Development and Characterization of an Ethyl Methane Sulfonate (EMS) Induced Mutant Population in Capsicum annuum L

Identification and characterization of Capsicum mutants using, biochemical, physiological, and single sequence repeat (SSR) markers

Identification and characterization of crop mutants through molecular marker analysis are imperious to develop desirable traits in mutation breeding programs. In the present study, macromolecular variations with altered morphological, quantitative, and biochemical traits were generated through chemically induced mutagenesis via alkylating agents and heavy metals. Statistical analysis based on quantitative traits indicating enhanced mean value in mutant lines selected from the M4 generation as compared to previous generations. Identification and characterization of morphology in selected mutant lines are based on altered phenotypes (e.g. tall and dwarf mutant with high yield, fruits with thick texture and bold seeds, etc.) in comparison to control populations. The useful mutations were recorded in phytochemicals (e.g. capsaicin and dihydrocapsaicin) and macro and micro nutrients profile (e.g. protein, iron, copper, cadmium and zinc) in selected mutant lines of Capsicum annuum L. Single Sequence Repeats (SSRs) markers analysis in selected mutant lines revealed genetic diversity in Capsicum. annuum L. The total of 44 alleles were observed with average number of allele 4.00. The Unweighted Pair Group Arithmetic Mean Method (UPGMA) showed maximum dissimilarity was recorded between mutant A-III and F-III followed by mutant G-III and C-III, while mutant B-III and G-III showed the lowest dissimilarity to each other followed by mutant L-III and mutant J-III. Correlation and Principal Component Analysis (PCA) revealed genetic diversity among mutant lines indicating their prioritization over other traits in indirect selection and also revealed that mutants treated with lower and medium concentrations were divergent. These mutant lines could be suitable in crop improvement programs for the broadening the genetic base of C. annuum L. Hierarchical Cluster Analysis (HCA) grouped the mutants into two clusters with variable euclidean distance indicated heterogeneous mutant lines developed from induced mutagenic treatments. Thus beneficial mutations could be induced in chilli genotypes via mutation breeding to enhance genetic variability in limited resources, period, and efforts.

Current knowledge and breeding strategies for management of aphid-transmitted viruses of pepper (Capsicum spp.) in Africa

Aphid-transmitted viruses cause significant losses in pepper production worldwide, negatively affecting yield and quality. The emergence of new aphid-transmitted viruses or development of variants as well as the occurrence in mixed infections make management a challenge. Here, we overview the current status of the distribution, incidence and phylogeny of aphids and the viruses they transmit in pepper in Africa; outline the available genetic resources, including sources of resistance, resistance genes and molecular markers; and discuss the recent advances in understanding the genetic basis of resistance to the predominant African viruses infecting pepper. Pepper veinal mottle virus (PVMV; Potyvirus); Potato virus Y (PVY; Potyvirus), Chili veinal mottle virus (ChiVMV; Potyvirus), Cucumber mosaic virus (CMV; Cucumovirus) and Pepper veins yellow virus (PeVYV; Polerovirus) have been reported to be the most widespread and devastating aphid-transmitted viruses infecting pepper across Africa. Co-infection or mixed infection between aphid-transmitted viruses has been detected and the interrelationship between viruses that co-infect chili peppers is poorly understood. Establishing and evaluating existing and new diversity sets with more genetic diversity is an important component of developing host resistance and implementing integrated management strategies. However, more work needs to be done to characterize the aphid-transmitted viral strains across Africa and understand their phylogeny in order to develop more durable host resistance. In addition, a limited number of QTLs associated with resistance to the aphid-transmitted virus have been reported and QTL data are only available for PVY, ChiVMV and CMV mainly against European and Asian strains, although PVMV is likely the most important aphid-transmitted viral disease in Africa. There is a need to identify germplasm resources with resistance against various aphid-transmitted virus strains, and subsequent pyramiding of the resistance using marker-assisted selection could be an effective strategy. The recent advances in understanding the genetic basis of the resistance to the virus and the new breeding techniques that can be leveraged to accelerate breeding for aphid-transmitted virus in pepper are proposed as strategies to more efficiently develop resistant cultivars. The deployment of multi-genetic resistances in pepper is an effective and desirable method of managing viral-diseases in Africa and limit losses for farmers in a sustainable manner.

