Arun K. Shanker

Drought stress responses in crops

Among the effects of impending climate change, drought will have a profound impact on crop productivity in the future. Response to drought stress has been studied widely, and the model plant Arabidopsis has guided the studies on crop plants with genome sequence information viz., rice, wheat, maize and sorghum. Since the value of functions of genes, dynamics of pathways and interaction of networks for drought tolerance in plants can only be judged by evidence from field performance, this mini-review provides a research update focussing on the current developments on the response to drought in crop plants. Studies in Arabidopsis provide the basis for interpreting the available information in a systems biology perspective. In particular, the elucidation of the mechanism of drought stress response in crops is considered from evidence-based outputs emerging from recent omic studies in crops.

Optimization of Agrobacterium mediated genetic transformation of cotyledonary node explants of Vigna radiata

A reproducible and highly efficient protocol for genetic transformation mediated by Agrobacterium has been established for greengram (Vigna radiata L. Wilczek). Double cotyledonary node (DCN) explants were inoculated with Agrobacterium tumefaciens strain LBA 4404 harboring a binary vector pCAMBIA 2301 containing neomycin phosphotransferase (npt II) gene as selectable marker, β-glucuronidase (GUS) as a reporter (uidA) gene and annexin 1 bj gene. Important parameters like optical density of Agrobacterium culture, culture quantity, infection medium, infection and co-cultivation time and acetosyringone concentration were standardized to optimize the transformation frequency. Kanamycin at a concentration of 100 mg/l was used to select transformed cells. Transient and stable GUS expressions were studied in transformed explants and regenerated putative plants, respectively. Transformed shoot were produced on regeneration medium containing 100 mg/l kanamycin and 250 mg/l cefotaxime and rooted on ½ MS medium. Transient and constitutive GUS expression was observed in DCN explants and different tissues of T0 and T1 plants. Rooted T0 and T1 shoots confirming Polymerase Chain Reaction (PCR) positive for npt II and annexin 1bj genes were taken to maturity to collect the seeds. Integration of annexin gene into the greengram genome was confirmed by Southern blotting.

Dryland Agriculture: Bringing Resilience to Crop Production Under Changing Climate

Drylands of the world are affected in addition to the impending climate change by various other inherent biotic and abiotic limitations like water availability, declining soil quality and pest and disease infestations. The challenges facing dryland agriculture, global food security and the sustainable management of natural resources are many and are interrelated. Productivity of dryland crops can be increased only if the problems are understood well and in turn combated effectively. Major dryland agro ecological regions of the world and their problems are outlined in this chapter. Sustainable Natural Resource Management (SNRM) is stressed here as an important way to addresses the problems faced by these regions of the world. Resilience to predicted climate change will depend on increasing agricultural productivity with available water resources; refining technologies and timely deployment of affordable strategies to accomplish potential levels of arable land and water productivity. An account into the adaptation strategies to increase resilience to combat climate change related effects by management of water, soil and biodiversity are detailed here. We propose here that research on adaptive capability of crops by increasing their resilience to abiotic stresses, pests and diseases will have to expand to new horizons with a systems biology perspective.

Overview of Plant Stresses: Mechanisms, Adaptations and Research Pursuit

Biotic and abiotic stresses in crops are a major hurdle in attaining potential yield worldwide. Finding an approach to sustain high yields of crop plants under biotic and abiotic stresses is an important goal of agriculture researchers and stakeholders alike. Among the abiotic stresses, drought, salinity, temperature and heavy metal accumulation are the major environmental stresses, which adversely affect plant growth and productivity. In addition, biotic stresses primarily, plant diseaseses are a significant constraint to the production of about 25 important food and fiber crops. Changing climate compounds these adverse effects of stresses on crops. To cope with biotic and abiotic stress it is of paramount significance to understand plant responses to these stresses that disturb the homeostatic equilibrium at cellular and molecular level in order to identify a common mechanism for multiple stress tolerance at least in the case of abiotic stresses. An integrated systems approach is essential in the study of complex quantitative traits governing tolerance to multiple biotic and abiotic stresses. A detailed account of specially abiotic stresses and combating strategies to effectively counter them are discussed in this chapter.

