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Plant exposed to heat stress (35/33 °C) and control (27/16 °C) in JL-3 (sensitive) and PDL-2 (tolerant) genotypes at seedling stage in growth chamber under hydroponic conditions.
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The present study reports the role of morphological, physiological and reproductive attributes viz. membrane stability index (MSI), osmolytes accumulations, antioxidants activities and pollen germination for heat stress tolerance in contrasting genotypes. Heat stress increased proline and glycine betaine (GPX) contents, induced superoxide dismutase...
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... °C (day/night) conditions. Ribonucleic acid (RnA) extraction and complementary deoxyribonucleic acid (cDnA) library preparation. Three biological replicates from each of tolerant and sensitive genotypes under control and heat stress conditions were sampled. Each replicate consisted of 12 seedlings which were pooled together (Additional File 1. Fig. S1). Leaf samples were frozen in liquid nitrogen and preserved at −80 °C and were used for RNA extraction for Illumina library construction and quantitative real time polymerase chain reaction (RT-qPCR). TRIZOL reagent (Takara, Japan) was used for extraction of total RNA from control and treated leaf samples followed by RNA integrity test ...
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... tolerant treated vs sensitive treated revealed 15,156 and 15,457 genes, respectively (Fig. 6). Similarly, in tolerant treated vs tolerant control and sensitive treated vs sensitive control comparison groups, a total of 13,508;16,807 and 16,262;15,335 up regulated and down regulated genes were identified, respectively (Additional File 11. Fig. S11 and Additional File 12. Fig. S12 Tolerant- Treated_1 6.1 22536460 93705 500 16470 1437 985 1770 3005 Tolerant-Treated _2 5.9 24355081 91926 500 16818 1426 978 1766 3006 Tolerant-Treated_3 5.7 23604075 90267 500 15500 1423 980 1760 2978 Sensitive- www.nature.com/scientificreports www.nature.com/scientificreports/ highest components in ...
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... treated revealed 15,156 and 15,457 genes, respectively (Fig. 6). Similarly, in tolerant treated vs tolerant control and sensitive treated vs sensitive control comparison groups, a total of 13,508;16,807 and 16,262;15,335 up regulated and down regulated genes were identified, respectively (Additional File 11. Fig. S11 and Additional File 12. Fig. S12 Tolerant- Treated_1 6.1 22536460 93705 500 16470 1437 985 1770 3005 Tolerant-Treated _2 5.9 24355081 91926 500 16818 1426 978 1766 3006 Tolerant-Treated_3 5.7 23604075 90267 500 15500 1423 980 1760 2978 Sensitive- www.nature.com/scientificreports www.nature.com/scientificreports/ highest components in addition to number of genes per ...
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... and downregulated DEGs with tolerant and sensitive genotypes under control and stressed conditions (Fig. 7). MapMan (MapManVersion 3.6.0RC1) represented www.nature.com/scientificreports www.nature.com/scientificreports/ overall views of metabolic pathways involved under heat stress for different combination (Fig. 8, Additional File 13. Fig. S13 and Additional File 14. Fig. S14). For the combination tolerant treated vs sensitive treated, MapMan showed involvement of nearly all the pathways. Among the major pathways, cell wall and secondary metabolite had highest number of BINs which represented the functional categories to which genes were assigned (Fig. ...
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... with tolerant and sensitive genotypes under control and stressed conditions (Fig. 7). MapMan (MapManVersion 3.6.0RC1) represented www.nature.com/scientificreports www.nature.com/scientificreports/ overall views of metabolic pathways involved under heat stress for different combination (Fig. 8, Additional File 13. Fig. S13 and Additional File 14. Fig. S14). For the combination tolerant treated vs sensitive treated, MapMan showed involvement of nearly all the pathways. Among the major pathways, cell wall and secondary metabolite had highest number of BINs which represented the functional categories to which genes were assigned (Fig. ...
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... enzyme 5 peroxisomal www.nature.com/scientificreports www.nature.com/scientificreports/ Validation of g-SSRs. All 55 g-SSRs gave amplification in 96 genotypes. Among which, 18 markers were found to be polymorphic. Primer 10 had highest number of allele, genetic diversity as well as Polymorphism Information Content (PIC) (Additional File 15. Fig. S15). Major allelic frequency, PIC, number of alleles, genetic diversity and heterozygosity were deduced using power marker (Additional File 21. Table ...