Evaluation of the Impact of Chemical Mutagens on the Phenological and Biochemical Characteristics of Two Varieties of Soybean (Glycine max L.)

Mutagenic effectiveness and efficiency are the most important factors determining the success of mutation breeding, a coherent tool for quickly enhancing diversity in crops. This study was carried out at Lovely Professional University's agricultural research farm in Punjab, India, during the year 2023. The experimental design followed a randomized complete block design (RCBD) with three replications. The experiment aimed to assess the effect of three chemical mutagens, sodium azide (SA), ethyl methyl sulphonates (EMSs), and methyl methane sulfonate (MMS), at three different concentrations (0.2%, 0.4%, and 0.6%), in SL958 and SL744 soybean varieties to select the mutant exhibiting the highest yield. The data were collected and analysed using a two-way ANOVA test through SPSS software (version 22), and the means were separated using Duncan's multiple range test (DMRT) at the 5% level of significance. Between the two varieties, the highest seed germination percentage (76.0% seedlings/plot) was recorded in SL958 (0.4% SA), while the lowest (30.33% seedlings/plot) was observed in 0.6% MMS as compared to the control (53% and 76% in SL744 and SL958 at 10 days after sowing, respectively). Several weeks after sowing, the average plant height was observed to be higher (37.84 ± 1.32 cm) in SL958 (0.4% SA) and lower (20.58 ± 0.30 cm) in SL744 (0.6% SA), as compared to the controls (SL958: 26.09 ± 0.62 cm and SL744: 27.48 ± 0.74 cm). The average leaf count was the highest (234.33 ± 3.09 tetrafoliate leaves/plant) in SL958 (0.4% SA) while it was the lowest (87 leaves/plant) in 0.6% MMS as compared to the control (SL744 180.00 ± 1.63 and SL958 160.73 ± 1.05). The highest total leaf areas recorded in the SL958 and SL744 M1plants were 3625.8 ± 1.43 cm2 and 2311.03 ± 3.65 cm2, respectively. Seeds of the SL958 variety treated with 0.4% SA resulted in the development of tetrafoliate leaves with a broad leaf base and the maximum yield (277.55 ± 1.37 pods/plant) compared to the narrow pentafoliate leaves obtained through the treatment with EMS. Meanwhile, in the SL744 variety, the same treatment led to tetrafoliate leaves with a comparatively lower yield of 206.54 ± 23.47 pods/plant as compared to the control (SL744 164.33 ± 8.58 and SL958 229.86 ± 0.96). The highest protein content (47.04 ± 0.87% TSP) was recorded in the SL958 (0.4% SA) M2 seeds followed by a content of 46.14 ± 0.64% TSP in the SL744 (0.4% SA) M2 seeds, whereas the lowest content (38.13 ± 0.81% TSP) was found in SL958 (0.6% MMS). Similar observations were recorded for the lipid and fibre content. The 0.4% SA treatment in SL958 proved to be efficient in generating the highest leaf area (tetrafoliate leaves) and a reasonable yield of M1 (the first generation after mutation) plants.

Genetic characterization of a locus responsible for low pungency using EMS-induced mutants in Capsicum annuum L

