Elucidating the callus-to-shoot-forming mechanism in Capsicum annuum 'Dempsey' through comparative transcriptome analyses.

BACKGROUND: The formation of shoots plays a pivotal role in plant organogenesis and productivity. Despite its significance, the underlying molecular mechanism of de novo regeneration has not been extensively elucidated in Capsicum annuum 'Dempsey', a bell pepper cultivar. To address this, we performed a comparative transcriptome analysis focusing on the differential expression in C. annuum 'Dempsey' shoot, callus, and leaf tissue. We further investigated phytohormone-related biological processes and their interacting genes in the C. annuum 'Dempsey' transcriptome based on comparative transcriptomic analysis across five species. RESULTS: We provided a comprehensive view of the gene networks regulating shoot formation on the callus, revealing a strong involvement of hypoxia responses and oxidative stress. Our comparative transcriptome analysis revealed a significant conservation in the increase of gene expression patterns related to auxin and defense mechanisms in both callus and shoot tissues. Consequently, hypoxia response and defense mechanism emerged as critical regulators in callus and shoot formation in C. annuum 'Dempsey'. Current transcriptome data also indicated a substantial decline in gene expression linked to photosynthesis within regenerative tissues, implying a deactivation of the regulatory system governing photosynthesis in C. annuum 'Dempsey'. CONCLUSION: Coupled with defense mechanisms, we thus considered spatial redistribution of auxin to play a critical role in the shoot morphogenesis via primordia outgrowth. Our findings shed light on shoot formation mechanisms in C. annuum 'Dempsey' explants, important information for regeneration programs, and have broader implications for precise molecular breeding in recalcitrant crops.

Transcriptome and Metabolome Reveal Key Genes from the Plant Hormone Signal Transduction Pathway Regulating Plant Height and Leaf Size in Capsicum baccatum.

Plant structure-related agronomic traits like plant height and leaf size are critical for growth, development, and crop yield. Defining the types of genes involved in regulating plant structure size is essential for the molecular-assisted breeding of peppers. This research conducted comparative transcriptome analyses using Capsicum baccatum germplasm HNUCB0112 and HNUCB0222 and their F2 generation as materials. A total of 6574 differentially expressed genes (DEGs) were detected, which contain 379 differentially expressed transcription factors, mainly including transcription factor families such as TCP, WRKY, AUX/IAA, and MYB. Seven classes of DEGs were annotated in the plant hormone signal transduction pathway, including indole acetic acid (IAA), gibberellin (GA), cytokinin (CK), abscisic acid (ABA), jasmonic acid (JA), ethylene (ET), and salicylic acid (SA). The 26 modules were obtained by WGCNA analysis, and the MEpink module was positively correlated with plant height and leaf size, and hub genes associated with plant height and leaf size were anticipated. Differential genes were verified by qRT-PCR, which was consistent with the RNA-Seq results, demonstrating the accuracy of the sequencing results. These results enhance our understanding of the developmental regulatory networks governing pepper key traits like plant height and leaf size and offer new information for future research on the pepper plant architecture system.

Potassium silicate and vinasse enhance biometric characteristics of perennial sweet pepper (Capsicum annuum) under greenhouse conditions.

An effective strategy for enhancing fruit production continuity during extended sweet pepper season involves adopting innovative biostimulants such as potassium silicate (PS) and vinasse. Adjusting PS and vinasse concentrations are crucial for maintaining the balance between vegetative and fruit growth, particularly in sweet pepper with a shallow root system, to sustain fruiting over prolonged season. However, the interaction between PS and vinasse and the underlying physiological mechanisms that extend the sweet pepper season under greenhouse conditions remain unclear. This study aimed to investigate the impact of PS and vinasse treatments on the yield and biochemical constituents of perennial pepper plants cultivated under greenhouse conditions. For two consecutive seasons [2018/2019 and 2019/2020], pepper plants were sprayed with PS (0, 0.5, and 1 g/l) and drenched with vinasse (0, 1, 2, and 3 l/m3). To estimate the impact of PS and vinasse on the growth, yield, and biochemical constituents of pepper plants, fresh and dry biomass, potential fruit yield, and some biochemical constituents were evaluated. Results revealed that PS (0.5 g/l) coupled with vinasse (3 l/m3) generated the most remarkable enhancement, in terms of plant biomass, total leaf area, total yield, and fruit weight during both growing seasons. The implementation of vinasse at 3 l/m3 with PS at 0.5 and 1 g/l demonstrated the most pronounced augmentation in leaf contents (chlorophyll index, nitrogen and potassium), alongside improved fruit quality, including total soluble solid and ascorbic acid contents, of extended sweet pepper season. By implementing the optimal combination of PS and vinasse, growers can significantly enhance the biomass production while maintaining a balance in fruiting, thereby maximizing the prolonged fruit production of superior sweet pepper under greenhouse conditions.

