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Summary Verticillium dahliae, one of the most destructive fungal pathogens of several crops, challenges the sustainability of cotton productivity worldwide because very few widely‐cultivated Upland cotton varieties are resistant to Verticillium wilt (VW). Here, we report that REVEILLE2 (RVE2), the Myb‐like transcription factor, confers the novel function in resistance to VW by regulating the jasmonic acid (JA) pathway in cotton. RVE2 expression was essentially required for the activation of JA‐mediated disease‐resistance response. RVE2 physically interacted with TPL/TPRs and disturbed JAZ proteins to recruit TPL and TPR1 in NINJA‐dependent manner, which regulated JA response by relieving inhibited‐MYC2 activity. The MYC2 then bound to RVE2 promoter for the activation of its transcription, forming feedback loop. Interestingly, a unique truncated RVE2 widely existing in D‐subgenome (GhRVE2D) of natural Upland cotton represses the ability of the MYC2 to activate GhRVE2A promoter but not GausRVE2 or GbRVE2. The result could partially explain why Gossypium barbadense popularly shows higher resistance than Gossypium hirsutum. Furthermore, disturbing the JA‐signalling pathway resulted into the loss of RVE2‐mediated disease‐resistance in various plants (Arabidopsis, tobacco and cotton). RVE2 overexpression significantly enhanced the resistance to VW. Collectively, we conclude that RVE2, a new regulatory factor, plays a pivotal role in fine‐tuning JA‐signalling, which would improve our understanding the mechanisms underlying the resistance to VW.

Exposing genetic material with physical mutagens can create novel genetic resources capable of combating different stresses. High throughput GBS-DArTseq™ assay was deployed to estimate genetic diversity of 33 newly developed stable wheat mutants as compared to the wild type. The identified 1,57,608 PAVs markers were randomly distributed across wheat chromosomes and sub-genomes with the highest number detected on Chr-7D (2877) and Chr-7B (2711). The B sub-genome contained the most PAVs followed by D and A-sub genome. Among mutant lines, Pb-M-2061 and Pb-M-59 had the highest PAV count, while Pb-M-605 and Pb-M-196 had the lowest. A total of 7,910 PAVs were consistently present over all replicates, with 3,252 specifically present in mutants and absent in wild type. The maximum PAVs (1480) were found in Pb-M-1027 and Pb-M-1323 (656). Functional characterization revealed that out of 3,252, 1,238 were found in wheat transcriptome database that contained 152 characterized and 1,196 uncharacterized genes. COGs and GO-terms analysis linked many PAVs with pathways involving signaling, metabolism and defense. Maximum number of gene-containing PAVs were identified in Pb-M-1027, Pb-M-2302 and Pb-M-1323 which were involved in tolerance to diseases and abiotic stresses, improved photosynthetic efficiency, larger grain size, increased grain yield and harvest index pathways. This study provides valuable insights into the genetic diversity and potential agronomic benefits of PAVs in wheat mutant lines. These findings can help molecular geneticist and breeders for exploiting the induced genetic diversity for unravelling the genetic circuits as well as exploiting in wheat breeding for developing resilient cultivars.

At the dawn of new millennium, policy makers and researchers focused on sustainable agricultural growth, aiming for food security and enhanced food quality. Several emerging scientific innovations hold the promise to meet the future challenges. Nanotechnology presents a promising avenue to tackle the diverse challenges in agriculture. By leveraging nanomaterials, including nano fertilizers, pesticides, and sensors, it provides targeted delivery methods, enhancing efficacy in both crop production and protection. This integration of nanotechnology with agriculture introduces innovations like disease diagnostics, improved nutrient uptake in plants, and advanced delivery systems for agrochemicals. These precision-based approaches not only optimize resource utilization but also reduce environmental impact, aligning well with sustainability objectives. Concurrently, genetic innovations, including genome editing and advanced breeding techniques, enable the development of crops with improved yield, resilience, and nutritional content. The emergence of precision gene-editing technologies, exemplified by CRISPR/Cas9, can transform the realm of genetic modification and enabled precise manipulation of plant genomes while avoiding the incorporation of external DNAs. Integration of nanotechnology and genetic innovations in agriculture presents a transformative approach. Leveraging nanoparticles for targeted genetic modifications, nanosensors for early plant health monitoring, and precision nanomaterials for controlled delivery of inputs offers a sustainable pathway towards enhanced crop productivity, resource efficiency, and food safety throughout the agricultural lifecycle. This comprehensive review outlines the pivotal role of nanotechnology in precision agriculture, emphasizing soil health improvement, stress resilience against biotic and abiotic factors, environmental sustainability, and genetic engineering.

