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Singh, C.M.; Singh, P.; Tiwari, C.; Purwar, S.; Kumar, M.; Pratap, A.; Singh, S.; Chugh, V.; Mishra, A.K. Multi-Omics Approaches for Drought Tolerance. Encyclopedia. Available online: https://encyclopedia.pub/entry/41496 (accessed on 15 June 2024).
Singh CM, Singh P, Tiwari C, Purwar S, Kumar M, Pratap A, et al. Multi-Omics Approaches for Drought Tolerance. Encyclopedia. Available at: https://encyclopedia.pub/entry/41496. Accessed June 15, 2024.
Singh, Chandra Mohan, Poornima Singh, Chandrakant Tiwari, Shalini Purwar, Mukul Kumar, Aditya Pratap, Smita Singh, Vishal Chugh, Awdhesh Kumar Mishra. "Multi-Omics Approaches for Drought Tolerance" Encyclopedia, https://encyclopedia.pub/entry/41496 (accessed June 15, 2024).
Singh, C.M., Singh, P., Tiwari, C., Purwar, S., Kumar, M., Pratap, A., Singh, S., Chugh, V., & Mishra, A.K. (2023, February 21). Multi-Omics Approaches for Drought Tolerance. In Encyclopedia. https://encyclopedia.pub/entry/41496
Singh, Chandra Mohan, et al. "Multi-Omics Approaches for Drought Tolerance." Encyclopedia. Web. 21 February, 2023.
Multi-Omics Approaches for Drought Tolerance
Edit

Drought stress is considered a severe threat to crop production. It adversely affects the morpho-physiological, biochemical and molecular functions of the plants, especially in short duration crops like mungbean. Significant progress has been made towards enhancing climate resilience in legumes through classical and next-generation breeding coupled with omics approaches. Various defence mechanisms have been reported as key players in crop adaptation to drought stress. Many researchers have identified potential donors, QTLs/genes and candidate genes associated to drought tolerance-related traits. 

drought genome editing multi-omics approaches

1. Introduction

Mungbean is the third most important grain legume after chickpea and pigeon pea. It is predominantly cultivated across the Asian countries and has also expanded to some parts of Africa, Australia and South America [1][2]. It is a diploid, self-pollinating, fast-growing and short-duration crop and helps in the effective utilization of summer fellows to enhance the cropping intensity and crop production [3]. Mungbean has a wider adaptability and low input requirements [4]. It has a strong root system architecture, which is actively involved in fixing the atmospheric nitrogen into the soil (about 58–109 kg/ha) via symbiosis with Rhizobium [5][6]. Therefore, it plays a vital role in improving soil fertility and sustaining productivity [7][8]. It is an excellent source of vegetable proteins, micro-nutrients and antioxidants like flavonoids and phenolics [9][10][11] and has multifarious uses as a food [12][13], feed, fodder [14] and green manure crop. Despite being an economically important crop, the productivity of mungbean is stagnant due to erratic weather conditions coupled with various biotic and abiotic stresses [15][16]. Among the abiotic stresses, drought is the most limiting factor for mungbean cultivation that hampers its growth and yield. However, varieties respond deferentially to drought stress as per duration of the stress, crop growth stage and genetic potential of a variety that lead to moderate to severe yield loss [17]. Drought stress affects various morpho-physiological processes associated with growth and molecular functions, which lead to poor grain yield [18][19][20][21]. At the initial stage, drought stress affects seed germination and impaired seedling establishment due to affected cell division and cell elongation, leading to poor crop growth [22]. It also limits cell growth due to the function of loss of turgor pressure [23]. Drought stress leads to imbalanced assimilates and decreases sucrose content, ultimately reducing the export rate from source to sink and dry matter partitioning by stress [24]. Zare et al. [25] observed 51% to 85.50% yield reduction due to drought stress in the mungbean. The flowering and the post-flowering stages have been found most sensitive than the vegetative stage in drought [26].
Yield is a complex character, which is highly affected by the genotype and its interaction with environmental factors [3][27][28][29][30]. Simultaneously, it also depends upon the expression of different morpho-physiological functions. These morpho-physiological processes are highly affected by drought stress, which exhibit impact on yield. The characters like plant height, leaf size, pod filling index, seed weight, root architecture and crop yield are significantly reduced under the drought stress conditions in mungbean and other legumes [31]. Drought stress also greatly impacts the nutrients up-taken by plant roots system along with water [32][33] due to reduced root growth in drought conditions. Furthermore, symbiotic association plays an important role in nutrient relations of legumes, which also affects the nitrogen-fixing ability and plant growth. Due to interactive effects, the nutrient relations are more complicated; therefore, this requires detailed research at molecular level. Hence, there is an utmost need to develop drought-tolerant varieties to improve crop productivity to ensure farmers’ nutritional and livelihood security, especially under the changing climate. The diverse mechanisms such as drought escape, drought avoidance, and drought tolerance are involved in the adoption of drought stress that enables the plants to survive, accumulate dry matter and produce seed [34].