In silico targeted genome mining and comparative modelling reveals a putative protein similar to an Arabidopsis drought tolerance DNA binding transcription factor in Chromosome 6 of Sorghum bicolor genome.

Arabidopsis Thaliana HARDY (AtHRD) is a gene with an APETELA 2 / Ethylene Responsive Factor (AP2/ERF) domain linked to improved performance under drought in rice. We hypothesized that the sorghum genome could possess a similar gene product and were motivated to conduct a computational genome scale mining for the protein and analyse its structural and functional properties. AtHRD sequence was used as a query to BLAST against the sorghum genome dataset followed by multiple alignment analysis. A homology model of the target was built using a template detected based on the pair-wise comparison of hidden Markov models for alignments. DNA docking with a matrix of homologous interface contacts was done. Functional and structural analysis of the query and target was conducted using various online servers.A High-scoring segment pair from Chromosome 6 of the sorghum genome in the region between 54948120 and 54948668 had 68 amino acid similarities out of the 184 residues and was 1.4% above twilight zone threshold. The homology model showed 86.8% residues in most favoured regions. The target protein which had an AP2/ERF domain when docked with GCC box DNA motif had conserved residues involved in binding; it had a long unstructured region beyond the AP2 domain with several motifs for the recognition of serine/threonine protein kinase group. The protein model showed that it could bind to a GCC box which is present in several drought responsive genes. The presence of possible signalling domains and intrinsic disorder in the target protein suggest that this could play a role in drought tolerance which is an inherent character of sorghum. These results offer a jumpstart for validation experiments which could pave the way for cis/trans genic improvement of a range of crops.

Predicting Irrigated and Rainfed Rice Yield Under Projected Climate Change Scenarios in the Eastern Region of India

Numerous estimates for the coming decades project changes in precipitation resulting in more frequent droughts and floods, rise in atmospheric CO2 and temperature, extensive runoff leading to leaching of soil nutrients, and decrease in freshwater availability. Among these changes, elevated CO2 can affect crop yields in many ways. It is imperative to understand the consequences of elevated CO2 on the productivity of important agricultural crop species in order to devise adaptation and mitigation strategies to combat impending climate change. In this study, we have modeled rice phenology, growth phase, and yield with the “Decision Support System for Agrotechnology Transfer (DSSAT) CERES rice model” and arrived at predicted values of yield under different CO2 concentrations at four different locations in Eastern India out of which three locations were irrigated and one location was rainfed. The ECHAM climate scenario, Model for Interdisciplinary Research on Climate (MIROC)3.0 climate scenario, and ensemble models showed different levels of yield increase with a clear reduction in yield under rainfed rice as compared to irrigated rice. A distinct regional and cultivar difference in response of rice yield to elevated CO2 was seen in this study. Results obtained by simulation modeling at different climate change scenarios support the hypothesis that rice plant responses to elevated CO2 are through stimulation of photosynthesis. Realization of higher yields is linked with source sink dynamics and partitioning of assimilates wherein sink capacity plays an important role under elevated CO2 conditions.

Chlorophyll fluorescence induction kinetics and yield responses in rainfed crops with variable potassium nutrition in K deficient semi-arid alfisols.

Optimum potassium (K) nutrition in semi-arid regions may help crop plants to overcome constraints in their growth and development such as moisture stress, leading to higher productivity of rainfed crops, thus judicious K management is essential. A study was conducted to evaluate the importance of K nutrition on physiological processes like photosynthesis through chlorophyll a fluorescence and chlorophyll fluorescence induction kinetics (OJIP) of rainfed crops viz., maize (Zea mays L.), pearl millet (Pennisetum glaucum), groundnut (Arachis hypogaea), sunflower (Helianthus annuus), castor (Ricinus communis L.) and cotton (Gossypium hirsutum) under water stress conditions by studying their growth attributes, water relations, yield, K uptake and use efficiency under varied K levels. Highest chlorophyll content was observed under K60 in maize and pearl millet. Narrow and wide Chl a:b ratio was observed in castor and groundnut respectively. The fluorescence yield decreased in the crops as K dosage increased, evidenced by increasing of all points (O, J, I and P) of the OJIP curves. The fluorescence transient curve for K60 was lower than K0 and K40 for all the crops. Potassium levels altered the fluorescence induction and impaired photosynthetic systems in all the crops studied. There was no distinct trend observed in leaf water potential of crops under study. Uptake of K was high in sunflower with increased rate of K application. Quantitatively, K uptake by castor crop was lesser compared to all other crops. Our results indicate that the yield reduction under low K was due to the low capacity of the crops to translocate K from non-photosynthetic organs such as stems and petioles to upper leaves and harvested organs and this in turn influenced the capacity of the crops to produce a high economic yield per unit of K taken up thus reducing utilization efficiency of K.

