Identification of salt-tolerant wild Oryza : physiological and molecular investigation

Soil salinity is a major abiotic stress constraining global crop production. Salinity is already affecting more than 800 million hectares (Mha) of total global land area, where 20 Mha and 4 Mha are in Australia and India, respectively. Salinity stress is thought to be only secondary to the drought stress in hindering rice productivity in the major rice-growing regions. Rice (Oryza sativa L.) is highly susceptible to salinity stress. Improvement in rice salinity tolerance using existing cultivars is facing bottlenecks of narrow genetic diversity and negative linkage between key salinity tolerance traits and yield and quality traits. Wild rice preserved wide diversity of genetic pools in undisturbed natural habitats, which draws a lot of attention from the plant breeders for its outstanding performance under different environmental stresses including salinity. In this Ph.D. thesis, salinity tolerance of ten Oryza species was explored using agronomical, physiological, and molecular approaches to expand the understanding of salinity tolerance in rice. I studied the agronomic, physiological, electrophysiological, and molecular responses of three rice cultivars (Koshihikari, Doongara, and Reiziq) differing in salt tolerance to NaCl treatment in both greenhouse and field experiments. The assessment was also conducted in the wild Oryza species to evaluate if the observed relation between salinity tolerance and the measured parameters in O. sativa, can also be validated in wild Oryza species. I then studied the adaptation mechanism of leaf tissue of the only halophytic Oryza species - O. coarctata and evaluated whether different leaf tissues of O. coarctata had a specific contribution to the overall tissue tolerance to NaCl using physiological, cell biological, and transcriptomic approaches. This study provides useful insights into physiological and molecular mechanisms of salinity response in the Oryza genus. I also suggest the potential use of traits and genes from wild rice species, especially those with the C genome and the halophyte O. coarctata, in breeding for salt-tolerant rice cultivars. Outcomes of this Ph.D. project will not only improve the understanding of the complex salt tolerance mechanisms in wild and cultivated rice species but also guide future research towards a more sustainable rice production by improving tolerance of cultivated rice with the salt-tolerant traits of their wild relatives

Alleviation of drought and salt stress in vegetables : crop responses and mitigation strategies

In recent decades, the demand for vegetables has increased signifcantly due to the blooming global population. Climate change has afected vegetable production by increasing the frequencies and severity of abiotic and biotic stresses. Among the abiotic stresses, drought and salinity are the major issues that possess severe threats on vegetable production. Many vegetables (e.g., carrot, tomato, okra, pea, eggplant, lettuce, potato) are usually sensitive to drought and salt stress. The defence mechanisms of plants against salt and drought stress have been extensively studied in model plant species and feld crops. Better understanding of the mechanisms of susceptibility of vegetables to drought and salt stresses will help towards the development of more tolerant genotypes as a long-term strategy against these stresses. However, the intensity of the challenges also warrants more immediate approaches to mitigate these stresses and enhance vegetable production in the short term. Therefore, this review enlightens the updated knowledge of responses (physiological and molecular) against drought and salinity in vegetables and potentially efective strategies to enhance production. Moreover, we summarized diferent technologies such as seed priming, genetic transformation, biostimulants, nanotechnology, and cultural practices adopted to enhance vegetable production under drought and salinity stress. We propose that approaches of conventional breeding, genetic engineering, and crop management should be combined to generate drought and salt resistance cultivars and adopt smart cultivation practices for sustainable vegetable production in a changing climate

Evolutionary significance of NHX family and NHX1 in salinity stress adaptation in the genus Oryza

