Raising crops for dry and saline lands: Challenges and the way forward.

Abstract

Plants are continuously exposed to various environmental stresses. Of these, soil salinity and drought are considered to be the most important environmental stresses globally because they have a negative impact on plant growth and crop productivity. Drought and salinity thus threaten global food and nutritional security. The estimated annual global loss in crop production due to saline soils in irrigated areas is approximately US$27.3 billion (Qadir et al., 2014). Drought caused direct losses to the developing world's agriculture in the order of US$ 29 billion between 2005 and 2015 (FAO, 2018). Conversely, there is an increasing pressure to enhance agricultural production by 70% to feed a predicted increase in the world population of 9.7 billion by 2050. Hence, agriculture systems must become extremely productive and less wasteful throughout the world. Achieving this goal will be extremely challenging under the prevailing environmental conditions coupled with reductions in arable land and freshwater availability, together with climate change-induced environmental uncertainties. Over the past six decades, classical plant breeding technologies have played a major role in increasing crop performance and productivity. However, the consensus of scientific opinion is that most major crops have reached their maximum yield potential. Hence, the challenge for plant science is to develop improved crop varieties that can achieve sustainable higher yields with limited soil water availability and on saline soils. Recent developments in gene editing and innovative plant breeding technologies are crucial to the nature-based roadmap for sustainable agriculture intensification and climate resilience. Salinity and drought disturb ionic and osmotic homeostasis in plant cells. However, plants possess a network of molecular and physiological mechanisms to cope with these stresses (Karan et al., 2009). Ionic stress triggers a burst of Ca2+ ions in the cytoplasm of root cells, which activates the Salt Overly Sensitive (SOS) signaling pathway comprised of three major proteins: SOS1, SOS2, and SOS3. These proteins protect cells from the toxic effects of excessive Na+ ion accumulation (Ji et al., 2013). In addition, proton pumps such as plasma membrane-localized P-type ATPases and tonoplast-localized H+-ATPases play important roles in cellular ion homeostasis and Na+ sequestration. An appropriate balance between cellular Na+ and K+ levels is important for maintaining metabolic functions under salt stress. Members of the Na+/H+ exchanger (NHXs) protein family, such as the plasma membrane-localized SOS1/NHX7 transporter, are able to facilitate Na+ transport out of cells. In addition, potassium (K+) and Na+ can be transported by other members of the NHX family that are localized in distinct intracellular compartments. Osmotic stress is first perceived by the roots. This triggers a molecular signal that moves from roots to the shoots. The phytohormone abscisic acid (ABA) is synthesized in leaves in response to this signal. The accumulation of ABA triggers drought stress responses leading to tolerance through processes such as stomatal closure and drought-responsive gene expression (Takahashi et al., 2020). Osmotic stress responses are regulated in an ABA-dependent and an ABA-independent manner. Stomatal closure takes place in an ABA-dependent manner in response to osmotic stress in most species (Vishwakarma et al., 2017). However, osmotic stress-induced stomatal closure in glycophytes and ferns is regulated in an ABA-independent manner (Brodribb & McAdam, 2011). Secondary stress symptoms that occur as a result of the imposition of drought and salt stresses are complex, and they are associated with oxidative and nitrosative stress. Plants trigger antioxidant pathways to combat the increased production of oxidants such as hydrogen peroxide. Plant responses to these secondary stress symptoms occur at the molecular level and are governed by ABA-dependent and ABA-independent signaling pathways, in which the regulation of transcription factors (TFs) plays an important role in regulating the expression of effector genes. In recent years, significant advances have been witnessed in our understanding of plant responses to drought and salinity stresses at a systems level. Such studies have revealed that tolerance to environmental stresses is the result of the integrated and coordinated action of stress-responsive genes and gene networks in plants, reflecting the multi-genic nature of the stress tolerance traits. Progress in genomics, molecular biology, and genetic engineering has enabled the identification and functional characterization of key regulatory genes that can be deployed in crops to enhance drought and salinity tolerance. The literature contains numerous reports documenting significant improvements in plant tolerance to drought and salt stress. This special issue specifically highlights the significant achievements, collates original research and review articles that advance our current understanding of plant responses to drought and salinity stress, describing the potential development of