2. Genomics Approaches

Understanding the genetics of any trait is very important to any crop improvement programme. As drought stress is a quantitatively inherited trait and is highly influenced by genotype x environment interaction (GEI), it remains a challenge for researchers [35]. Genetic control of drought tolerance-related traits requires integrated approaches to determine the genes/QTLs underlying them at a specific crop growth stage. The stage-specific drought stress-related traits need to be focused upon to improve the drought tolerance. Linkage mapping for QTL detection requires robust drought-tolerant donors. Yuliasti et al. [36] evaluated five mutant lines along with their parents for drought tolerance and found nine SSR-markers viz., MBSS R033; satt137; MBSSR008; MBSSR203; MBSSR013; MBSSR021; MBSSR016; MBSSR136; and DMBSSR013 linked to drought stress tolerance. A recent report by Liu et al. [37] describes the linkage of SSR loci associated with drought tolerance through linkage mapping. They detected two QTLs, qPHI4.1 and qPHI4.2 accounting for 7.85% and 21.60% phenotypic variations for each locus. Likewise, two QTLs (qBMI8.1 and qPHI8.2) for drought tolerance index of biomass were mapped on LG08, with each locus accounting for 7.11% and 5.64% of the total phenotypic variations. Nonetheless, very few reports are available on this aspect, indicating the lack of QTL information for drought tolerance in mungbean. Sholihin et al. [38] identified QTLs for RWC under drought conditions. In contrast, QTL mapping in mungbean for various resistant traits such as resistance to bruchids [39][40][41][42], powdery mildew [43][44], mungbean yellow mosaic virus [45], mungbean yellow mosaic India virus [40][46][47][48] and Cercospora leaf spot [49], have been worked out which indicates the efficiency and importance of mapping approach. Despite several studies carried out for biotic stresses, limited information is available for abiotic stress tolerance in the mungbean, therefore requiring more focus.
Although several gene mapping techniques like QTL-hotspot detection, association mapping, nested association mapping, AB-QTL approach have been evolved, the studies on gene mapping for targeted traits for drought tolerance in mungbean are still meagre. Exploring “QTL-hotspot” for drought tolerance could be a milestone for introgression of associated QTLs. Varshney et al. [50] transferred a “QTL-hotspot” for several root and drought tolerance traits through marker-assisted backcrossing into chickpea. Varshney et al. [51] identified a QTL-hotspot region in chickpea that consisted of 13 main-effect QTLs controlling 12 drought-related traits. A similar kind of hot-spot QTL identification and exploitation approach is also needed in mungbean for improving drought tolerance. Furthermore, while earlier workers have reported several QTLs for various traits, only few of them have been characterized, cloned and incorporated in breeding programs [52]. Therefore, to elucidate genetic and molecular mechanisms underlying drought tolerance in mungbean, the identified QTLs need to be cloned and characterized for their effective utilization in a breeding programme.
Genotyping by sequencing (GBS) is one of the most powerful approaches in plant breeding [53][54], which will allow plant breeders to implement GWAS, molecular diversity analysis, linkage analysis, marker discovery and marker-assisted selection [55][56][57][58][59][60]. GBS has proven to be robust for genotyping and SNP discovery [53][61]. GWAS detects marker–trait associations with higher precision by combining genotypic and phenotypic data on the natural population [62]. Sai et al. [63] prepared the GBS-based linkage map for MYMIV-resistance in mungbean. Mathivathana et al. [64] used the genotyping-by-sequencing (GBS) platform to develop the genetic linkage map using an interspecific population of V. radiata × V. umbellata (mungbean × rice bean), comprising of 538 SNP markers, with an average marker distance of 2.40 cM. Likewise, Schafleitner et al. [42] adopted GBS approach for detecting QTLs for bruchid resistance in mungbean. Noble et al., [65] characterized a mungbean panel consisting of 466 cultivated and 16 wild accessions by conducting a pilot genome-wide association study of seed coat color. Thiel et al. [66] developed SSR markers using MISA tool, which can be used in molecular breeding of mungbean against biotic and abiotic stresses. Jiao et al. [67] performed resequencing of two accessions, namely Salu and AL127, via the Illumina HiSeq 2500 platform (Illumina Technologies) for mapping lma locus. Genomic selection (GS) is a novel approach compared to MAS, which combines molecular markers with phenotype and pedigree to increase the breeding accuracy and efficiency of genomics-assisted breeding [53][68][69].
In recent years, phenomics has appeared as a novel approach to enhance the efficiency of breeding programs. Modern plant phenotyping methods help to increase the accuracy, precision and throughput at all levels, which reduce the costs through automation, remote sensing, data integration and experimental design [70]. Many next-generation and high throughput plant phenotyping platforms (HTPPs) have been developed to measure various trait values more precisely through imaging techniques to record complex traits [70][71][72][73][74][75]. These tools will help in improving the phenotyping efficiently as similar to high-throughput genomics tools [76]. Integration of these high throughput phonemics tools with genomics will accelerate the efficiency of breeding programmes.

