Comparative Analysis of Fruit Metabolites and Pungency Candidate Genes Expression between Bhut Jolokia and Other Capsicum Species

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.

The Influence of Different Factors on the Metabolism of Capsaicinoids in Pepper (Capsicum annuum L.)

Pepper is a globally cultivated vegetable known for its distinct pungent flavor, which is derived from the presence of capsaicinoids, a class of unique secondary metabolites that accumulate specifically in pepper fruits. Since the accumulation of capsaicinoids is influenced by various factors, it is imperative to comprehend the metabolic regulatory mechanisms governing capsaicinoids production. This review offers a thorough examination of the factors that govern the metabolism of capsaicinoids in pepper fruit, with a specific focus on three primary facets: (1) the impact of genotype and developmental stage on capsaicinoids metabolism, (2) the influence of environmental factors on capsaicinoids metabolism, and (3) exogenous substances like methyl jasmonate, chlorophenoxyacetic acid, gibberellic acid, and salicylic acid regulate capsaicinoid metabolism. The findings of this study are expected to enhance comprehension of capsaicinoids metabolism and aid in the improvement of breeding and cultivation practices for high-quality pepper in the future.

A multifunctional role for riboflavin in the yellow nectar of Capsicum baccatum and Capsicum pubescens

A few Capsicum (pepper) species produce yellow-colored floral nectar, but the chemical identity and biological function of the yellow pigment are unknown. A combination of analytical biochemistry techniques was used to identify the pigment that gives Capsicum baccatum and Capsicum pubescens nectars their yellow color. Microbial growth assays, visual modeling, and honey bee preference tests for artificial nectars containing riboflavin were used to assess potential biological roles for the nectar pigment. High concentrations of riboflavin (vitamin B2) give the nectars their intense yellow color. Nectars containing riboflavin generate reactive oxygen species when exposed to light and reduce microbial growth. Visual modeling also indicates that the yellow color is highly conspicuous to bees within the context of the flower. Lastly, field experiments demonstrate that honey bees prefer artificial nectars containing riboflavin. Some Capsicum nectars contain a yellow-colored vitamin that appears to play roles in (1) limiting microbial growth, (2) the visual attraction of bees, and (3) as a reward to nectar-feeding flower visitors (potential pollinators), which is especially interesting since riboflavin is an essential nutrient for brood rearing in insects. These results cumulatively suggest that the riboflavin found in some Capsicum nectars has several functions.

Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation

Pepper (Capsicum spp.) is one of the earliest cultivated crops and includes five domesticated species, C. annuum var. annuum, C. chinense, C. frutescens, C. baccatum var. pendulum and C. pubescens. Here, we report a pepper graph pan-genome and a genome variation map of 500 accessions from the five domesticated Capsicum species and close wild relatives. We identify highly differentiated genomic regions among the domesticated peppers that underlie their natural variations in flowering time, characteristic flavors, and unique resistances to biotic and abiotic stresses. Domestication sweeps detected in C. annuum var. annuum and C. baccatum var. pendulum are mostly different, and the common domestication traits, including fruit size, shape and pungency, are achieved mainly through the selection of distinct genomic regions between these two cultivated species. Introgressions from C. baccatum into C. chinense and C. frutescens are detected, including those providing genetic sources for various biotic and abiotic stress tolerances.

Antioxidant potential and factors influencing the content of antioxidant compounds of pepper: A review with current knowledge

The use of natural food items as antioxidants has gained increasing popularity and attention in recent times supported by scientific studies validating the antioxidant properties of natural food items. Peppers (Capsicum spp.) are also important sources of antioxidants and several studies published during the last few decades identified and quantified various groups of phytochemicals with antioxidant capacities as well as indicated the influence of several pre- and postharvest factors on the antioxidant capacity of pepper. Therefore, this review summarizes the research findings on the antioxidant activity of pepper published to date and discusses their potential health benefits as well as the factors influencing the antioxidant activity in pepper. The major antioxidant compounds in pepper include capsaicinoids, capsinoids, vitamins, carotenoids, phenols, and flavonoids, and these antioxidants potentially modulate oxidative stress related to aging and diseases by targeting reactive oxygen and nitrogen species, lipid peroxidation products, as well as genes for transcription factors that regulate antioxidant response elements genes. The review also provides a systematic understanding of the factors that maintain or improve the antioxidant capacity of peppers and the application of these strategies offers options to pepper growers and spices industries for maximizing the antioxidant activity of peppers and their health benefits to consumers. In addition, the efficacy of pepper antioxidants, safety aspects, and formulations of novel products with pepper antioxidants have also been covered with future perspectives on potential innovative uses of pepper antioxidants in the future.