KEY MESSAGE

The pepper mutants ('221-2-1a' and '1559-1-2h') with very low pungency were genetically characterized. The Pun4 locus, responsible for the reduced pungency of the mutant fruits, was localized to a 208 Mb region on chromosome 6. DEMF06G16460, encoding 3-ketoacyl-CoA synthase, was proposed as a strong candidate gene based on the genetic analyses of bulked segregants, DEG, and expression analyses. Capsaicinoids are unique alkaloids present in pepper (Capsicum spp.), synthesized through the condensation of by-products from the phenylpropanoid and branched-chain fatty acid pathways, and accumulating in the placenta. In this study, we characterized two allelic ethyl methanesulfonate-induced mutant lines with extremely low pungency ('221-2-1a' and '1559-1-2h'). These mutants, derived from the pungent Korean landrace 'Yuwolcho,' exhibited lower capsaicinoid content than Yuwolcho but still contained a small amount of capsaicinoid with functional capsaicinoid biosynthetic genes. Genetic crosses between the mutants and Yuwolcho or pungent lines indicated that a single recessive mutation was responsible for the low-pungency phenotype of mutant 221-2-1a; we named the causal locus Pungency 4 (Pun4). To identify Pun4, we combined genome-wide polymorphism analysis and transcriptome analysis with bulked-segregant analysis. We narrowed down the location of Pun4 to a 208-Mb region on chromosome 6 containing five candidate genes, of which DEMF06G16460, encoding a 3-ketoacyl-CoA synthase associated with branched-chain fatty acid biosynthesis, is the most likely candidate for Pun4. The expression of capsaicinoid biosynthetic genes in placental tissues in Yuwolcho and the mutant was consistent with the branched-chain fatty acid pathway playing a pivotal role in the lower pungency observed in the mutant. We also obtained a list of differentially expressed genes in placental tissues between the mutant and Yuwolcho, from which we selected candidate genes using gene co-expression analysis. In summary, we characterized the capsaicinoid biosynthesis-related locus Pun4 through integrated of genetic, genomic, and transcriptome analyses. These findings will contribute to our understanding of capsaicinoid biosynthesis in pepper.

Leaky mutations in the zeaxanthin epoxidase in Capsicum annuum result in bright-red fruit containing a high amount of zeaxanthin

Fruit color is one of the most important traits in peppers due to its esthetic value and nutritional benefits and is determined by carotenoid composition, resulting from diverse mutations of carotenoid biosynthetic genes. The EMS204 line, derived from an EMS mutant population, presents bright-red color, compared with the wild type Yuwolcho cultivar. HPLC analysis indicates that EMS204 fruit contains more zeaxanthin and less capsanthin and capsorubin than Yuwolcho. MutMap was used to reveal the color variation of EMS204 using an F3 population derived from a cross of EMS204 and Yuwolcho, and the locus was mapped to a 2.5-Mbp region on chromosome 2. Among the genes in the region, a missense mutation was found in ZEP (zeaxanthin epoxidase) that results in an amino acid sequence alteration (V291 → I). A color complementation experiment with Escherichia coli and ZEP in vitro assay using thylakoid membranes revealed decreased enzymatic activity of EMS204 ZEP. Analysis of endogenous plant hormones revealed a significant reduction in abscisic acid content in EMS204. Germination assays and salinity stress experiments corroborated the lower ABA levels in the seeds. Virus-induced gene silencing showed that ZEP silencing also results in bright-red fruit containing less capsanthin but more zeaxanthin than control. A germplasm survey of red color accessions revealed no similar carotenoid profiles to EMS204. However, a breeding line containing a ZEP mutation showed a very similar carotenoid profile to EMS204. Our results provide a novel breeding strategy to develop red pepper cultivars containing high zeaxanthin contents using ZEP mutations.

A large sequenced mutant library - valuable reverse genetic resource that covers 98% of sorghum genes

Mutant populations are crucial for functional genomics and discovering novel traits for crop breeding. Sorghum, a drought and heat-tolerant C4 species, requires a vast, large-scale, annotated, and sequenced mutant resource to enhance crop improvement through functional genomics research. Here, we report a sorghum large-scale sequenced mutant population with 9.5 million ethyl methane sulfonate (EMS)-induced mutations that covered 98% of sorghum's annotated genes using inbred line BTx623. Remarkably, a total of 610 320 mutations within the promoter and enhancer regions of 18 000 and 11 790 genes, respectively, can be leveraged for novel research of cis-regulatory elements. A comparison of the distribution of mutations in the large-scale mutant library and sorghum association panel (SAP) provides insights into the influence of selection. EMS-induced mutations appeared to be random across different regions of the genome without significant enrichment in different sections of a gene, including the 5' UTR, gene body, and 3'-UTR. In contrast, there were low variation density in the coding and UTR regions in the SAP. Based on the Ka /Ks value, the mutant library (~1) experienced little selection, unlike the SAP (0.40), which has been strongly selected through breeding. All mutation data are publicly searchable through SorbMutDB (https://www.depts.ttu.edu/igcast/sorbmutdb.php) and SorghumBase (https://sorghumbase.org/). This current large-scale sequence-indexed sorghum mutant population is a crucial resource that enriched the sorghum gene pool with novel diversity and a highly valuable tool for the Poaceae family, that will advance plant biology research and crop breeding.