3. Exploring Gene Families and Transcriptional Factors as Drought-Responsive Markers

Functional genomics has revolutionized understanding of gene function and gene interaction through genome-wide approaches and planning better strategies for improving tolerance towards abiotic stresses [77]. Modern biotechnology tools like transcriptomic and next-generation sequencing technologies have a great role in identification and cloning drought-responsive candidate genes [59][78], which would provide helpful insights into the molecular mechanisms of stress tolerance [79][80]. Transcriptome studies under various stresses in Vigna species have been performed by several workers [81][82][83]. The candidate genes from other model and related crops have been presented. RNA-sequencing (RNA-seq) is an efficient tool that has been used for gene discovery, their annotation and development of molecular markers including EST-SSRs [84][85]. Tian et al. [82] suggested the possible role of late embryogenesis abundant (LEA) and heat shiock proteins (HSPs), in drought tolerance in mungbean. In this post-genomics era, Vigna species have also been engineered against various abiotic stresses [86]. Many studies have suggested that the transcriptional factors consisting of sequence-specific DNA-binding domains bind to the promoter and/or enhancer of target genes and modulate the stress responses [87]. Wang et al. [88] identified 54 and 50 genome-wide bZIP proteins in V. radiata and V. angularis, respectively. Another TF-superfamily APETALA2/ethylene-responsive element factor binding proteins (AP2/ERF) are also known to enhance drought-stress tolerance in plants. The AP2/ERF superfamily is classified into different subfamilies such as AP2, ERF, RAV (related to AB13/VP), DREB (dehydration responsive element binding proteins). Labbo et al. [89] characterized 71 AP2/ERF superfamily in the mungbean genome by comparing Arabidopsis as a model system using BLAST and prediction of conserved domains with SMART. Out of 71 genes of AP2/ERF TF-families, sixteen VrDREB genes were significantly upregulated under drought stress, and proved that these genes participate in pathways leading to drought tolerance in mungbean. Similarly, WRKY TFs also have great significance acting as positive, as well as negative regulators of stress responses [90]. Srivastava et al. [91] identified 84 VaWRKY genes and 85 VrWRKY genes in adzuki bean and mungbean, respectively. Besides, there are numbers of transcription factors like NAC, BZR, etc. identified in legumes, although such studies in mungbean are yet to be undertaken. NAC have been functionally characterized in common bean [92], chickpea [93] and soybean [94]. These studies revealed that NAC expression enhances plant abiotic stresses and defence responses, such as salt, wound, cold and drought. Another gene family, Brassinazole-Resistant (BZR), is reported as a positive regulator in the biosynthesis of brassinosteroids that are actively involved in organ development and respond to drought and salt stresses [60]. Li et al. [95] worked on the expression profile of receptor for activated C-kinase 1 (RACK1) in soybean, a versatile scaffold protein that binds to numerous proteins to regulate diverse cellular pathways Arabidopsis. Their analysis revealed that GmRACK1 was expressed at different levels in all tissues and was strongly down-regulated in drought stress. Manna et al. [96] recently summarized the drought responsive genes in plants and suggested the role of those genes and transcriptional factors such as bZIP, DREB, DOF, HSF, MYB, NAC-TF, TCP-TF and WRKY gene families in modulating stress response. The DREB and HSFs are characterized, whereas many more families need to be characterized for elucidating the possible pathways and signalling channels for improving the drought stress tolerance in mungbean.
Among different pathways of GB synthesis, the most suitable target for metabolic engineering of GB is the COD pathway that changes choline into GB in a single step because of their involvement in the transfer of a single gene codA. This signifies the role of the GB-biosynthetic pathway as accomplished by codA gene encoding for choline oxidase for improving stress tolerance in mungbean. It needs hours to accelerate research in the field of molecular biology toward identifying and characterizing different keys gene, which have metabolic or regulatory roles [77][86]. In view of the facts, it is evident that in comparison to other legumes, the genetic and molecular information is still lagging behind. Therefore, an in-depth research is required on identification and characterization of genes involved in detoxification, osmolyte bio-synthesis, proteolysis of cellular substrates, water channel, ion transporter, heat shock protein (HSP) and late embryogenesis abundant (LEA) protein along with regulatory mechanisms primarily comprising of TFs, signalling protein kinases and protein phosphatases, which synchronize signal transduction and expression of genes during stress responses and that contribute toward drought stress response. Surprisingly, even after more than six years of genome sequencing of mungbean, very little progress has been made in characterizing gene families, which needs to be expedited.
The candidate genes discovered in grain legumes until date are understood to ameliorate drought stress resistance through enhancing the extent of well suited solutes like proline, starch, sugars and many others, consequently providing cellular osmotic adjustment, stabilization of membrane integrity and various enzymes/proteins and ROS detoxification [97]. Drought stress-responsive candidate genes have been reported in many grain legumes such as chickpea, common bean, soybean, cowpea and pigeon pea [98][99]. However, isolation of such candidate genes has not been reported from mungbean till date [100]. Chen et al. [101] suggested that heterologous expression of VrDREB2A isolated from mungbean led to an increased expression of DREB2A target, stress-inducible genes and ameliorated salt and drought stress tolerance of transgenic Arabidopsis, which provides a useful tool. Bharadwaj et al. [102] cloned a stress-responsive candidate gene SKP1 from mungbean. Stable transformation and expression of transgene (codA gene) for an osmoprotectant glycine betaine have also been achieved in mungbean through Agrobacterium mediated transformation system to improve the drought tolerance response [103]. Since drought stress is a quantitatively inherited trait, engineering crop for single gene integration is practically not feasible. In such conditions, engineering of TFs can affect the expression of many genes simultaneously, which will be a more effective approach and therefore, needs to be given a focussed attention.