Characterization of phenolics and tocopherol profile, capsaicinoid composition and bioactive properties of fruits in interspecies (Capsicum annuum X Capsicum frutescens) recombinant inbred pepper lines (RIL)

In this study, 104 RIL (Recombinant Inbred Pepper Lines: F6) populations which generated by selfing Capsicum annuum (Long pepper) × Capsicum frutescens (PI281420) F6 population were characterized in terms of detailed bioactive properties, major phenolic composition, tocopherol and capsaicinoid profile. Total phenolics, flavonoid and total anthocyanin contents of the red pepper lines were in the range of 7.06-17.15 mg gallic acid equivalent (GAE)/g dw, 1.10-5.46 mg catechin equivalent (CE)/g dw and 7.9-516.6 mg/kg dw extract, respectively. Antiradical activity and antioxidant capacity values also ranged between 18.99 and 49.73% and 6.97-16.47 mg ascorbic acid equivalent (AAE)/kg dw, respectively. Capsaicin and dihydrocapsaicin levels showed a wide variance with the range of 27.9-1405.9 and 12.3-640.4 mg/100 g dw, respectively. Scoville heat unit revealed that the 95% of the peppers were highly pungent. The major tocopherol was alpha tocopherol for the pepper samples with the highest level of 1078.4 µg/g dw. The major phenolics were detected as p-coumaric acid, ferulic acid, myricetin, luteolin and quercetin. Pepper genotypes showed significant differences in terms of the characterized properties and principal component analysis was applied successfully to reveal the similar genotypes.

MYB24 Negatively Regulates the Biosynthesis of Lignin and Capsaicin by Affecting the Expression of Key Genes in the Phenylpropanoid Metabolism Pathway in Capsicum chinense

The wide application of pepper is mostly related to the content of capsaicin, and phenylpropanoid metabolism and its branch pathways may play an important role in the biosynthesis of capsaicin. The expression level of MYB24, a transcription factor screened from the transcriptome data of the pepper fruit development stage, was closely related to the spicy taste. In this experiment, CcMYB24 was cloned from Hainan Huangdenglong pepper, a hot aromatic pepper variety popular in the world for processing, and its function was confirmed by tissue expression characteristics, heterologous transformation in Arabidopsis thaliana, and VIGS technology. The results showed that the relative expression level of CcMYB24 was stable in the early stage of pepper fruit development, and increased significantly from 30 to 50 days after flowering. Heterologous expression led to a significant increase in the expression of CcMYB24 and decrease in lignin content in transgenic Arabidopsis thaliana plants. CcMYB24 silencing led to a significant increase in the expression of phenylpropanoid metabolism pathway genes PAL, 4CL, and pAMT; lignin branch CCR1 and CAD; and capsaicin pathway CS, AT3, and COMT genes in the placenta of pepper, with capsaicin content increased by more than 31.72% and lignin content increased by 20.78%. However, the expression of PAL, pAMT, AT3, COMT, etc., in the corresponding pericarps did not change significantly. Although CS, CCR1, and CAD increased significantly, the relative expression amount was smaller than that in placental tissue, and the lignin content did not change significantly. As indicated above, CcMYB24 may negatively regulate the formation of capsaicin and lignin by regulating the expression of genes from phenylpropanoid metabolism and its branch pathways.

Integrated analysis of DNA methylation, transcriptome, and global metabolites in interspecific heterotic Capsicum F1 hybrid

Hybrid breeding is one of the efficacious methods of crop improvement. Here, we report our work towards understanding the molecular basis of F1 hybrid heterosis from Capsicum chinense and C. frutescens cross. Bisulfite sequencing identified a total of 70597 CG, 108797 CHG, and 38418 CHH differentially methylated regions (DMRs) across F₁ hybrid and parents, and of these, 4891 DMRs showed higher methylation in F₁ compared to the mid-parental methylation values (MPMV). Transcriptome analysis showed higher expression of 46–55% differentially expressed genes (DE-Gs) in the F₁ hybrid. The qRT-PCR analysis of 24 DE-Gs with negative promoter methylation revealed 91.66% expression similarity with the transcriptome data. A few metabolites and 65–72% enriched genes in metabolite biosynthetic pathways showed overall increased expression in the F₁ hybrid compared to parents. These findings, taken together, provided insights into the integrated role of DNA methylation, and genes and metabolites expression in the manifestation of heterosis in Capsicum.