Rice (Oryza sativa), a staple crop for a substantial part of the world’s population, is highly sensitive to soil salinity; however, some wild Oryza relatives can survive in highly saline environments. Sodium/hydrogen antiporter (NHX) family members contribute to Na+ homeostasis in plants and play a major role in conferring salinity tolerance. In this study, we analyzed the evolution of NHX family members using phylogeny, conserved domains, tertiary structures, expression patterns, and physiology of cultivated and wild Oryza species to decipher the role of NHXs in salt tolerance in Oryza. Phylogenetic analysis showed that the NHX family can be classified into three subfamilies directly related to their subcellular localization: endomembrane, plasma membrane, and tonoplast (vacuolar subfamily, vNHX1). Phylogenetic and structural analysis showed that vNHX1s have evolved from streptophyte algae (e.g., Klebsormidium nitens) and are abundant and highly conserved in all major land plant lineages, including Oryza. Moreover, we showed that tissue tolerance is a crucial trait conferring tolerance to salinity in wild rice species. Higher Na+ accumulation and reduced Na+ effluxes in leaf mesophyll were observed in the salt-tolerant wild rice species O. alta, O. latifolia, and O. coarctata. Among the key genes affecting tissue tolerance, expression of NHX1 and SOS1/NHX7 exhibited significant correlation with salt tolerance among the rice species and cultivars. This study provides insights into the evolutionary origin of plant NHXs and their role in tissue tolerance of Oryza species and facilitates the inclusion of this trait during the development of salinity-tolerant rice cultivars

Coal tailings as a soil conditioner : evaluation of tailing properties and effect on tomato plants

The global coal industry yields a vast amount of tailings waste, and the utilisation of these tailings necessitates innovative eforts contributing to the United Nations Sustainable Development Goals. One of such novel initiatives is to reuse coal tailings (CT) safely, ecofriendly, and cost-efectively in agroecosystems as a soil conditioner to enhance the productivity of lands. This study aimed to evaluate the potential utilisation of coal tailings waste in the soil amelioration to improve plant performance. The physico–chemical characteristics of coal tailings from two Australian mining sites (CT1 and CT2) showed that the tailings samples are alkaline with loamy and loamy sand textures, respectively. The tailings have ~ 3% of macronutrients, high carbon (C), and low heavy metals and metalloids (As, Cd, Se, Cu, Zn, and Pb). The germination rate of tomato seeds was improved in the low-rate CT treatment. Greenhouse tomato plants exhibited an increase in leaf’s K, Ca, and Mg contents in CT1 and CT2 treatments. More importantly, the CT treatment-induced accumulation of heavy metals in plants was mostly insignifcant in both CT treatments. Therefore, we highlight the potential application of coal tailings as a soil conditioner because of the benefcial efect of improved carbon and nutrients (N, P, K, Mg, and Ca) in tomato leaves. Further amendment of the coal tailings should focus on the adjustment of pH and the addition of other benefcial materials for the improvement of soil properties for crops in both the greenhouse and the feld

Proto Kranz-like leaf traits and cellular ionic regulation are associated with salinity tolerance in a halophytic wild rice

Species of wild rice (Oryza spp.) possess a wide range of stress tolerance traits that can be potentially utilized in breeding climate-resilient cultivated rice cultivars (Oryza sativa) thereby aiding global food security. In this study, we conducted a greenhouse trial to evaluate the salinity tolerance of six wild rice species, one cultivated rice cultivar (IR64) and one landrace (Pokkali) using a range of electrophysiological, imaging, and whole-plant physiological techniques. Three wild species (O. latifolia, O. officinalis and O. coarctata) were found to possess superior salinity stress tolerance. The underlying mechanisms, however, were strikingly different. Na+ accumulation in leaves of O. latifolia, O. officinalis and O. coarctata were significantly higher than the tolerant landrace, Pokkali. Na+ accumulation in mesophyll cells was only observed in O. coarctata, suggesting that O. officinalis and O. latifolia avoid Na+ accumulation in mesophyll by allocating Na+ to other parts of the leaf. The finding also suggests that O. coarctata might be able to employ Na+ as osmolyte without affecting its growth. Further study of Na+ allocation in leaves will be helpful to understand the mechanisms of Na+ accumulation in these species. In addition, O. coarctata showed Proto Kranz-like leaf anatomy (enlarged bundle sheath cells and lower numbers of mesophyll cells), and higher expression of C4-related genes (e.g., NADPME, PPDK) and was a clear outlier with respect to salinity tolerance among the studied wild and cultivated Oryza species. The unique phylogenetic relationship of O. coarctata with C4 grasses suggests the potential of this species for breeding rice with high photosynthetic rate under salinity stress in the future