Exploiting new genetic resources is an effective way to achieve sustainable wheat production. To this end, we exposed wheat seeds of the “Punjab-11” cultivar to gamma rays. A total of 32 stable mutants (M7) were developed, followed by characterization by conducting multilocation trials over two seasons. Principal component analysis (PCA) showed that the first six components accounted for 90.28% of the total variation among the plant height, tillers per plant, 1000-kernel weight, grain yield, and quality traits. All mutants were grouped into three clusters based on high yield index values. The genotype by trait (GT) bi-plot revealed significant associations between yield and its components among the mutants. Positive correlations were estimated for tillers per plant, plant height, 1000-kernel weight, and grain yield; however, yield components showed negative associations with protein, moisture, and gluten contents. The mutant lines Pb-M-59 waxy, Pb-M-1272 waxy, Pb-M-2260, Pb-M-1027 waxy, Pb-M-1323 waxy, and Pb-M-1854 exhibited maximum grain yield, 1000-grain weight, and tillers per plant values. Likewise, Pb-M-2725, Pb-M-2550, and Pb-M-2728 were found to be the best mutant lines in terms of grain quality; thus, the use of gamma radiation is effective in improving the desirable traits, including yield and grain quality. It is suggested that these traits can be improved beyond the performance of corresponding traits in their parent genotypes. The newly produced mutants can also be used to explore the genetic mechanisms of complex traits in the future.

Wheat is a staple food crop of many countries. Improving resilience to biotic and abiotic stresses remain key breeding targets. Among these, rust diseases are the most detrimental in terms of depressing wheat production. In the present study, chemical mutagenesis was used to induce mutations in the wheat variety NN-Gandum-1. This cultivar is moderately resistant to leaf and yellow rust. The aim of mutagenesis was to improve resistance to the disease as well as to study function of genes conferring resistance to the disease. In the present investigation, a 0.8% EMS dose was found optimum for supporting 45-55% germination of NN-Gandum-1. A total of 3,634 M2 fertile plants were produced from each of the M1 plant. Out of these, 33 (0.91%) and 20 plants (0.55%) showed absolute resistance to leaf and yellow rust, respectively. While 126 (3.46%) and 127 plants (3.49%) exhibited high susceptibility to the leaf and yellow rust, respectively. In the M4 generation, a total of 11 M4 lines (nine absolute resistant and two highly susceptible) and one wild type were selected for NGS-based exome capture assay. A total of 104,779 SNPs were identified that were randomly distributed throughout the wheat sub genomes (A, B and D). Induced mutations in intronic sequences predominated. The highest total number of SNPs detected in this assay were mapped to chr.2B (14,273 SNPs), which contains the highest number of targeted base pairs in the assay. The average mutation density across all regions interrogated was estimated to be one mutation per 20.91 Mb. The highest mutation frequency was found in chr.2D (1/11.7 kb) and the lowest in chr.7D (1/353.4 kb). Out of the detected mutations, 101 SNPs were filtered using analysis criteria aimed to enrich for mutations that may affect gene function. Out of these, one putative SNP detected in Lr21 were selected for further analysis. The SNP identified in chimeric allele (Lr21) of a resistant mutant (N1-252) was located in a NBS domain of chr.1BS at 3.4 Mb position. Through computational analysis, it was demonstrated that this identified SNP causes a substitution of glutamic acid with alanine, resulting in a predicted altered protein structure. This mutation, therefore, is a candidate for contributing to the resistance phenotype in the mutant line. Based on this work, we conclude that the wheat mutant resource developed is useful as a source of novel genetic variation for forward-genetic screens and also as a useful tool for gaining insights into the important biological circuits of different traits of complex genomes like wheat.