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... with three technical replicates using RT-qPCR. Degree of expression of genes amplified using RT-qPCR is represented in Fig. 9. Log2 fold change was deduced from the raw data and when compared to that of RNA Seq data, it exhibited a close association and concordance with differential expression results of genes under heat stress conditions (Fig. ...
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... field conditions. Hence, hydroponics is one of the best approaches to reveal true genes responsible for heat stress. In present study, plants were subjected to heat stress continuous at 35/33 °C for 3 d. As a result, plants of sensitive genotype showed marked wilting of leaves along with lodging of stems when compared to plants of tolerant one (Fig. 1). This indicated that 3 d continuous heat exposure is sufficient to discriminate genotypes as tolerant or sensitive, in addition to the fact that the genotypes has already been selected from a whole spectrum of 119 genotypes by Singh et al. 1 . Same duration of heat stress did not affect the basic metabolism in tolerant genotype which ...
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... S3). RT-qPCR results showed that expression of all these DEGs were similar to those obtained from Illumina sequencing analysis (Figs 9 and 10). Besides, the fold changes obtained by DEGs were generally higher than those obtained by RT-qPCR, which was a comprehensive phenomenon in some studies. ...
Citations
... Furthermore, acute hindrance of the flowering process causes abnormal pro-embryo growth, hindering seed and fruit production. For instance, at a temperature ≤20 • C or ≥32 • C, lentils reportedly exhibited pod abortion, fewer flowers, a shorter flowering period, diminished pollen viability, pollen germination, stigmatic function, ovule viability, and pollen tube elongation (which are symptoms of a pollen deficiency in a plant), leading to a severe reduction in seed size (Singh et al., 2019). ...
The increase in cash crop productivity has helped improve farmers, communities, and economic streams and has served as a source of income. However, the erratic global climate change deeply affects crops' productivity due to the exacerbating high temperatures predominant in some geographical regions, which has translated into other environmental issues. Combinatorial impacts of these climate-associated problems have exposed agricultural lands to multiple abiotic stresses, placing massive pressure on cultivatable arable lands and reducing crop productivity. Agronomists, through an understanding of single abiotic stressors, have innovated new concepts like nanotechnology, molecular modified and cross-bred varieties to unravel these problems. However, the complexity, toxicity, and resistance development associated with these approaches have consistently left the search window open for novel, natural, and more sustainable alternatives. To this end, the roles of root microbiomes, particularly root endophytes, in ensuring plant growth promotion through siderophore production, phytohormone release and regulation, and nutrient fertilization have been harnessed in an effort to resolve single, double, and multiple abiotic stressors without a complete understanding of the pathways involved in each mechanism of plant growth promotion. Thus, to successfully leverage root endophytes for growth promotion during multi-stresses, this review is targeted to reveal single abiotic stress mechanism for each cash crop group, as this could help conceptualize the details involved in stress control and the alleviation of multi-stresses through nutrient fertilization pathways.
... The nutritional pro le of lentil seeds is very rich, offering high levels of protein, dietary ber, and essential micronutrients like folate, iron, and zinc (Foodstruct, 2023). Moreover, regular consumption of lentils is associated with a reduced risk of chronic diseases, including cardiovascular conditions and diabetes, and metabolic disorders (Singh et al, 2019). Despite these bene ts, lentil cultivation is frequently challenged by biotic stresses including rust, bruchid, wilt etc (Rubio Teso et al., 2022; Barilli and Rubiales, 2023) and abiotic stresses, such as drought, salinity, and extreme temperatures which, can severely limits its yield (Sehgal et al., 2017;Noor et al., 2024). ...