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Global methylation identified significantly different proportions of mCs in hybrid

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Of common DMRs, 33.08% showed different methylation in hybrid from the mid-parental value

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Negatively correlated DEG pDMR-genes were enriched in metabolic pathways

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Significant higher expression of metabolites and DE-Gs were identified in the F₁ hybrid

Integrated omics analysis identified genes and their splice variants involved in fruit development and metabolites production in Capsicum species

To date, several transcriptomic studies during fruit development have been reported; however, no comprehensive integrated study on expression diversity, alternative splicing, and metabolomic profiling was reported in Capsicum. This study analyzed RNA-seq data and untargeted metabolomic profiling from early green (EG), mature green (MG), and breaker (Br) fruit stages from two Capsicum species, i.e., C. annuum (Cann) and C. frutescens (Cfrut) from Northeast India. A total of 117,416 and 96,802 alternatively spliced events (AltSpli-events) were identified from Cann and Cfrut, respectively. Among AltSpli-events, intron retention (IR; 32.2% Cann and 25.75% Cfrut) followed by alternative acceptor (AA; 15.4% Cann and 18.9% Cfrut) were the most abundant in Capsicum. Around 7600 genes expressed in at least one fruit stage of Cann and Cfrut were AltSpli. The study identified spliced variants of genes including transcription factors (TFs) potentially involved in fruit development/ripening (Aux/IAA 16-like, ETR, SGR1, ARF, CaGLK2, ETR, CaAGL1, MADS-RIN, FUL1, SEPALLATA1), carotenoid (PDS, CA1, CCD4, NCED3, xanthoxin dehydrogenase, CaERF82, CabHLH100, CaMYB3R-1, SGR1, CaWRKY28, CaWRKY48, CaWRKY54), and capsaicinoids or flavonoid biosynthesis (CaMYB48, CaWRKY51), which were significantly differentially spliced (DS) between consecutive Capsicum fruit stages. Also, this study observed that differentially expressed isoforms (DEiso) from 38 genes with differentially spliced events (DSE) were significantly enriched in various metabolic pathways such as starch and sucrose metabolism, amino acid metabolism, cysteine cutin suberin and wax biosynthesis, and carotenoid biosynthesis. Furthermore, the metabolomic profiling revealed that metabolites from aforementioned pathways such as carbohydrates (mainly sugars such as D-fructose, D-galactose, maltose, and sucrose), organic acids (carboxylic acids), and peptide groups significantly altered during fruit development. Taken together, our findings could help in alternative splicing-based targeted studies of candidate genes involved in fruit development and ripening in Capsicum crop.

Characterization of 75 Cultivars of Four Capsicum Species in Terms of Fruit Morphology, Capsaicinoids, Fatty Acids, and Pigments

Fruit quality has long been well known as an important prerequisite for evaluating pepper resources. In the study, 75 cultivars belonging to four Capsicum species were investigated on the bases of fruit morphology and concentrations of fruit secondary metabolites. The results showed that C. annuum had a greater variation than C. chinense and C. frutescens in terms of fruit weight, size and contents of carotenoids, anthocyanidins, and capsaicinoids. Moreover, there were significant differences in the concentrations of total phenol, total soluble sugar, total soluble solids, titratable acid, and total soluble protein of all samples. Capsaicin and dihydrocapsaicin were the most important capsaicinoids components in pepper fruits, of which C. chinense both had the highest levels, whereas some accessions of C. annuum were not detected. Eighteen fatty acids were detected in pepper fruits, and the dominant member was linoleic acid (a polyunsaturated fatty acid) therein. We integrated a set of methods for metabolites, and the results indicated that there was a positive correlation between concentrations of capsaicinoids and fatty acids. Four accessions had the highest contents of quality-related compounds, two of which belonged to C. chinense (S23 and S24) and possessed high levels of capsaicin. However, S67 had a high level of β-carotene and S68 contained higher contents of total fatty acid and ascorbic acid, and both of them belonged to C. annuum. This work could provide a valid experimental basis for the potential application value of the four accessions mentioned above.