Current status, breeding strategies and future prospects for managing chilli leaf curl virus disease and associated begomoviruses in Chilli (Capsicum spp.)

Chilli leaf curl virus disease caused by begomoviruses, has emerged as a major threat to global chilli production, causing severe yield losses and economic harm. Begomoviruses are a highly successful and emerging group of plant viruses that are primarily transmitted by whiteflies belonging to the Bemisia tabaci complex. The most effective method for mitigating chilli leaf curl virus disease losses is breeding for host resistance to Begomovirus. This review highlights the current situation of chilli leaf curl virus disease and associated begomoviruses in chilli production, stressing the significant issues that breeders and growers confront. In addition, the various breeding methods used to generate begomovirus resistant chilli cultivars, and also the complicated connections between the host plant, vector and the virus are discussed. This review highlights the importance of resistance breeding, emphasising the importance of multidisciplinary approaches that combine the best of traditional breeding with cutting-edge genomic technologies. subsequently, the article highlights the challenges that must be overcome in order to effectively deploy begomovirus resistant chilli varieties across diverse agroecological zones and farming systems, as well as understanding the pathogen thus providing the opportunities for improving the sustainability and profitability of chilli production.

Mutation and sequencing-based cloning and functional studies of a rust resistance gene in sunflower (Helianthus annuus)

Rust, caused by the fungus Puccinia helianthi Schwein., is one of the most devastating diseases of sunflower (Helianthus annuus L.), affecting global production. The rust R gene R₁₁ in sunflower line HA-R9 shows broad-spectrum resistance to P. helianthi virulent races and was previously mapped to an interval on sunflower chromosome 13 encompassing three candidate genes annotated in the XRQr1.0 reference genome assembly. In the current study, we combined ethyl methane sulfonate (EMS) mutagenesis with targeted region capture and PacBio long-read sequencing to clone the R₁₁ gene. Sequencing of a 60-kb region spanning the R₁₁ locus from the R₁₁ -HA-R9 rust-resistant line and three EMS-induced susceptible mutants facilitated the identification of R₁₁ and definition of induced mutations. The R₁₁ gene is predicted to have a single 3996-bp open reading frame and encodes a protein of 1331 amino acids with CC-NBS-LRR domains typical of genes conferring plant resistance to biotrophic pathogens. Point mutations identified in the R₁₁ rust-susceptible mutants resulted in premature stop codons, consistent with loss of function leading to rust susceptibility. Additional functional studies using comparative RNA sequencing of the resistant line R₁₁ -HA-R9 and R₁₁ -susceptible mutants revealed substantial differences in gene expression patterns associated with R₁₁ -mediated resistance at 7 days post-inoculation with rust, and uncovered the potential roles of terpenoid biosynthesis and metabolism in sunflower rust resistance.

Stress Management in Plants: Examining Provisional and Unique Dose-Dependent Responses

The purpose of this review is to critically evaluate the effects of different stress factors on higher plants, with particular attention given to the typical and unique dose-dependent responses that are essential for plant growth and development. Specifically, this review highlights the impact of stress on genome instability, including DNA damage and the molecular, physiological, and biochemical mechanisms that generate these effects. We provide an overview of the current understanding of predictable and unique dose-dependent trends in plant survival when exposed to low or high doses of stress. Understanding both the negative and positive impacts of stress responses, including genome instability, can provide insights into how plants react to different levels of stress, yielding more accurate predictions of their behavior in the natural environment. Applying the acquired knowledge can lead to improved crop productivity and potential development of more resilient plant varieties, ensuring a sustainable food source for the rapidly growing global population.