The WRKY gene family plays a very important role in plant growth, development, and response to both biotic and abiotic stresses. Despite its importance, WRKY gene family is yet to be explored in lentil ( Lentil culinaris Medikus), an important legume cultivated worldwide. This study presents the first in-depth analysis of WRKY genes in lentil with respect to their genomic organization, evolution, and expression patterns. A total of 105 LcWRKY genes were identified, distributed across seven chromosomes, and classified into six subgroups based on conserved motifs and phylogenetic relationships. Promoter analysis revealed cis-regulatory elements associated with hormone signalling and stress responses underscoring the role of LcWRKY genes in stress adaptation. Chromosome mapping showed uneven LcWRKY gene distribution, with chromosome 5 hosting the most, indicating gene duplication's events might have played role in their evolution. Synteny analysis with Arabidopsis further confirmed the evolutionary conservation of this gene family. In silico gene expression profiling revealed 16 LcWRKY genes that were significantly upregulated under both salt and drought stress conditions, supporting their involvement in stress tolerance. Notably, LcWRKY46 and LcWRKY73 showed significant upregulation in response to salt stress, whereas LcWRKY22 and LcWRKY47 were significantly upregulated under drought conditions, indicating their critical roles in enhancing stress tolerance in lentil. This study not only advances our understanding of the organization and evolution of the LcWRKY gene family but also provides insights into its potential role in stress adaptation, which can be utilized by lentil researchers to design stress-tolerant varieties.
... The advent of NGS technologies has enabled quicker and more cost-effective mapping of genes and QTLs by mining SNPs (Sharpe et al. 2013). Additionally, recent transcriptome research using NGS has generated more SNPs from the coding regions of the lentil genome (Singh et al. 2017a(Singh et al. , 2019. Drawing on these diverse marker systems, Lens species can be readily differentiated from one another. ...
Climate change has negatively impacted lentil growth and production, necessitating advanced omics tools for trait characterization and genetic improvement. Traditional breeding methods have reached their limits, making high-throughput omics technologies, biotechnology, and bioinformatics essential. Despite their benefits, efforts targeting lentils have been limited. Genomics and transcriptomics studies have identified linkage maps, quantitative-trait loci (QTLs), and stress tolerance genes. The use of phenotyping techniques has expanded, but lentil has not yet made full use of these state-of-the-art procedures under stress conditions. Lentil proteomics has used 2-D gel electrophoresis to discover seed-specific proteomes, but lacks research on stress impacts. Lentil ionomics has involved the analysis of elemental composition and the examination of changes in response to various stresses. Metabolomics has revealed key stress-related pathways and genes. The review suggests integrating omics discoveries into a systems approach to enhance lentil productivity and resilience.
... Transcriptome analysis using RNA sequencing (RNA-seq) is another powerful application of NGS that enables researchers to investigate gene expression patterns under different conditions, including salt stress. RNA-seq generates a comprehensive profile of all the transcripts expressed in a particular tissue at a given time, allowing for the identification of differentially expressed genes (DEGs) in response to salinity [101]. For instance, RNA-seq studies in Arabidopsis thaliana have identified thousands of DEGs under salt stress, including those involved in osmoprotection, ion transport, and ROS scavenging [102]. ...
Salt stress is a major abiotic stressor that limits plant growth, development, and agricultural productivity, especially in regions with high soil salinity. With the increasing salinization of soils due to climate change, developing salt-tolerant crops has become essential for ensuring food security.This review consolidates recent advances in plant genetics, transcription factors (TFs), and nextgeneration
sequencing (NGS) technologies that are pivotal for enhancing salt stress tolerance in crops. It highlights critical genes involved in ion homeostasis, osmotic adjustment, and stress signaling pathways, which contribute to plant resilience under saline conditions. Additionally, specific TF families, such as DREB, NAC (NAM, ATAF, and CUC), and WRKY, are explored for their roles in activating salt-responsive gene networks. By leveraging NGS technologies—including genome-wide association studies (GWASs) and RNA sequencing (RNA-seq)—this review provides insights into
the complex genetic basis of salt tolerance, identifying novel genes and regulatory networks that underpin adaptive responses. Emphasizing the integration of genetic tools, TF research, and NGS, this review presents a comprehensive framework for accelerating the development of salt-tolerant crops, contributing to sustainable agriculture in saline-prone areas.
