abundance methods. The N fertilizer use efficiency of sorghum was unaltered by the cropping system, while that of the pigeonpea was greatly reduced by intercropping. Although intercropping increased the fractional contribution of fixed N to the pigeonpeas, no significant difference was observed between the cropping systems in total symbiotically fixed N. There was no evidence of a significant transfer of N from the pigeonpea to the sorghum. This study showed that use of soil N and fertilizer N by pigeonpeas was almost the same as that by sorghum in sole cropping, indicating the potential competence of pigeonpeas to exploit soil N. However, when N was exhausted by a companion crop in intercropping, the pigeonpea crop increased its dependency on atmospheric N2 fixation. We conclude that knowledge of how N from different sources is shared by companion crops is a prerequisite to establishing strategies to increase N use, and consequently land productivity, in intercropping systems.

“Fallow Band System,” a land management practice for controlling desertification and improving crop production in the Sahel, West Africa. 1. Effectiveness in desertification control and soil fertility improvement

Wind erosion is a major contributor to desertification in the Sahel. Although three effective countermeasures for wind erosion (i.e. ridging, mulching with post-harvest crop residue, and windbreaks) have been proposed, they are not practical for Sahelian farmers. Therefore, we designed a new land management practice, termed the “Fallow Band System,” which can be used for both controlling wind erosion and improving soil fertility and crop production. This method does not impose additional expense and labor requirements on Sahelian farmers who are economically challenged and have limited manpower. The objective of this study was to evaluate the effects of this system on wind-erosion control and soil-fertility improvement. We conducted field experiments at the International Crops Research Institute for the Semi-Arid Tropics West and Central Africa and showed that (i) a fallow band can capture 74% of wind-blown soil particles and 58% of wind-blown coarse organic matter, which suggests that it can effectively control wind erosion, (ii) the amount of soil nutrients available for crops in a former fallow band was increased by the decomposition of trapped soil materials containing considerable amounts of nutrients, and (iii) the amount of soil water available for crops in a former fallow band was increased by the trapped wind-blown soil materials through improvement of rainwater infiltration into surface soil. These results lead to the conclusion that the “Fallow Band System” can be useful for preventing desertification and improving soil fertility in the Sahel, West Africa.

Spatial distribution of root activity and nitrogen fixation in sorghum/pigeonpea intercropping on an Indian Alfisol

A medium-duration pigeonpea cultivar (ICP 1–6) and a hybrid sorghum (CSH 5) were grown on a shallow Alfisol in monocropping and intercropping systems. Using a monolith method, spatial distribution of nodulation, acetylene reduction activity (ARA) and root respiration were measured. The number, mass and ARA of nodules decreased exponentially with distance from the plant base except at the late reproductive stage. Nodulation and ARA tended to be higher in the intercrop than in the monocrop.

Response of short-duration pigeonpea to nitrogen application after short-term waterlogging on a Vertisol

Abstract Short-duration pigeonpea suffers from waterlogging damage following heavy rainfall at the pre-flowering stage on soils with high clay content, such as Vertisols. Effects of short-term waterlogging (3 d) on shoot and root growth of short-duration pigeonpea grown on a Vertisol field were quantified, and the alleviation of waterlogging damage by top-dressing of nitrogen fertilizer was examined. Reduced leaf chlorophyll, increased senescence and abscission of lower leaves were observed within 3 d of the initiation of waterlogging. Root growth and symbiotic N2 fixation were also severely impaired. Root distributions of waterlogged plants were shallower than those of the control during the subsequent recovery period because new adventitious roots were formed in the shallow rather than deep soil layer. Yield of waterlogged crops was significantly smaller than the control. Top-dressing of nitrogen at one day after the termination of waterlogging alleviated waterlogging damage either completely or partially. Leaf chlorophyll and shoot dry mass of waterlogged plants were 78 and 84% of the values in control plants immediately after waterlogging but recovered to 92 and 98% of the control values at the pod-filling stage with a top-dressing of 50 kg N ha−1. Nitrogen application promoted root growth in the shallow soil layers during the first 11 d after application, and in the deeper soil layers during the subsequent 16 d. Total nodule activity was significantly reduced by 100 kg N ha−1, but increased by 50 kg N ha−1 around one month after the top-dressing. The reduction in seed yield was largely compensated for by 50 kg N ha−1, because of recovery from waterlogging damage to shoot and root growth involving increased nodule activity.

Sediment catcher to trap coarse organic matter and soil particles transported by wind.