Environmental abiotic stresses challenge food security by depressing crop yields often exceeding 50% of their annual production. Different methods, including conventional as well as genomic-assisted breeding, mutagenesis, and genetic engineering have been utilized to enhance stress resilience in several crop species. Plant breeding has been partly successful in developing crop varieties against abiotic stresses owning to the complex genetics of the traits as well as the narrow genetic base in the germplasm. Irrespective of the fact that genetic engineering can transfer gene(s) from any organism(s), transgenic crops have become controversial mainly due to the potential risk of transgene-outcrossing. Consequently, the cultivation of transgenic crops is banned in certain countries, particularly in European countries. In this scenario, the discovery of the CRISPR tool provides a platform for producing transgene-free genetically edited plants—similar to the mutagenized crops that are not extensively regulated such as genetically modified organisms (GMOs). Thus, the genome-edited plants without a transgene would likely go into the field without any restriction. Here, we focused on the deployment of CRISPR for the successful development of abiotic stress-tolerant crop plants for sustaining crop productivity under changing environments.

Virus-induced gene silencing (VIGS) by deploying viral-based vectors such as tobacco rattle virus (TRV) is a homology-based gene silencing technique in post-transcriptional gene silencing (PTGS) and transcriptional gene silencing (TGS) to validate the function of particular genes. The study presented here showed the induction of DNA methylation in the promoter regions of three phenotypic marker genes in different cotton accessions, including two endogenous genes such as phytoene desaturase (PDS) and phytoene synthase (PSY), and an exogenous gene, such as green fluorescent protein (GFP). First, DNA methylation was established in transgenic GFP cotton where methylation persisted up to S3 generation. Afterward, the promoter of PSY was targeted following the same conditions. Significant silencing of PSY was observed and methylation of the promoter was found up to S2 generation in red leaf cotton as detected in GFP cotton. Silencing of PDS resulted in a photobleaching phenotype; interestingly, the strength of this phenotype was diverse within the plants and was not observed in the next generation. Bisulfite sequencing results showed methylation percentage of the cytosine residues was high at CG and CHG sites of the targeted promoter sequences in the silenced plants. The findings of this paper suggest that TRV-based vector system can be used to monitor DNA methylation for both exogenous and endogenous gene levels in cotton and offer a very useful tool for plant epigenetic modification.

Key message Different kinship and resistance to cotton leaf curl disease (CLCuD) and heat were found between upland cotton cultivars from China and Pakistan. 175 SNPs and 82 InDels loci related to yield, fiber quality, CLCuD, and heat resistance were identified. Elite alleles found in Pakistani accessions aided local adaptation to climatic condition of two countries. Adaptation of upland cotton ( Gossypium hirsutum ) beyond its center of origin is expected to be driven by tailoring of the genome and genes to enhance yield and quality in new ecological niches. Here, resequencing of 456 upland cotton accessions revealed two distinct kinships according to the associated country. Fiber quality and lint percentage were consistent across kinships, but resistance to cotton leaf curl disease (CLCuD) and heat was distinctly exhibited by accessions from Pakistan, illustrating highly local adaption. A total of 175 SNP and 82 InDel loci related to yield, fiber quality, CLCuD and heat resistance were identified; among them, only two overlapped between Pakistani and Chinese accessions underscoring the divergent domestication and improvement targets in each country. Loci associated with resistance alleles to leaf curl disease and high temperature were largely found in Pakistani accessions to counter these stresses prevalent in Pakistan. These results revealed that breeding activities led to the accumulation of unique alleles and helped upland cotton become adapted to the respective climatic conditions, which will contribute to elucidating the genetic mechanisms that underlie resilience traits and help develop climate-resilient cotton cultivars for use worldwide.