... This gene has also been reported to restrain the seed size by negatively regulating the elongation of integument cells (Yu et al. 2014). Candidate gene with SNP (SNP3927) annotated as retrovirus-related Pol polyprotein from transposon TNT 1-94 has been reported in legumes such as Cajanus cajan (Singh et al. 2019b), V. umbellata (Sahu et al. 2024) and Lens culinaris (Singh et al. 2019a). This protein is reported to be associated with heat stress in tomato (Cappetta et al. 2021), lentil (Singh et al. 2019a) and V. umbellata (Sahu et al. 2024). ...
... Candidate gene with SNP (SNP3927) annotated as retrovirus-related Pol polyprotein from transposon TNT 1-94 has been reported in legumes such as Cajanus cajan (Singh et al. 2019b), V. umbellata (Sahu et al. 2024) and Lens culinaris (Singh et al. 2019a). This protein is reported to be associated with heat stress in tomato (Cappetta et al. 2021), lentil (Singh et al. 2019a) and V. umbellata (Sahu et al. 2024). This protein might also play an important role in providing heat stress resilience to moth bean. ...
Moth bean is a small-seeded, protein-rich, and abiotic stress-resilient legume grown in arid and semi-arid areas of South Asia. Cultivation of this underutilized legume can reduce the dependency on commercialized Vigna species for food and nutrient security in underdeveloped countries. However, low yield remains one of the major limitations in the wider adoption of the crop among farmers in South Asian countries. To address this challenge, the present study employs genome-wide association studies to dissect the genetic basis of seed weight, a very important trait directly related to seed size and yield. The study used a diverse panel of 327 genotypes, which were phenotyped for 100-seed weight trait across three environments. By employing four multi-locus GWAS methods and 8518 SNP markers, we identified 17 significant SNPs across the genome associated with seed weight. The important seed size/seed development-associated candidate genes anchoring these SNPs were S-protein-like protein, purple acid phosphatase, kinetochore protein spc25 isoform X2 and CBL-interacting protein kinase 8-like protein. Four trait-associated SNPs/genomic regions identified in this study exhibited significant effects on the 100-seed weight trait. Genes associated with two of these SNPs (SNP2374: “g20155.t2” encoding purple acid phosphatase, and SNP5696: “g29506.t1” encoding kinetochore protein spc25 isoform X2) showed prominent upregulation in flower and early developing seed tissues/pod development stages suggesting their role in regulating seed size in moth bean. Trait-based markers developed from these candidate genes could potentially accelerate the marker-assisted breeding program to enhance seed weight and overall productivity of moth bean.
... NGS technology has advanced our comprehension of genetic diversity by facilitating the representative sequencing of cultivars genome over a shorter period of time through the genotyping by sequencing (GBS) approach [41,42,43]. Furthermore, the examination of the transcriptome under various situations has yielded a more profound understanding of gene expression patterns [44,45]. The progress made in this field has made it easier to identify quantitative trait loci (QTLs) and has resulted in the finding of several molecular markers, including simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) [44,45,46,47,48,49]. ...
... Furthermore, the examination of the transcriptome under various situations has yielded a more profound understanding of gene expression patterns [44,45]. The progress made in this field has made it easier to identify quantitative trait loci (QTLs) and has resulted in the finding of several molecular markers, including simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) [44,45,46,47,48,49]. Apart from these, several other marker systems have also been used to assess genetic diversity and characterize Lens species, including inter-simple sequence repeat (ISSR), directed amplification of minisatellite DNA (DAMD), inter-primer binding site (iPBS), and sequence-related amplified polymorphism (SRAP) [50,51,52]. ...
... A study reported the transformation of two microsperma seeded lentil varieties namely, Bari Masur-4 and Bari Masur-5 in Bangladesh using A. tumefaciens strain LBA4404 [127]. The development of lentil transgenic plants can also benefit from the recent advancement in next generation sequencing technologies with the identification of putative genes for traits such as drought tolerance [44,128], heat tolerance [45,129,130], cold acclimation [131], disease resistance [132,133], and agronomical traits [134] through transcriptomic analysis. Apart from these genes, functionally characterized and validated genes from several heterologous systems, such as WRKY transcription factor genes [135,136], NAC transcription factor genes [137], and DREB transcription factors genes [138], may also be used for abiotic and biotic stress tolerance. ...