crops with improved tolerance to these stresses through genetic engineering and gene editing approaches. This special issue contains 31 excellent articles, including seven reviews and twenty-four original research papers. The study of plant stress response at multiple levels, from whole plant physiology and biochemistry to molecular biology and genetics, is essential for the elucidation of stress tolerance mechanisms and identification of essential underlying genes and pathways. Physiological analysis coupled with comparative proteomics was used to study two pearl millet (Pennisetum glaucum L.) genotypes with contrasting levels of salt tolerance. This analysis uncovered key physiological parameters and pathways responsible for the higher level of salt tolerance in the salt-tolerant genotype (Jha et al., 2022). Similarly, physiological responses and the levels of miRNAs were compared in pearl millet genotypes with contrasting drought tolerance in response to low and high vapor pressure deficits (Palakolanu et al., 2022). In addition, a range of physiological parameters such as root and shoot length, shoot and root fresh and dry weights, and the germination percentage were screened in 314 wheat genotypes at the seedling stage to evaluate salt stress tolerance as part of a wheat breeding program (Choudhary et al., 2021). Comparative transcriptomics can be used to reveal key details of plant stress responses and identify key regulatory genes. A comparative transcriptomics analysis of the flag leaves, panicles, and roots (at heading stage) was performed in drought-tolerant (Nagina 22) and drought-sensitive (IR64) rice varieties by Gour et al. (2022). Of the differentially expressed genes (DEGs), many were found to co-localize within the drought-related QTLs responsible for grain yield and drought tolerance (Gour et al., 2022). Similarly, the high-throughput sequencing of suppression subtractive hybridization-enriched transcripts in Saccharum spontaneum, a drought and salt-tolerant wild relative of sugarcane, identified 314 transcripts that were differentially expressed in response to salinity stress (Kasirajan et al., 2022). In addition, phenomics and metabolomics approaches were employed to understand the metabolic basis of drought tolerance in a Tef (Eragrostis tef) accession, Enatite (Ent). A greater canopy area, together with a higher accumulation of flavonoids, amino acids, sugars, and fatty acids were shown to increase drought tolerance in Ent compared with other accessions (Girija et al., 2022). Advances in genome sequencing and associated computational pipelines to increase the performance of high-throughput data analytics have been documented during the last two decades. Such improvements have facilitated the rapid sequencing of the whole genomes of a large number of plant species, leading to the identification and characterization of new and important genes, alleles, and molecular markers. Bhat et al. (2022) used the whole-genome resequencing (WGRS) data obtained from 178 peanut genotypes to identify more than 4.3 million SNPs. Of these, 2488 SNPs had a high impact due to the gain of stop codons, variations in splice acceptors and splice donors, and the loss of start codons. Similarly, analysis of WGRS data obtained from nine chickpea genotypes (3 of which were drought-sensitive and 6 were drought-tolerant) led to the identification of 36,406 SNPs and 3407 insertions or deletions that distinguish the drought-sensitive and drought-tolerant genotypes (Rajkumar et al., 2022). Moreover, Tang et al. (2022) identified 66 U-box genes encoding ubiquitin ligases in the potato genome. Many of these genes were found to be abiotic stress-responsive. A study to identify Meta-QTLs governing traits related to salt tolerance in rice revealed genomic regions with roles in seedling stage salinity tolerance (Prakash et al., 2022). Transgenic approaches have been widely used to characterize the functions of genes of interest that might improve stress tolerance in model plants and crop species. The overexpression of the E. coli hchA gene, which encodes a functional GLYOXALASE III (EcGly-III), conferred salinity tolerance in tobacco (Ghosh et al., 2022). The ectopic expression of this glyoxalase III increased the capacity for detoxification of methylglyoxal, which is a cytotoxic molecule, without depleting the cellular pools of reduced glutathione (GSH) or NADPH because the enzyme does not require these reductants as cofactors (Ghosh et al., 2022). The rice OsPSKR15 gene encoding a phytosulfokine receptor confers drought tolerance by regulating the reactive oxygen species (ROS)-mediated pathway of ABA signaling in Arabidopsis guard cells (Nagar et al., 2022). Similarly, overexpression of the mitochondrial alternate oxidase (AOX) in Arabidopsis conferred salinity tolerance by mitigating nitro-oxidative stress (Manbir et al., 2022). The functional characterization of Arabidopsis AtUSP17 gene, which encodes a universal stress protein, revealed that AtUSP17 is a negative regulator of salinity tolerance (Bhuria et al., 2022). Several articles report the results of gene overexpression in crop plants. For example, the overexpression of the HaHB4 transcription factor in