Capsicum chinense MYB Transcription Factor Genes: Identification, Expression Analysis, and Their Conservation and Diversification With Other Solanaceae Genomes

Myeloblastosis (MYB) genes are important transcriptional regulators of plant growth, development, and secondary metabolic biosynthesis pathways, such as capsaicinoid biosynthesis in Capsicum. Although MYB genes have been identified in Capsicum annuum, no comprehensive study has been conducted on other Capsicum species. We identified a total of 251 and 240 MYB encoding genes in Capsicum chinense MYBs (CcMYBs) and Capsicum baccatum MYBs (CbMYBs). The observation of twenty tandem and 41 segmental duplication events indicated expansion of the MYB gene family in the C. chinense genome. Five CcMYB genes, i.e., CcMYB101, CcMYB46, CcMYB6, CcPHR8, and CcRVE5, and two CaMYBs, i.e., CaMYB3 and CaHHO1, were found within the previously reported capsaicinoid biosynthesis quantitative trait loci. Based on phylogenetic analysis with tomato MYB proteins, the Capsicum MYBs were classified into 24 subgroups supported by conserved amino acid motifs and gene structures. Also, a total of 241 CcMYBs were homologous with 225 C. annuum, 213 C. baccatum, 125 potato, 79 tomato, and 23 Arabidopsis MYBs. Synteny analysis showed that all 251 CcMYBs were collinear with C. annuum, C. baccatum, tomato, potato, and Arabidopsis MYBs spanning over 717 conserved syntenic segments. Using transcriptome data from three fruit developmental stages, a total of 54 CcMYBs and 81 CaMYBs showed significant differential expression patterns. Furthermore, the expression of 24 CcMYBs from the transcriptome data was validated by quantitative real-time (qRT) PCR analysis. Eight out of the 24 CcMYBs validated by the qRT-PCR were highly expressed in fiery hot C. chinense than in the lowly pungent C. annuum. Furthermore, the co-expression analysis revealed several MYB genes clustered with genes from the capsaicinoid, anthocyanin, phenylpropanoid, carotenoid, and flavonoids biosynthesis pathways, and related to determining fruit shape and size. The homology modeling of 126 R2R3 CcMYBs showed high similarity with that of the Arabidopsis R2R3 MYB domain template, suggesting their potential functional similarity at the proteome level. Furthermore, we have identified simple sequence repeat (SSR) motifs in the CcMYB genes, which could be used in Capsicum breeding programs. The functional roles of the identified CcMYBs could be studied further so that they can be manipulated for Capsicum trait improvement.

Shear wave imaging and classification using extended Kalman filter and decision tree algorithm

Shear wave ultrasound elastography is a quantitative imaging approach in soft tissues based on viscosity-elastic properties. Complex shear modulus (CSM) estimation is an effective solution to analyze tissues' physical properties for elasticity and viscosity based on the wavenumber and attenuation coefficient. CSM offers a way to detect and classify some types of soft tissues. However, CSM-based elastography inherits some obstacles, such as estimation precision and calculation complexity. This work proposes an approach for two-dimensional CSM estimation and soft tissue classification using the Extended Kalman Filter (EKF) and Decision Tree (DT) algorithm, named the EKF-DT approach. CSM estimation is obtained by applying EKF to exploit shear wave propagation at each spatial point. Afterward, the classification of tissues is done by a direct and efficient decision tree algorithm categorizing three types of normal, cirrhosis, and fibrosis liver tissues. Numerical simulation scenarios have been employed to illustrate the recovered quality and practicality of the proposed method's liver tissue classification. With the EKF, the estimated wave number and attenuation coefficient are close to the ideal values, especially the estimated wave number. The states of three liver tissue types were automatically classified by applying the DT coupled with two proposed thresholds of elasticity and viscosity: (2.310 kPa, 1.885 Pa.s) and (3.620 kPa 3.146 Pa.s), respectively. The proposed method shows the feasibility of CSM estimation based on the wavenumber and attenuation coefficient by applying the EKF. Moreover, the DT can automate the classification of liver tissue conditions by proposing two thresholds. The proposed EKF-DT method can be developed by 3D image reconstruction and empirical data before applying it in medical practice.