Genetic tapestry of Capsicum fruit colors: a comparative analysis of four cultivated species.

KEY MESSAGE: Genome-wide association study of color spaces across the four cultivated Capsicum spp. revealed a shared set of genes influencing fruit color, suggesting mechanisms and pathways across Capsicum species are conserved during the speciation. Notably, Cytochrome P450 of the carotenoid pathway, MYB transcription factor, and pentatricopeptide repeat-containing protein are the major genes responsible for fruit color variation across the Capsicum species. Peppers (Capsicum spp.) rank among the most widely consumed spices globally. Fruit color, serving as a determinant for use in food colorants and cosmeceuticals and an indicator of nutritional contents, significantly influences market quality and price. Cultivated Capsicum species display extensive phenotypic diversity, especially in fruit coloration. Our study leveraged the genetic variance within four Capsicum species (Capsicum baccatum, Capsicum chinense, Capsicum frutescens, and Capsicum annuum) to elucidate the genetic mechanisms driving color variation in peppers and related Solanaceae species. We analyzed color metrics and chromatic attributes (Red, Green, Blue, L*, a*, b*, Luminosity, Hue, and Chroma) on samples cultivated over six years (2015-2021). We resolved genomic regions associated with fruit color diversity through the sets of SNPs obtained from Genotyping by Sequencing (GBS) and genome-wide association study (GWAS) with a Multi-Locus Mixed Linear Model (MLMM). Significant SNPs with FDR correction were identified, within the Cytochrome P450, MYB-related genes, Pentatricopeptide repeat proteins, and ABC transporter family were the most common among the four species, indicating comparative evolution of fruit colors. We further validated the role of a pentatricopeptide repeat-containing protein (Chr01:31,205,460) and a cytochrome P450 enzyme (Chr08:45,351,919) via competitive allele-specific PCR (KASP) genotyping. Our findings advance the understanding of the genetic underpinnings of Capsicum fruit coloration, with developed KASP assays holding potential for applications in crop breeding and aligning with consumer preferences. This study provides a cornerstone for future research into exploiting Capsicum's diverse fruit color variation.

Fresh bell peppers consumed in cities: Unveiling the environmental impact of urban and rural food supply systems.

Agriculture and its supply chain pose significant environmental threats. This study employs Life Cycle Assessment (LCA) to explore the environmental impact of fresh bell pepper production and distribution, comparing Urban and Peri-Urban Agriculture (UPA) with Rural Long-Distance Food Supply Systems (RLDFS). Four UPA scenarios (hydroponics, soil-based greenhouse, open-field conventional, and organic) and two RLDFS scenarios (soil-based greenhouse and open-field conventional) are evaluated using SimaPro, incorporating inputs from UPA practitioners and rural farmers. Results reveal an energy demand range of 0.011 to 5.5 kWh/kg eq., with urban greenhouses exhibiting the lowest consumption and hydroponics the highest due to lighting, ventilation, and irrigation. Hydroponics exhibits a global warming potential of 7.24 kg of CO2 eq·kg-1, with energy demand contributing over 95 %, surpassing other scenarios by 7-25 times, necessitating reduction for sustainability. RLDFS's environmental impact is dominated by transportation (over 70 %), meanwhile other UPA systems are influenced by irrigation, infrastructure, and fertilizers. Despite challenges, UPA-hydroponics proves to be 1.7 to 4.3 times more land-use-efficient than other scenarios, emphasizing its potential. The study highlights the need to address electricity usage in UPA-hydroponics for carbon footprint reduction. Despite challenges, hydroponics could contribute to sustainable food security, and RLDFS does not significantly lag in environmental performance compared to UPA other than Ozone layer depletion criteria attributed to fossil fuel usage in transportation. These insights offer valuable guidance for urban development and policy formulation, promoting sustainable agricultural practices and supporting policies for agronomic and supply chain sustainability.

Direct Application of Coffee Pulp Vermicompost Produced from Epigeic Earthworms and Its Residual Effect on Vegetative and Reproductive Growth of Hot Pepper (Capsicum annuum L.).