soybean (Minussi Winck et al., 2022) and the CaPDZ1 gene in chickpea (Lande et al., 2022) confers drought tolerance. Moreover, the overexpression of OsCYP2-P, which encodes an active cyclophilin, conferred salinity tolerance in rice by maintaining ion homeostasis and preventing membrane damage (Roy et al., 2022). Several studies involved the simultaneous overexpression of several genes, including γ-TOCOPHEROL METHYLTRANSFERASE (γ-TMT) and GLYOXALASE I (gly I) in Brassica juncea (Kumar et al., 2022a). The following transgenes were found to confer salinity and drought tolerance in transgenic crop plants: a cowpea VuTCP9 gene that encodes a nuclear-localized class-I TCP transcription factor (Mishra et al., 2022a), a rice DTH8 (days to heading) gene that encodes a putative HAP3/NF-YB/CBF subunit of the CCAAT-box binding protein (Mishra et al., 2022b), and OsSOS2 that encodes a serine/threonine kinase (Kumar et al., 2022b). The overexpression of a salt and drought stress-inducible banana NAC gene (MusaATAF2) was shown to induce leaf senescence by promoting chlorophyll catabolism and H2O2 accumulation (Bhakta et al., 2022), suggesting that this gene plays a role in stress-induced leaf senescence. The use of beneficial microbes to enhance stress tolerance is often considered to be a sustainable and eco-friendly approach to crop improvement. Inoculation with four Pseudomonas strains that have 1-aminocyclopropane 1-carboxylic acid (ACC) deaminase activity, as well as the ability to produce gibberellic acid, abscisic acid, indole acetic acid, as well as exopolysaccharides was shown to confer drought tolerance in Arabidopsis (Yasmin et al., 2022). Similarly, inoculation of Brevibacterium linens RS16 that has ACC deaminase activity conferred heat stress tolerance in rice by reducing ethylene emissions, thereby decreasing ROS accumulation and enhancing the expression of HSP16 and HSP26 (Choi et al., 2022). In addition to a rich array of innovative research articles, this Special Issue contains seven authoritative review articles that concisely summarize the current state of knowledge and concepts while highlighting unresolved issues and gaps in our understanding. The review by González Guzmán et al. (2022) provides an expert analysis of green strategies, such as chemical priming and root-associated microorganisms, to improve stress tolerance, as well as the application of advanced technologies such as genome-editing and high-throughput phenotyping to develop improved crop varieties with better stress tolerance. The well-formulated perspective provided by Kandhol et al. (2022) focuses on the use of nanoparticles as effective and promising tools to engineer sustainable crop yields under drought stress. A consideration of the regulatory mechanisms and key components that can be used to remodel root system architecture (RSA) to enhance drought stress tolerance is provided in the expert review by Ranjan et al. (2022). The central role of ion transporters and their associated signaling mechanisms in regulating salt tolerance are discussed in the interesting and informative review by Joshi et al. (2022). The mechanisms of hydrogen sulfide-mediated alleviation of salinity tolerance signaling cross talk with other signaling pathways are considered in the review by Srivastava et al. (2022), while Verma et al. (2022) discuss the literature concerning the role of AUXIN RESPONSE FACTORS (ARFs) in auxin-mediated drought and salinity stress response. The approaches that have been used to identify the transcription factors with a potential role in salinity stress tolerance are presented in the review by Tiwari et al. (2022), which also discusses the functions of key transcription factors families such as AP2/EREBP, bZIP, NAC, WRKY, MYB, and zinc finger proteins, in salinity tolerance in rice seedlings. In summary, this Special Issue contains a wealth of current information, expert opinions, and insights, as well as novel findings that together will facilitate rapid advances in fundamental research and applied crop design to improve salinity and drought stress tolerance. The articles cover a wide range of state-of-the-art approaches, from genomics and transgenic approach to the application of bacterial inoculants and nanoparticles. Many articles present crucial new evidence of the functions of novel genes and the application of molecular markers that can assist plant breeders. The guest editors of this special issue are indebted to the authors of the articles in this Special Issue that present new and interesting contributions either as research findings or as review articles. We also thank all the reviewers for their generous gift of time and constructive opinions and suggestions for improvement of the articles covered in this Special Issue. We consider that the content of this Special Issue will appeal to the wide readership of the Journal, as well as experts in the field. We also trust that the contents of this Special Issue will lay the foundations for new directions in research into stress tolerance mechanisms and provide researchers at all levels with the inspiration and enthusiasm to further explore crop improvement with a special emphasis on abiotic stress tolerance.