Role of Traditional Ethnobotanical Knowledge and Indigenous Communities in Achieving Sustainable Development Goals

The sustainable development goals (SDGs) are a set of 17 goals with 169 targets. The Agenda 2030 of the United Nations envisages a holistic approach to achieve these goals by focusing on humankind and the planet. In this review, we analyzed the scientific literature and technical reports of international bodies such as the United Nations and Food and Agriculture Organization relating to traditional ethnobotanical knowledge (TEK). The literature on TEK was mapped with the targets of the SDGs to determine the role of traditional knowledge in the realization of selected goals and targets. Our extensive and systematic reviewing of available literatures suggests that, of the 17 goals, at least seven goals are associated with TEK. To achieve these seven goals, a thorough understanding is required to disentangle the intricacies involving TEK, indigenous people holding TEK, and their future role in achieving the SDGs. Our review points towards the role of TEK in achieving goals linked to poverty, health and wellbeing, responsible consumption and production, climate action, life on land, and partnerships. In summary, we argue that achieving the intended outcomes of the SDGs and the targets requires concerted efforts of all relevant stakeholders, including indigenous communities, common citizens, scientists, policy makers, and world leaders.

Supercritical fluid extraction of Bhut Jolokia oleoresin and its quality analysis

The present study focuses on the standardization of the supercritical fluid extraction of the Bhut Jolokia (Capsicum chinense) which is abundantly grown in the north eastern region of India. The effect of process parameters pressure (75–225 bar), temperature (40–60 °C) and time (30–90 min) of oleoresin extraction process was studied. The standardized condition to obtain maximum extraction of Bhut Jolokia oleoresin was found to be 207 bar, 60 °C and 73 min. The oleoresin extract was analyzed for its antimicrobial, antioxidant and total phenolics content. Four strains of bacteria namely Escherichia coli (ATCC -11,229), Bacillus subtilis (ATCC- 11,774), Salmonella typhimurium (ATCC- 14,028) and Staphylococcus aureus (12,600) were used for the antimicrobial assay. It was observed that the highest inhibition was seen against E. coli, moderate inhibition was seen against S.aureus and S. typhi and partial/no zone of inhibition was observed against B. subtilis. The extract of Bhut Jolokia oleoresin showed radical scavenging activity of 58.6 ± 3.86% and total phenolics content of 4250 ± 2.26 mg GAE/100 g sample indicating Bhut Jolokia oleoresin as a good antioxidant and is also a good source of phenolic compounds.

Integrative Analysis of the Metabolome and Transcriptome of a Cultivated Pepper and Its Wild Progenitor Chiltepin (Capsicum annuum L. var. glabriusculum) Revealed the Loss of Pungency During Capsicum Domestication

Pungency is a unique characteristic of chili peppers (Capsicum spp.) caused by capsaicinoids. The evolutionary emergence of pungency is thought to be a derived trait within the genus Capsicum. However, it is not well-known how pungency has varied during Capsicum domestication and specialization. In this study, we applied a comparative metabolomics along with transcriptomics analysis to assess various changes between two peppers (a mildly pungent cultivated pepper BB3 and its hot progenitor chiltepin) at four stages of fruit development, focusing on pungency variation. A total of 558 metabolites were detected in two peppers. In comparison with chiltepin, capsaicinoid accumulation in BB3 was almost negligible at the early stage. Next, 412 DEGs associated with the capsaicinoid accumulation pathway were identified through coexpression analysis, of which 18 genes (14 TFs, 3 CBGs, and 1 UGT) were deemed key regulators due to their high coefficients. Based on these data, we speculated that downregulation of these hub genes during the early fruit developmental stage leads to a loss in pungency during Capsicum domestication (from chiltepin to BB3). Of note, a putative UDP-glycosyltransferase, GT86A1, is thought to affect the stabilization of capsaicinoids. Our results lay the foundation for further research on the genetic diversity of pungency traits during Capsicum domestication and specialization.

González-de-Peredo A, Espada-Bellido E, Ferreiro-González M, Palma M, Garcés-Claver A, F. Barbero G. Content of Capsaicinoids and Capsiate in "Filius" Pepper Varieties as Affected by Ripening

Peppers are fruits with wide genetic variability and multiple ways of being consumed that hold a relevant position in the human diet. Nowadays, consumers are interested in new gastronomic experiences provided by pepper cultivars that present new shapes, colors, and flavors while preserving their bioactive compounds, such as their capsaicinoids and capsinoids. However, numerous changes take place during their development that may alter their biological properties. Therefore, this work evaluates the capsaicinoid and capsiate contents in two traditional varieties of ornamental peppers ("Filius Blue" and "Filius Green'") during fruit maturation. The aim is to determine the ideal harvesting moment depending on the farmer's objective (e.g., achieving a specific color, shape, or flavor; achieving the maximum concentrations of bioactive compounds). The capsaicinoid contents followed different patterns in the two varieties analyzed. The "Filius Blue" variety exhibited increasing concentrations of capsaicinoids up to the 41st day post-anthesis (dpa), from which point on this trend was reversed. The concentrations in the "Filius Green" variety increased and decreased several times, reaching maximum concentrations on the 69th dpa. Regarding capsiate contents, both varieties varied in the same way, reaching maximum concentrations on the 34th dpa and then decreasing.