Lentil (Lens culinaris Medik) is an essential pulse crop that is widely grown for its high nutritional value, notably its high protein content, making it an important dietary component for vegetarians and vegans. Despite being the world's fifth most produced pulse, with large contributions from Canada and India, lentil production confronts obstacles such as poor productivity due to limited genetic improvement against biotic and abiotic stresses under rainfed cultivation conditions. Recent advances in lentil genetics and genomics, such as the discovery of genes related to yield, disease resistance, and nutritional content, have boosted breeding efforts to generate improved lentil Review Article Kesari et al.; J. Exp.
... Furthermore, plant ameliorates metabolism by cyclic transport of electrons around PSI and photorespiration (Johnson 2011) by consumption of excess NADPH and free electrons to maintain homeostasis of ATP/NADPH, thereby protecting photosystems from heat stress (Kramer and Evans 2011). Singh et al. (2019b) reported that thermo-tolerant genotypes maintain net and gross photosynthesis due to maintaining the maximum quantum efficiency of PSII and depend upon night respiration, which relies on the availability of substrate and repair of ROS damage by antioxidant activity. It also observed that a reduction in net photosynthesis due to HNT has no association with photorespiration. ...
Rice (Oryza sativa) faces challenges to yield and quality due to urbanisation, deforestation and climate change, which has exacerbated high night temperature (HNT). This review explores the impacts of HNT on the physiological, molecular and agronomic aspects of rice growth. Rise in minimum temperature threatens a potential 41% reduction in rice yield by 2100. HNT disrupts rice growth stages, causing reduced seed germination, biomass, spikelet sterility and poor grain development. Recent findings indicate a 4.4% yield decline for every 1°C increase beyond 27°C, with japonica ecotypes exhibiting higher sensitivity than indica. We examine the relationships between elevated CO2, nitrogen regimes and HNT, showing that the complexity of balancing positive CO2 effects on biomass with HNT challenges. Nitrogen enrichment proves crucial during the vegetative stage but causes disruption to reproductive stages, affecting grain yield and starch synthesis. Additionally, we elucidate the impact of HNT on plant respiration, emphasising mitochondrial respiration, photorespiration and antioxidant responses. Genomic techniques, including CRISPR-Cas9, offer potential for manipulating genes for HNT tolerance. Plant hormones and carbohydrate enzymatic activities are explored, revealing their intricate roles in spikelet fertility, grain size and starch metabolism under HNT. Gaps in understanding genetic factors influencing heat tolerance and potential trade-offs associated with hormone applications remain. The importance of interdisciplinary collaboration is needed to provide a holistic approach. Research priorities include the study of regulatory mechanisms, post-anthesis effects, cumulative HNT exposure and the interaction between climate variability and HNT impact to provide a research direction to enhance rice resilience in a changing climate.
... These markers have been used for various genetic studies in various crops including soybean [13], and chickpea [14]. However, in lentils, the InDels are very scantily reported in the public databases [15][16][17] and no PCR-based InDel markers have been developed till now. This study used QTL-seq to map QTLs and identify the candidate genes associated with earliness and identify and validate the PCR-based InDel markers linked with earliness trait in lentils. ...
The systematic identification of insertion/deletion (InDel) length polymorphisms from the entire lentil genome can be used to map the quantitative trait loci (QTL) and also for the marker-assisted selection (MAS) for various linked traits. The InDels were identified by comparing the whole-genome resequencing (WGRS) data of two extreme bulks (early- and late-flowering bulk) and a parental genotype (Globe Mutant) of lentil. The bulks were made by pooling 20 extreme recombinant inbred lines (RILs) each, derived by crossing Globe Mutant (late flowering parent) with L4775 (early flowering parent). Finally, 734,716 novel InDels were identified, which is nearly one InDel per 5,096 bp of lentil genome. Furthermore, 74.94% of InDels were within the intergenic region and 99.45% displayed modifier effects. Of these, 15,732 had insertions or deletions of 20 bp or more, making them amenable to the development of PCR-based markers. An InDel marker I-SP-356.6 (chr. 3; position 356,687,623; positioned 174.5 Kb from the LcFRI gene) was identified as having a phenotypic variance explained (PVE) value of 47.7% for earliness when validated in a RIL population. Thus, I-SP-356.6 marker can be deployed in MAS to facilitate the transfer of the earliness trait to other elite late-maturing cultivars. Two InDel markers viz., I-SP-356.6 and I-SP-383.9 (chr. 3; linked to LcELF3a gene) when tested in 9 lentil genotypes differing for maturity duration, clearly distinguished three early (L4775, ILL7663, Precoz) and four late genotypes (Globe Mutant, MFX, L4602, L830). However, these InDels could not be validated in two genotypes (L4717, L4727), suggesting either absence of polymorphism and/or presence of other loci causing earliness. The identified InDel markers can act as valuable tools for MAS for the development of early maturing lentil varieties.