Since 6000 BC, cotton has been cultivated for lint fiber, which now dominates the natural textile industry worldwide. Common resources such as an integrated web database, a microsatellite database, and comparative quantitative trait loci (QTL) resources for Gossypium have accelerated the progress towards quantifying the impact of repeated human dispersals and selection regimes on various gene pools of the genus Gossypium. Out of 50 Gossypium species, four have been domesticated—two diploids and two tetraploids—for elimination of hard seed coat, improvement in lint percentage of about 40% and fiber length of 22%, larger boll size, and day-neutral reproductive habit. The major drawback of domestication is the lack of genetic diversity. This lack of genetic diversity is observed more in Gossypium hirsutum L. cultivars characterizing upland cotton than in Gossypium barbadense, typical of Pima and Egyptian cotton. Much of the genetic diversity among G. barbadense cultivars is attributed to the introgression of G. hirsutum alleles. This process highlights the importance of introgression of new alleles from accessions of all the Gossypium species into cultivated cotton species. Among the genomic resources, about 16,162 publicly available SSRs and 312 mapped cotton RFLP sequences containing simple sequence repeat (SSR), restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), and random amplified polymorphic DNA (RAPD) markers have been surveyed on numerous mapping populations, and developed about 26 linkage maps (SSR, RFLP, AFLP, and RAPD). Reports show the identification of DNA markers associated with over 29 important traits or QTLs such as fiber quality and yield, leaf and flower morphology, trichome density and their distribution, and disease resistance. In comparative mapping studies, 432 QTLs mapped on 11 different mapping populations were aligned on a high-density reference map containing 3,475 loci. In a meta-analysis study of over 1,000 QTLs obtained from backcross population and recombinant inbred line populations derived from the same parents, most consistent meta-clusters were reported for fiber color, fineness, and length. For exploring the function of genes, the targeting induced local lesions in genomes (TILLING) approach—avoiding gene transfer process was used for identifying a brassino steroid receptor gene that is involved in fiber development. Lastly, cotton genome has been enriched with genes isolated from distantly related organisms using various transformation methods. For example, Cry1Ac, Cry1Ab, and herbicide-resistant genes were transformed in cotton that covered a vast majority of cotton acreage worldwide. Here the authors discuss investigations for improving the efficacy of transformation and regeneration systems, and for searching new genes or silencing the unwanted cotton genes using RNAi technology. We suggest initiating projects on sequencing the diploid and tetraploid genomes for exploring the extent of genetic variations, developing TILLING populations, initiating nested association mapping studies, and developing third generation genetically modified cotton, collectively setting the stage for sustaining cotton production under continually changing production conditions, climates, and human needs.

Background Abiotic stresses such as drought and salinity significantly constrain peanut productivity. However, their underlying molecular response mechanisms remain unclear. Results This study identified the AhGST23 gene, together with its involvement in glutathione metabolism and the ascorbic acid-glutathione (AsA-GSH) cycle, as a key component in alleviating drought and salt stresses in peanut. Under drought (15% PEG6000 for 6 days) and salt (200 mM NaCl for 6 days) stresses, peanut seedlings exhibited a marked reduction in biomass, net photosynthetic rate, transpiration rate, and chlorophyll fluorescence parameters. Concurrently, levels of H 2 O 2 , O 2 − , and malondialdehyde (MDA), as well as the activities of antioxidant enzymes (APX, GR, SOD, POD, and CAT), were significantly elevated in both leaves and roots. RNA-seq analysis identified 3,780 and 5,019 shared differentially expressed genes (DEGs) in leaves and roots, respectively, which were enriched in pathways including plant hormone signal transduction, starch and sucrose metabolism, glutathione metabolism, and MAPK signaling. The key gene families involved in the glutathione metabolism ( AhGSTs , AhGPXs ) and AsA-GSH cycle ( AhGRs , AhAPXs , and AhMDHARs ) were highlighted as central players in the antioxidant system. Silencing AhGST23 disrupted glutathione-related metabolism in peanut. This disruption was manifested by reduced contents of ascorbic acid (AsA), dehydroascorbate (DHA), glutathione (GSH), and oxidized glutathione (GSSG), as well as decreased activities of ascorbate eroxidase (APX), glutathione S-transferases (GST), dehydroascorbate reductase (DHAR), and monodehydroascorbate reductase (MDHAR). These disruptions impaired ROS scavenging capacity and heightened sensitivity to drought and salt stresses. Conclusions In summary, the glutathione-related metabolism, with AhGST23 as a key functional gene, plays an essential role in conferring drought and salt stresses tolerance in peanut. These findings offer novel insights into antioxidant defense mechanisms and provide valuable genetic resources for enhancing peanut stress resilience.