Nanoselenium Foliar Applications Enhance the Nutrient Quality of Pepper by Activating the Capsaicinoid Synthetic Pathway

Increasing the crop quality through enhancement of plant health is a challenging task. In this study, nanoselenium (nano-Se) was sprayed on pepper leaves, and the pepper components were compared to those of selenite. It was found that nano-Se (20 mg/L) resulted in a greater performance of plant health. It increased the chlorophyll and soluble sugar levels, which could activate phenylpropane and branched-chain fatty acid pathways, as well as AT3-related enzymes and gene expressions. These led to an enhancement for the synthesis of capsaicinoids, flavonoids, and total phenols. The nano-Se treatment also significantly promoted the expression of phyto-hormones synthesis genes, and consequently increased jasmonic, abscisic, and salicylic acid levels. Proline pathway-related compounds were increased, which could decrease the malondialdehyde and hydroxyl radical levels in crops. This study shows that nano-Se activated capsaicinoid pathways by enhancing photosynthesis and raising soluble sugar levels. The capsaicinoid contents in peppers were then increased, which consequently promoted the accumulation of secondary metabolites and antioxidants.

Phytochemical Assessment of Native Ecuadorian Peppers (Capsicum spp.) and Correlation Analysis to Fruit Phenomics

In this work, the impact of pepper (Capsicum spp.) fruits morphology on their composition for health-promoting compounds was investigated. For that purpose, pepper accessions from Ecuador, one of the hotspots in Capsicum's origin, were analyzed for ascorbic acid, polyphenols, capsaicinoids, and prevention of cholesterol oxidation. Plant and fruit phenomics were assessed with conventional descriptors and Tomato Analyzer digital traits. Significant differences among accessions and species revealed a large diversity within the collection. The Capsicum frutescens group displayed the highest levels of capsaicinoids, whereas the polyphenols shortly varied among the five domesticated species. Capsicum pubescens exhibited the lowest content of ascorbic acid. The conventional descriptors describing the magnitude of plants and fruits, as well as digital attributes under the categories of size, shape index, and latitudinal section, mostly explained the variance among Capsicum groups. Correlation test revealed that phytochemical components were negatively correlated with the morphometric fruit attributes, suggesting that huge fruits contained lower amounts of nutraceutical compounds. Multivariate analysis showed that parameters related to fruit size, shape, and nutraceutical composition primarily contribute to the arrangement of pepper accessions. Such results suggested that those traits have been subjected to higher selection pressures imposed by humans.

Placenta, Pericarp, and Seeds of Tabasco Chili Pepper Fruits Show a Contrasting Diversity of Bioactive Metabolites

Chili pepper (Capsicum spp.) is one of the most important horticultural crops worldwide, and its unique organoleptic properties and health benefits have been established for centuries. However, there is little knowledge about how metabolites are distributed throughout fruit parts. This work focuses on the use of liquid chromatography coupled with high resolution mass spectrometry (UHPLC-ESI-HRMS) to estimate the global metabolite profiles of the pericarp, placenta, and seeds of Tabasco pepper fruits (Capsicum frutescens L.) at the red mature stage of ripening. Our main results putatively identified 60 differential compounds between these tissues and seeds. Firstly, we found that pericarp has a higher content of glycosides, showing on average a fold change of 5 and a fold change of 14 for terpenoids when compared with other parts of the fruit. While placenta was the richest tissue in capsaicinoid-related compounds, alkaloids, and tocopherols, with a 35, 3, and 7 fold change, respectively. However, the seeds were richer in fatty acids and saponins with fold changes of 86 and 224, respectively. Therefore, our study demonstrates that a non-targeted metabolomic approach may help to improve our understanding of unexplored areas of plant metabolism and also may be the starting point for a detailed analysis in complex plant parts, such as fruits.