Value-added products as soil conditioners for sustainable agriculture

Due to the intensive use of fertilisers, soil degradation has become a global problem, leading to the depletion of organic matter and soil fertility. Meanwhile, the intensification of agriculture accompanied by urbanisation and industrialisation has drastically accelerated the waste generation rate. For instance, coal mining produces wastes in a large quantity globally, the majority of which end up in landfills or dump into storage dams. Accordingly, sustainable food production is driving global innovations to better utilise various waste materials to make value added products, such as soil conditioners. Nowadays, soil conditioners are of great importance to improve plant growth and soil health and reduce chemical fertiliser use. This paper comprehensively reviews the soil conditioners derived from various agro-wastes and coal by-products. The process of producing soil conditioners and their sustainable applications in agriculture are also reviewed. Furthermore, sustainable approaches to recycle coal wastes are gaining increasing interest, and co-pelletisation of coal waste with agro-waste as a value-added soil conditioner to supplement soil nutrients in the agro-ecosystem has been proposed to improve the productivity of lands towards sustainable agricultural applications. This review highlights the possibility of turning coal wastes and organic wastes into revenue-earning products of environmental and economic values in the form of pellets for soil conditioning. But a multidisciplinary approach should be adopted to utilise the natural resources eco-friendly and cost-effectively, contributing to the United Nations Sustainable Development Goals

Back to the wild: on a quest for donors toward salinity tolerant rice

Salinity stress affects global food producing areas by limiting both crop growth and yield. Attempts to develop salinity-tolerant rice varieties have had limited success due to the complexity of the salinity tolerance trait, high variation in the stress response and a lack of available donors for candidate genes for cultivated rice. As a result, finding suitable donors of genes and traits for salinity tolerance has become a major bottleneck in breeding for salinity tolerant crops. Twenty-two wild Oryza relatives have been recognized as important genetic resources for quantitatively inherited traits such as resistance and/or tolerance to abiotic and biotic stresses. In this review, we discuss the challenges and opportunities of such an approach by critically analyzing evolutionary, ecological, genetic, and physiological aspects of Oryza species. We argue that the strategy of rice breeding for better Na exclusion employed for the last few decades has reached a plateau and cannot deliver any further improvement in salinity tolerance in this species. This calls for a paradigm shift in rice breeding and more efforts toward targeting mechanisms of the tissue tolerance and a better utilization of the potential of wild rice where such traits are already present. We summarize the differences in salinity stress adaptation amongst cultivated and wild Oryza relatives and identify several key traits that should be targeted in future breeding programs. This includes: (1) efficient sequestration of Na in mesophyll cell vacuoles, with a strong emphasis on control of tonoplast leak channels; (2) more efficient control of xylem ion loading; (3) efficient cytosolic K retention in both root and leaf mesophyll cells; and (4) incorporating Na sequestration in trichrome. We conclude that while amongst all wild relatives, O. rufipogon is arguably a best source of germplasm at the moment, genes and traits from the wild relatives, O. coarctata, O. latifolia, and O. alta, should be targeted in future genetic programs to develop salt tolerant cultivated rice

Physiological and yield performance is partially linked to water use efficiency of eggplant genotypes in a high-tech glasshouse