RNA-seq Analysis of Irrigated vs. Water Stressed Transcriptomes of Zea mays Cultivar Z59

Maize (Zea mays) is one of the important food crops of India with other potential uses in preparation of livestock feed and biofuel. But production of maize in India is low compared to top maize producing countries due to abiotic stresses (Ranum et al., 2014). Among abiotic stresses affecting maize production in India, drought is the major limiting factor. In spite of extensive research on drought tolerance in maize no tangible achievements could be made due to the extreme complexity associated with drought tolerance (Ashraf, 2010). Availability of the maize genome and high throughput genomic methods have provided new tools for addressing the complexity associated with drought tolerance (Zivy et al., 2015). We have chosen the drought tolerant genotype Z59 and are developing transcriptomic resources for better understanding of drought tolerance of this cultivar. As part of this work, we have sequenced the irrigated and water stressed transcriptomes of Z59 cultivar and the dataset is reported here.

Physiological and Biochemical Basis of Extended and Sudden Heat Stress Tolerance in Maize

Effects of extended and sudden heat stress on various physiological and biochemical processes have been investigated in ten inbred lines of maize (Zea mays L.) at seedling stage. Among the various parameters studied, a significant decrease was observed in membrane stability, chlorophyll fluorescence and chlorophyll concentration under extended heat stress and sudden heat shock in sensitive genotypes which indicated their susceptibility to high temperature. However, heat tolerant genotypes exhibited less impact on these parameters which could be attributed to lesser oxidative stress injury. The free radical scavenging system in heat tolerant genotypes was observed to be better established as compared to heat sensitive genotypes. These findings suggested that the genotypes which performed better both under extended and sudden heat stress conditions could be partly due to their superior ability to cope up with oxidative damage caused by heat stress in maize.

Seasonal variation in expression pattern of genes in irrigated and water stressed transcriptomes of Zea mays Z59

Drought is the major limiting factor for maize cultivation in India. Though many drought tolerant genotypes have been developed, there is very poor understanding of the tolerance mechanisms in these genotypes. Whole genome transcriptome analysis is an established high throughput genomic method employed for understanding complex traits like drought tolerance. We have employed RNA-seq analysis for understanding the drought tolerance of maize inbred line Z59 grown in kharif (wet season) and rabi (dry season). The physiological parameters recorded during the plant growth show difference in the values for relative water content and proline level but no significant changes were seen in root and shoot length. Leaf sample of irrigated and water stressed plants at reproductive stage were sequenced, transcripts were assembled, and the abundance were calculated. The results showed overall difference in expression level of genes in kharif (wet season) and rabi (dry season). The data was comparatively analyzed for genes differentially expressed between the irrigated and water stressed plants in both seasons. Taking p ≥ 0.001 and at least fourfold change in expression, a total of 453 and 774 genes were found to be differentially expressed amongst the irrigated and water stressed plants grown in kharif (wet season) and rabi (dry season)seasons respectively. Out of the 453 genes in kharif (wet season) grown plants, 227 genes were found to be up regulated and 226 genes were down regulated and in the 774 differentially expressed genes in rabi (dry season) grown plants, 460 genes were found to be up regulated and 314 genes were down regulated, in the water stressed sample when compared to irrigated. Functional annotation of these genes showed upregulation of MYB DNA binding protein and pathogenesis related protein in irrigated and early drought induced protein, late embryogenesis protein in water stressed kharif (wet season) crops. Metallothionein and aspargine synthetase are upregulated in irrigated and ubiquitin family protein, serine/threonine-protein kinase in water stressed rabi (dry season)crops. Gene ontology analysis co relates with the physiological parameters as most of the differentially expressed genes belong to the functioning of the plant when compared to the structural genes.