In areas where coffee is growing, there is a huge potential to get coffee pulp, which produces a bad odor and air and water pollution. On the other hand, the farming practice in the study area is still traditional and highly dependent on artificial fertilizers. Therefore, this study aimed to evaluate the direct and residual effects of vermicompost on the vegetative and reproductive growth of hot pepper (Capsicum annuum L.). Factorial research was conducted in a randomized complete block design, where coffee pulp, animal waste, and Eisenia fetida and Dendrobaena veneta earthworms were used to produce coffee pulp vermicompost. The first factor was three types of vermicompost: coffee pulp Eisenia fetida vermicompost (CEV), coffee pulp Dendrobaena veneta vermicompost (CDV), and a combination of coffee pulp Eisenia fetida and Dendrobaena veneta vermicompost (CEV_CDV), and the second factor was three application rates (5 t/ha, 10 t/ha, and 15 t/ha) and a control treatment with three replications. Reproductive and vegetative growth parameters (number of leaves, number of fruits, single fruit length, total biomass weight, days to 50% flowering, and yield per hectare) were collected in two consecutive cropping seasons. The collected data were analyzed using R Statistical software. The results recorded in the direct application of 15 t/ha CEV were profoundly higher (P < 0.05), followed by the combined effects of both worms with an application rate of 15 t/ha. Generally, the three-way interaction effect of a media type, the application effect, and the application rate interaction effect were highly significant (P < 0.05) for the number of leaves per plant, the number of fruits per plant, and yield per hectare. The media type and the application rate interaction effect showed a significant (P < 0.05) difference in days to 50% flowering, fruit length, and fresh biomass weight. Likewise, the combined effect of the media type and application was statistically (P < 0.01) different in biomass weight and fruit length. In addition to reducing water and air pollution, utilizing coffee pulp vermicompost enhances soil fertility and hot pepper (Capsicum annuum L.) productivity.

Tomato zonate spot virus induced hypersensitive resistance via an auxin-related pathway in pepper.

Tomato zonate spotvirus (TZSV) often incurs significant losses in many food and ornamental crops in Yunnan province, China, and the surrounding areas. The pepper (Capsicum chinensePI152225)can develop hypersensitive resistance following infection with TZSV, through an as yet unknown mechanism. The transcriptome dataset showed a total of 45.81 GB of clean data were obtained from six libraries, and the average percentage of the reads mapped to the pepper genome was over 90.00 %. A total of 1403 differentially expressed genes (DEGs) were obtained after TZSV infection, including 825significantly up-regulated genes and 578 down-regulated genes. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that most up-regulated DEGs were involved in basal defenses. RT-qPCR, and virus induced gene silencing (VIGS) were used preliminarily to identifyBBC_22506 and BBC_18917, among total of 71 differentially expressed genes (DEGs), that play a key role in mediating the auxin-induced signaling pathway that might take part in hypersensitive response (HR) conferred resistance to viral infection in pepper (PI152225) byTZSV. This is the first study on the mechanism of auxin resistance, involved in defense responses of pepper against viral diseases, which lay the foundation for further study on the pathogenic mechanism of TZSV, as well as the mechanism of resistance to TZSV, in peppers.

Deciphering the influence of Bacillus subtilis strain Ydj3 colonization on the vitamin C contents and rhizosphere microbiomes of sweet peppers.

Bacillus subtilis strain Ydj3 was applied to sweet peppers to understand the influence of this bacterium on the growth, fruit quality, and rhizosphere microbial composition of sweet pepper. The promotion of seed germination was observed for sweet pepper seeds treated with the Ydj3 strain, indicating that Ydj3 promoted seed germination and daily germination speed (131.5 ± 10.8 seeds/day) compared with the control (73.8 ± 2.5 seeds/day). Strain Ydj3 displayed chemotaxis toward root exudates from sweet pepper and could colonize the roots, which enhanced root hair growth. Following the one-per-month application of strain Ydj3 to sweet pepper grown in a commercial greenhouse, the yield, fruit weight, and vitamin C content significantly increased compared with those of the control. Additionally, the composition of the rhizosphere bacterial community of sweet pepper changed considerably, with the Bacillus genus becoming the most dominant bacterial genus in the treated group. These results suggested that B. subtilis Ydj3 promotes seed germination and enhances fruit quality, particularly the vitamin C content, of sweet pepper. These effects may be partly attributed to the B. subtilis Ydj3 colonization of sweet pepper roots due to Ydj3 chemotaxis toward root exudates, resulting in the modulation of the rhizosphere bacterial community.

Synergistic effects of biochar and biostimulants on nutrient and toxic element uptake by pepper in contaminated soils.