... The initial DNA markers-based linkage maps developed in lentils were using RFLP and AFLP markers (Eujayl et al., 1998;Havey and Muehlbauer, 1989). Afterward, several PCR-based markers such as RAPD, SCAR, SSR, EST-SSRs, etc. have been deployed in lentil breeding programs across the globe (Mbasani-Mansi et al., 2019;Polanco et al., 2019;Singh et al., 2019a;Verma et al., 2014). However, next-generation sequencing (NGS) technologies speeded up the development of single nucleotide polymorphism (SNP) based markers in lentils, which are used to find out the linked markers with various traits including seed quality, disease resistance, and micronutrient (Lombardi et al., 2014;Sudheesh et al., 2016;Khazaei et al., 2016;Khazaei et al., 2017;Khazaei et al., 2018). ...
... Temel et al. (2014) used 50960 SNPs for the construction of a linkage map in lentil. NGS platforms have also been used for a number of RNA Seq analyses in lentils (Sharpe et al., 2013;Kaur et al., 2014;Singh et al., 2019a;Kumar et al., 2021) and identified a large number of SNPs in the coding region of the lentil genome. These have been used for genetic diversity analysis, the development of dense linkage maps, and the identification of genes/QTLs for traits of agronomic importance (see following text). ...
... Also, many genes responsible for the negative regulation of absicisic acid, GABA synthesis, cell wall protein, etc were downregulated in the tolerant genotypes. The molecular mechanism underlying heat stress using RNA Seq has revealed new genes, and pathways (Singh et al., 2019a). The tolerant genotype showed more DEGs than the sensitive genotype after 3 days of heat stress and most of the DEGs were related to secondary metabolic components and cell walls. ...
... 27 interactions of varied intensity were observed between chickpea MKKs and MAPKs. Singh et al. (2019) investigated the identification, taxonomy, chromosomal localization, evolutionary relationships, and expression analyses of the MAPK family, as well as their response to abiotic stresses. Phylogenetic analysis of a set of 19 putative MAPK genes identified were categorised into four groups . ...
Jasmonic Acid (JA), Salicylic Acid (SA) and its derivatives are important phytohormones that play fundamental roles in the plant defence mechanisms against various biotic and abiotic stresses. These hormones are essential in enabling plants to respond and adapt to challenging environmental conditions. They serve as key players in various plant signalling pathways and exhibit both antagonistic and synergistic effects on each other. JA primarily functions in defence against pathogenic organisms and herbivores, while SA plays a crucial role in combating biotrophic pathogens. Apart from biotic stresses, studies have shown that the application of JA and SA can enhance the resistance of pulses to abiotic stresses such as drought, temperature extremes, metal toxicity, and salt stress, which could be achieved through the regulation of specific gene expression. Under such conditions, the magnitude of JA and SA is regulated through a complex signalling system, which includes coordinated actions of transcriptional and post-transcriptional regulation of enzymes, as well as modification of key proteins by other molecules. The WRKY70 transcription factor (TF) plays a significant role in the post-transcriptional regulation and modulation of genes such as NPR1, VSP1 VSP2, PR2, and PR10, which are associated with stimulating the plant defence response in the pulse crops. The regulation of JA and SA signalling pathways in pulse crops under stress conditions is complex, requiring a deeper understanding of the underlying mechanisms. Therefore, developing well-organized strategies for the exogenous application of JA/SA and its derivatives in pulses becomes crucial in mitigating the impact of these stresses. This paper sheds light on the recent understanding on mechanism and application of JA/SA, which could help in improving the resilience and defence mechanisms of pulse crops, leading to better stress tolerance and overall crop productivity.