4. The Role of Long Non-Coding RNA (lncRNAs) and Micro-RNA (miRNAs) in Drought Stress

Considerable progress has been made in the high-throughput sequencing of small RNA libraries than the large-scale identification of non-coding RNA molecules, which has expanded the scope in the era of RNA sequencing [104][105]. It plays an important role in regulating various biological processes, including genome integrity maintenance, and developmental, metabolic and adaptive responses toward environmental stresses [106]. Long noncoding RNAs are the long nucleotide sequence of RNA (~200 nt) without or with less protein-coding potential [107], which serve as precursors of miRNAs and other small RNAs [108]. MicroRNAs (miRNAs) are short (~21-nucleotide), non-coding RNA molecules that play important role in post-transcriptional gene silencing and or translational modification. Evidence suggests the role of long noncoding RNAs (lncRNAs) that modulate the drought stress response in plants [109][110][111] and are believed to regulate the transcriptional modification of drought-responsive genes [112][113]. The drought-responsive lncRNAs have also been reported in various plant species namely Arabidopsis [114], tomato [115], rice [116] and maize [117]. Likewise, Barrera-Figueroa et al., [118] identified 44 drought-responsive miRNAs in cowpea which encode zinc finger family protein, serine/threonine-protein kinase and kelch containing F-box protein. Wu et al. [119] obtained 16 drought-responsive miRNAs and the corresponding target genes related to TFs and protein kinases in common beans. Paul and Pal [120] identified 56 potentially conserved microRNAs and 88 potential miRNA target transcripts belonging to 28 families, in which 3 miRNAs viz., vra-miR160a, vra-miR162b and vra-miR398b were validated. These predicted transcripts were found to be involved in different development, metabolism and stress responses. A literature survey indicated that only a few reports are available about lncRNAs and miRNAs in mungbean, which need to be explored. It provides a unique strategy for modulating differential gene expression under drought stress, thus emerging as the next-generation genetic engineering target for mungbean improvement. It also will facilitate in designing suitable strategies for enhancing drought tolerance with minimum trade-offs in mungbean. Another strategy is use of artificial miRNAs (amiRNAs) to suppress expression of a protein-coding mRNA of interest of target gene [121]. These strategies of integrating multi-omics approaches will help in improving the breeding efficiency and developing climate smart drought tolerant mungbean cultivars.

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