Eggplant (Solanum melongena L.) has become an increasingly common vegetable grown in glasshouses. This study emphasized on the physiological traits and productivity of three eggplant cultivars (Longa, Lydia, and Tracey) in a high-tech glasshouse to determine the genotypic differences of agronomical, morphological, and physiological responses. The physiological parameters as well as the productivity of these eggplant cultivars were evaluated. The results showed that Tracey had significantly higher leaf growth than Longa and Lydia. Longa exhibited significantly higher values of net CO2 assimilation (A), stomatal conductance (gs), and transpiration rate (Tr) than Tracey, whereas Tracey showed significantly larger gs, Tr, and intracellular CO2 concentration (Ci) than Lydia. Tracey showed a significantly higher number of flowers per node compared to the two other varieties, but the number of fruits did not statistically differ among cultivars. Tracy produced the highest yield (fruit weight and fruit yield per m2) due to the significantly higher leaf length and leaf expansion rate despite the lowest level of A among the three cultivars. Interestingly, the higher yield of Tracey translated into better water use efficiency (WUE) in the agronomic term, but its intrinsic WUE (A/gs) was the lowest among the three cultivars. However, significant correlations between photosynthetic parameters and WUE were only found in certain stages of eggplant growth. Therefore, further research work with an emphasis on the source and sink partitioning of a large number of eggplant genotypes is required to investigate the varietal performance of greenhouse eggplants. Then, the information can be translated into protected cropping to set up the growth benchmark for large-scale sustainable production of eggplants with better yield and less water consumption for the horticultural industry

Sodium sequestration confers salinity tolerance in an ancestral wild rice

Wild rice Oryza rufipogon, a progenitor of cultivated rice Oryza sativa L., possesses superior salinity tolerance and is a potential donor for breeding salinity tolerance traits in rice. However, a mechanistic basis of salinity tolerance in this donor species has not been established. Here, we examined salinity tolerance from the early vegetative stage to maturity in O. rufipogon in comparison with a salt-susceptible (Koshihikari) and a salt-tolerant (Reiziq) variety of O. sativa. We assessed their phylogeny and agronomical traits, photosynthetic performance, ion contents, as well as gene expression in response to salinity stress. Salt-tolerant O. rufipogon exhibited efficient leaf photosynthesis and less damage to leaf tissues during the course of salinity treatment. In addition, O. rufipogon showed a significantly higher tissue Na+ accumulation that is achieved by vacuolar sequestration compared to the salt tolerant O. sativa indica subspecies. These findings are further supported by the upregulation of genes involved with ion transport and sequestration [e.g. high affinity K+ transporter 1;4 (HKT1;4), Na+/H+ exchanger 1 (NHX1) and vacuolar H+-ATPase c (VHA-c)] in salt-tolerant O. rufipogon as well as by the close phylogenetic relationship of key salt-responsive genes in O. rufipogon to these in salt-tolerant wild rice species such as O. coarctata. Thus, the high accumulation of Na+ in the leaves of O. rufipogon acts as a cheap osmoticum to minimise the high energy cost of osmolyte biosynthesis and excessive ROS production. These mechanisms demonstrated that O. rufipogon has important traits that can be used for improving salinity tolerance in cultivated rice

Leaf mesophyll K+ and Cl- fluxes and reactive oxygen species production predict rice salt tolerance at reproductive stage in greenhouse and field conditions

Extensive research on salinity tolerance in rice has been mostly carried out at the seedling stage in single experimental trials. Here, we aimed to understand the roles of ion transport and oxidative responses of leaf mesophyll in salinity tolerance of rice (Oryza sativa L.) at its reproductive stage using comparative investigations in both greenhouse and field trials. Two experimental trials were conducted to assess the salt tolerance of three rice cultivars at their reproductive stage in greenhouse and field. We employed agronomic, physiological, electrophysiological, molecular and cell imaging techniques to compare physiological response of control and salinity stressed rice plants. Salinity had the most severe effect to Koshihikari, followed by Doongara and Reiziq. We found that K+ retention and low recovery Cl− efflux in mesophyll cells confers salt tolerance in rice. Moderate to strong correlations were found between growth parameters and net K+ flux (r2=0.45–0.60), and net Cl− flux (r2=0.47–0.72). Also, dynamic ROS production and regulation of the NADPH oxidase gene, OsRBOHD, in mesophyll cells is crucial for salt tolerance of rice at the reproductive stage. OsRBOHD expression was significantly correlated to recovery ion fluxes (r2=0.45–0.64). This study brings together, for the first time, potential links between cellular ionic stress and oxidative stress components of salinity tolerance in rice at the reproductive stage in both greenhouse and field conditions. Our study will provide guidance to examine crop salinity tolerance at reproductive stages in controlled environments and natural climatic conditions in the future