How Do Plants Cope with DNA Damage? A Concise Review on the DDR Pathway in Plants

DNA damage is induced by many factors, some of which naturally occur in the environment. Because of their sessile nature, plants are especially exposed to unfavorable conditions causing DNA damage. In response to this damage, the DDR (DNA damage response) pathway is activated. This pathway is highly conserved between eukaryotes; however, there are some plant-specific DDR elements, such as SOG1-a transcription factor that is a central DDR regulator in plants. In general, DDR signaling activates transcriptional and epigenetic regulators that orchestrate the cell cycle arrest and DNA repair mechanisms upon DNA damage. The cell cycle halts to give the cell time to repair damaged DNA before replication. If the repair is successful, the cell cycle is reactivated. However, if the DNA repair mechanisms fail and DNA lesions accumulate, the cell enters the apoptotic pathway. Thereby the proper maintenance of DDR is crucial for plants to survive. It is particularly important for agronomically important species because exposure to environmental stresses causing DNA damage leads to growth inhibition and yield reduction. Thereby, gaining knowledge regarding the DDR pathway in crops may have a huge agronomic impact-it may be useful in breeding new cultivars more tolerant to such stresses. In this review, we characterize different genotoxic agents and their mode of action, describe DDR activation and signaling and summarize DNA repair mechanisms in plants.

Current trends and insights on EMS mutagenesis application to studies on plant abiotic stress tolerance and development

Ethyl methanesulfonate (EMS)-induced mutagenesis is a powerful tool to generate genetic resource for identifying untapped genes and characterizing the function of genes to understand the molecular basis of important agronomic traits. This review focuses on application of contemporary EMS mutagenesis in the field of plant development and abiotic stress tolerance research, with particular focuses on reviewing the mutation types, mutagenesis site, mutagen concentration, mutagenesis duration, the identification and characterization of mutations responsible for altered stress tolerance responses. The application of EMS mutation breeding combined with genetic engineering in the future plant breeding and fundamental research was also discussed. The collective information in this review will provide good insight on how EMS mutagenesis is efficiently applied to improve abiotic stress tolerance of crops with the utilization of Next-generation sequencing (NGS) for mutation identification.

Optimization of Lipid Production by Schizochytrium limacinum Biomass Modified with Ethyl Methane Sulfonate and Grown on Waste Glycerol

One of the most promising avenues of biofuel research relates to using waste as a starting feedstock to produce liquid or gaseous energy carriers. The global production of waste glycerol by the refinery industry is rising year after year. The aim of the present study was to examine the effect of ethyl methane sulfonate (EMS) on the growth rates and intracellular lipid accumulation in heterotrophically-cultured Schizochytrium limacinum microalgae, grown on waste glycerol as the carbon source. The strain S. limacinum E20, produced by incubating a reference strain in EMS for 20 min, was found to perform the best in terms of producing biomass (0.054 g_DW/dm³·h) and accumulating intracellular bio-oil (0.021 g/dm³·h). The selected parameters proved to be optimal for S. limacinum E20 biomass growth at the following values: temperature 27.3 °C, glycerol level 249.0 g/dm³, oxygen in the culture 26%, and yeast extract concentration 45.0 g/dm³. In turn, the optimal values for lipid production in an S. limacinum E20 culture were: temperature 24.2 °C, glycerol level 223.0 g/dm³, oxygen in the culture 10%, and yeast extract concentration 10.0 g/dm³. As the process conditions are different for biomass growth and for intracellular lipid accumulation, it is recommended to use a two-step culture process, which resulted in a lipid synthesis rate of 0.41 g/dm³·h.

Identification of Schizosaccharomyces pombe ird Mutants Resistant to Glucose Suppression and Oxidative Stress

Glucose is both the favourite carbon and energy source and acts as a hormone that plays a regulating role in many biological processes. Calorie restriction extends the lifespan in many organisms, including Schizosaccharomyces pombe, while uptake of high glucose leads to undesired results, such as diabetes and aging. In this study, sequence analysis of Schizosaccharomyces pombe ird5 and ird11 mutants was performed using next-generation sequencing techniques and a total of 20 different mutations were detected. ird11 is resistant to oxidative stress without calorie restriction, whereas ird5 displays an adaptive response against oxidative stress. We selected nine candidate mutations located in the non-coding (6) and coding (3) region among a total of 20 different mutations. The nine candidate mutations, which are thought to be responsible for ird5 and ird11 mutant phenotypes, were investigated via forward and backward mutations by using various cloning techniques. The results of this study provide report-like information that will contribute to understanding the relationship between glucose sensing/ signalling and oxidative stress response components.