Wind can erode fertile topsoil and reduce soil fertility. Evaluating the effect of wind erosion on soil fertility is crucial to achieve sustainable agriculture in areas suffering from desertification caused by wind erosion. To estimate soil loss and associated soil nutrient loss by wind erosion, flux of coarse organic matter (COM) (defined here as free organic debris larger than 200 µm) and soil particles (defined as the other soil components) must be measured separately. This is because their modes of transport are different, and COM plays a prominent role in soil nutrient dynamics in some semiarid zones where COM accounts for a large percentage of the total soil carbon. Because the Big Spring Number Eight (BSNE) sampler can trap both COM and soil particles 0.05 m above the surface, we designed a sediment catcher, the Aeolian Materials Sampler (AMS), to trap these components below 0.05 m. This device can be manufactured easily at low cost. AMS performance was tested by wind tunnel experiments over a range of wind velocities typically observed in erosive storms and with six incident wind angles because the AMS is a buried-type sampler that is unable to rotate toward the wind. The trapping efficiency of the AMS for COM and soil particles was not 100%, but it can be calibrated easily using wind data. Therefore, we can estimate the mass flux of COM and soil particles and evaluate the effect of wind erosion on soil fertility using the AMS with the BSNE sampler.

Validation of soil organic carbon dynamics model in the semi-arid tropics in Niger, West Africa

The fertility of sandy soils in the Sahelian zone (SZ) is extremely low. This poor soil fertility is one of the limiting factors of crop production in the SZ. Therefore, it is imperative to improve or to maintain soil fertility through various agricultural management methods. Further, it is well known that soil organic matter plays an important role in improving the physico-chemical properties of these sandy infertile soils. Therefore, it is essential to develop a suitable tool for the appropriate evaluation of soil organic carbon (SOC) dynamics in the SZ. Therefore, the Rothamsted carbon model (Roth-C) was verified in 32 treatments of two long-term field experiments with and without crop residue application. These experiments were performed by ICRISAT. The performance of the model was evaluated by statistical methods using four indices (RMSE: root mean square error, LOFIT: lack of fit, r: correlation coefficient, and M: mean difference). As a result, the predicted SOC values in the case without crop residue management decreased with time in approximately 10 cultivated years. In contrast, in the case with crop residue application, the predicted SOC remained roughly equal to the initial SOC value during the term observed. Mostly, the Roth-C-modelled values agreed well with the actual value. RMSE and LOFIT, the statistical indicators of agreement between predicted and observed values, showed a significant conformity between the predicted and observed SOC values in all the 32 treatments. This fact means that Roth-C can estimate long-term SOC dynamics of several technical options that developed with short-term trials. Moreover the annual carbon requirement for SOC maintaining can be calculate if enough number of cases was estimated. And also analysis of regional carbon dynamics was made possible with using Roth-C model. It will contribute to show the sustainable development in SZ against global warming and other climatic changes.

Simulating root system development of short-duration pigeonpea

Length and weight of pigeonpea roots were measured weekly in different soil layers and compared with estimates obtained from a root simulation model using daily climatic data, soil physico-chemical properties and dry matter allocation to roots. Daily moisture content and temperature at different soil depths were well simulated using sub-routines from the CERES-Maize model. Daily allocation of dry matter to roots was calculated from logistic functions fitted to the growth data for shoots and roots. Although root length and weight tended to be underestimated by the model, regressions between measured and simulated root growth were highly significant so that the model could, with a few modifications, be used to predict root system development.

Technical Note: Aeolian Materials Sampler for Measuring Surface Flux of Soil Nitrogen and Carbon During Wind Erosion Events in the Sahel, West Africa

In the Sahel, determining the effects of wind erosion on soil fertility and soil carbon balance is crucial for achieving sustainable agriculture and for carbon sequestration, respectively. We designed the Aeolian Materials Sampler (AMS) to measure the surface flux of soil nitrogen and carbon, which limit crop production as well as water in the Sahel. The AMS should not be used alone, but with the Big Spring Number Eight (BSNE) sampler, which is a quasi-isokinetic sampler. We examined the performance of the AMS in estimating the surface flux of soil nitrogen and carbon by conducting wind-tunnel and field experiments. In the former experiment, we measured the trapping efficiency of the AMS for nitrogen and carbon content in coarse organic matter (COM) and soil particles. We observed that the AMS allows estimation of the surface flux of soil nitrogen and carbon associated with the movement of COM and soil particles; wind data and empirical equations were used for the estimation. In the field experiment, we assessed the contribution of the inherent error of the AMS to the total measurement error and found that the inherent error was negligible and did not increase the total measurement error in the estimation of the surface flux of soil nitrogen and carbon. Therefore, we concluded that the combination of the AMS and the BSNE sampler could be effectively used to evaluate the effects of wind erosion on soil fertility and soil carbon balance in the Sahel.