Capsaicinoids, Polyphenols and Antioxidant Activities of Capsicum annuum: Comparative Study of the Effect of Ripening Stage and Cooking Methods

Peppers (Capsicum annuum L.) are an important crop usually consumed as food or spices. Peppers contain a wide range of phytochemicals, such as capsaicinoids, phenolics, ascorbic acid, and carotenoids. Capsaicinoids impart the characteristic pungent taste. The study analyzed capsaicinoids and other bioactive compounds in different pepper cultivars at both the mature green and red stages. The effect of roasting on their nutritional content was also investigated. In the cultivars tested, the levels of capsaicin ranged from 0 to 3636 µg/g in the mature green stage and from 0 to 4820 µg/g in the red/yellow stage. The concentration of dihydrocapsaicin ranged from 0 to 2148 µg/g in the mature green stage and from 0 to 2162 µg/g in the red/yellow stage. The levels of capsaicinoid compounds in mature green and red /yellow stages were either reduced or increased after roasting depending on the cultivar. The ranges of total phenolic and total flavonoids compounds were 2096 to 7689, and 204 to 962 µg/g, respectively, in the green and red/yellow mature stage pods. Ascorbic acid levels in the peppers ranged from 223 to 1025 mg/ 100 g Dry Weight (DW). Both raw and roasted peppers possessed strong antioxidant activity as determined by 2,2-diphenyl-1-picrylhydrazyl) reagent (DPPH, 61–87%) and 2,2′-azino-bis (3-ethylbenzthiazoline-6-sulphonic acid) (ABTS, 73–159 µg/g) assays. Ascorbic acid and antioxidant activity decreased after roasting in the mature green and red stages, whereas total phenolics and flavonoids increased except in the mature green stage of Sweet Delilah and yellow stage of Canrio.

Natural variations in the MYB transcription factor MYB31 determine the evolution of extremely pungent peppers

Plants produce countless specialized metabolites crucial for their development and fitness, and many are useful bioactive compounds. Capsaicinoids are intriguing genus-specialized metabolites that confer a pungent flavor to Capsicum fruits, and they are widely applied in different areas. Among the five domesticated Capsicum species, Capsicum chinense has a high content of capsaicinoids, which results in an extremely hot flavor. However, the species-specific upregulation of capsaicinoid-biosynthetic genes (CBGs) and the evolution of extremely pungent peppers are not well understood. We conducted genetic and functional analyses demonstrating that the quantitative trait locus Capsaicinoid1 (Cap1), which is identical to Pun3 contributes to the level of pungency. The Cap1/Pun3 locus encodes the Solanaceae-specific MYB transcription factor MYB31. Capsicum species have evolved placenta-specific expression of MYB31, which directly activates expression of CBGs and results in genus-specialized metabolite production. The capsaicinoid content depends on MYB31 expression. Natural variations in the MYB31 promoter increase MYB31 expression in C. chinense via the binding of the placenta-specific expression of transcriptional activator WRKY9 and augmentation of CBG expression, which promotes capsaicinoid biosynthesis. Our findings provide insights into the evolution of extremely pungent C. chinense, which is due to natural variations in the master regulator, and offers targets for engineering or selecting flavor in Capsicum.

A MYB transcription factor is a candidate to control pungency in Capsicum annuum

Identification of a novel pungency-controlling gene Pun3, which acts as a master regulator of capsaicinoid biosynthetic genes in Capsicum annuum. Capsaicinoid is a unique compound that gives hot peppers (Capsicum spp.) their spicy taste. The Pun1 and Pun2 loci are known to control pungency in Capsicum species. Whereas Pun1 encodes an acyltransferase, the identity of Pun2 is currently unknown. Here, we used recombinant inbred lines and F₂ plants derived from a cross between the non-pungent C. annuum accession 'YCM334' and the pungent C. annuum cultivar 'Tean' to identify a novel non-pungency locus. Inheritance studies showed that non-pungency in C. annuum 'YCM334' is controlled by a single recessive gene, which we named Pun3. Using a high-density SNP map derived from genotyping-by-sequencing, Pun3 was mapped to chromosome 7. By comparing physical information about the Pun3 region in the C. annuum 'Zunla-1' and C. chinense 'PI159236' reference genomes, we identified candidate genes in this target region. One cDNA sequence from 'PI159236' was homologous to an unannotated gene in 'Zunla-1.' This sequence was also homologous to CaMYB31, which is expressed only in 'Tean' and harbors one stop codon in the non-pungent accession 'YCM334.' RNA-Seq analysis showed that major structural genes in the capsaicinoid biosynthetic pathway were significantly downregulated in 'YCM334' compared to pungent pepper. Therefore, CaMYB31 is a candidate gene for Pun3, which may act as a master regulator of capsaicinoid biosynthetic genes in pepper.

Identification of genes involved in fruit development/ripening in Capsicum and development of functional markers

The molecular mechanism of the underlying genes involved in the process of fruit ripening in Capsicum (family Solanaceae) is not clearly known. In the present study, we identified orthologs of 32 fruit development/ripening genes of tomato in Capsicum, and validated their expression in fruit development stages in C. annuum, C. frutescens, and C. chinense. In silico expression analysis using transcriptome data identified a total of 12 out of 32 genes showing differential expression during different stages of fruit development in Capsicum. Real time expression identified gene LOC107847473 (ortholog of MADS-RIN) had substantially higher expression (>500 folds) in breaker and mature fruits, which suggested the non-climacteric ripening behaviour of Capsicum. However, differential expression of Ehtylene receptor 2-like (LOC107873245) gene during fruit maturity supported the climacteric behaviour of only C. frutescens (hot pepper). Furthermore, development of 49 gene based simple sequence repeat (SSR) markers would help in selection of identified genes in Capsicum breeding.

Genetic diversity of Chilli veinal mottle virus infecting different chilli landraces in North East India indicates the possibility of transboundary movement of virus

Diverse chilli genetic resources of North East India occupy a unique niche in the Nation's chilli gene pool. Widely cultivated chilli landraces (King chilli: Capsicum chinense, bird eye chilli: Capsicum frutescens and Capsicum annuum) of North East India in general and Manipur in particular suffer from decline complex due to high incidence of viral diseases. With this background and the known prominent distribution of Chilli veinal mottle virus (ChiVMV) in Asian region, we studied its prevalence and association with diverse symptoms of chilli landraces. Molecular indexing of samples from 40 chilli plantation groves of Manipur using reverse transcription (RT)-PCR targeting the coat protein (CP) region of ChiVMV genome revealed a high incidence and wide prevalence. Out of a total of 127 chilli samples collected from different groves of Manipur, 81 chilli samples (63.78%) were positive for ChiVMV. Interestingly, ChiVMV infection rate was comparatively higher in the hilly groves (69.23% samples positive) compared to the valley groves (60% samples positive). Present study through the extensive surveys and molecular indexing work, conclusively reported the association of ChiVMV with diverse symptoms like cupping of leaf lamina with mottling, vein banding and puckering in different chilli landraces. Further, five representative ChiVMV isolates sampled from different groves of Manipur upon mechanical inoculation showed significant variation in symptom expression, indicating wide pathogenic diversity among them. Partial coat protein (CP) sequence analysis of five ChiVMV isolates from Manipur although indicated genetic homogeneity among them, but distinctiveness from ChiVMV isolates reported from the other parts of India. Phylogenetic clustering of ChiVMV isolates from Manipur near Chinese isolates rather than other Indian isolates suggested the possibility of transboundary movement.

QTL mapping and GWAS reveal candidate genes controlling capsaicinoid content in Capsicum

Capsaicinoids are unique compounds produced only in peppers (Capsicum spp.). Several studies using classical quantitative trait loci (QTLs) mapping and genomewide association studies (GWAS) have identified QTLs controlling capsaicinoid content in peppers; however, neither the QTLs common to each population nor the candidate genes underlying them have been identified due to the limitations of each approach used. Here, we performed QTL mapping and GWAS for capsaicinoid content in peppers using two recombinant inbred line (RIL) populations and one GWAS population. Whole-genome resequencing and genotyping by sequencing (GBS) were used to construct high-density single nucleotide polymorphism (SNP) maps. Five QTL regions on chromosomes 1, 2, 3, 4 and 10 were commonly identified in both RIL populations over multiple locations and years. Furthermore, a total of 109 610 SNPs derived from two GBS libraries were used to analyse the GWAS population consisting of 208 C. annuum-clade accessions. A total of 69 QTL regions were identified from the GWAS, 10 of which were co-located with the QTLs identified from the two biparental populations. Within these regions, we were able to identify five candidate genes known to be involved in capsaicinoid biosynthesis. Our results demonstrate that QTL mapping and GBS-GWAS represent a powerful combined approach for the identification of loci controlling complex traits.