BACKGROUND: Nowadays a significant amount of land contaminated with toxic elements is being used for agriculture, posing a serious risk of crop contamination and toxicity. Several methodologies are being used to remediate soil contamination, including the use of amendments such as biochar. This work evaluated the effects of biochar combined with different fertirrigations (water, a conventional fertilizer solution, or a fertilizer solution with a commercial biostimulant derived from leonardite) on the availability of toxic elements and nutrients for pepper cultivated in a soil contaminated with As, Cd, Pb, and Zn. RESULTS: Irrigation with fertilizer solutions improved plant growth regardless of the biochar amendment. Biochar decreased the bioavailability of Cu and Pb in soil and the Cu content in pepper leaves. Combined with fertilization, biochar also decreased plant As and Pb content. Biochar combined with biostimulant decreased the bioavailable content of Cd in soil and its uptake by pepper plants. CONCLUSION: The use of biochar and biostimulant presented advantages for plant production in a non-suitable scenario of nutrient scarcity and contamination. © 2021 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Nutritional composition changes in bell pepper as affected by the ripening stage of fruits at harvest or postharvest storage and assessed non-destructively.

BACKGROUND: Nutritional quality in bell pepper is related to the ripening stage of the fruit at harvest and postharvest storage. Its determination requires time-consuming, tissue-destructive, analytical laboratory techniques. The objective of this study was to investigate the effect of ripening stage and of postharvest storage period on fruit nutritional quality, and whether it is feasible to develop reliable models for assessing the nutritional components in peppers using non-destructive methods. The dry matter, soluble solids, ascorbic acid, phenolics, chlorophylls, carotenoids and the total antioxidant capacity were determined in bell pepper fruits at six ripening stages, from green to full red, during storage at 10 °C for 8 days. Color, chlorophyll fluorescence, visible/near infrared (Vis/NIR) spectroscopy, red-green-blue (R-G-B) and red-green-near infrared (R-G-NIR) digital imaging were tested for assessing the nutritional quality of peppers. RESULTS: The nutritional composition was mainly affected by the ripening stage of bell pepper fruits at harvest and only to a small degree by the storage period. Indeed, the more advanced ripening stage of fruit at harvest resulted in superior nutritional quality. Most of the non-destructive techniques reliably predicted the internal quality of the fruit. The genetic algorithm (GA), the variable importance in projection (VIP) scores, and the variable inflation factor (VIF) tests identified nine distinct regions and four specific wavelengths on the whole visible/NIR electromagnetic spectrum that exhibited the most significant effect in the assessment of the nutritional components. CONCLUSION: It is possible to predict individual nutritional components in bell pepper fruit reliably and non-destructively, and irrespective of the ripening stage of fruits at harvest. © 2021 Society of Chemical Industry.

Peppermint Essential Oil and Its Major Volatiles as Protective Agents against Soft Rot Caused by Fusarium sambucinum in Cera Pepper (Capsicum pubescens).

Cera pepper (Capsicum pubescens) is an exotic fruit considered as a rich source of nutraceuticals with known benefits for human health and also an economic resource for local producers in Mexico. The present investigation reports on the in vitro and in situ antifungal activity of the essential oil from Mentha piperita and its two major volatiles (menthol and menthone) against Fusarium sambucinum, which is a causal agent of soft rot in cera pepper. The application of these components in pepper fruits previously infected with F. sambucinum caused a significant delay (p<0.05) in the emergence of soft rot symptoms. This effect was reflected in the maintenance of pH and fruit firmness during a period of 10 days. The nutrimental content of the fruits (protein, fiber, fat and other proximate parameters) was conserved in the same period of time. The nutraceutical content of these fruits was estimated by the quantification of seven carotenoids (violaxanthin, cis-violaxanthin, luteoxanthin, antheraxanthin, lutein, zeaxanthin and ß-carotene), ascorbic acid and capsaicinoids (capsaicin and dihydrocapsaicin). According to our results, the essential oil from M. Piperita and its major volatiles exerted a preservative effect on these metabolites. Our findings demonstrated that the essential oil of M. Piperita and its major volatiles represent an ecological alternative for the control of fusariosis caused by F. sambucinum in cera peppers under postharvest conditions.

Plant growth promoting rhizobacteria improve growth and yield related attributes of chili under low nitrogen availability.

Nitrogen (N) is a macronutrient desired by crop plants in large quantities. However, hiking fertilizer prices need alternative N sources for reducing its requirements through appropriate management practices. Plant growth promoting rhizobacteria (PGPR) are well-known for their role in lowering N requirements of crop plants. This study assessed the impact of PGPR inoculation on growth, allometry and biochemical traits of chili under different N doses. Two PGPR, i.e., Azospirillum 'Er-20' (nitrogen fixing) and Agrobacterium 'Ca-18' (phosphorous solubilizing) were used for inoculation, while control treatment had no PGPR inoculation. Six N doses, i.e., 100, 80, 75, 70, 60 and 50% of the N required by chili were included in the study. Data relating to growth traits, biochemical attributes and yield related traits were recorded. Interaction among N doses and PGPR inoculation significantly altered all growth traits, biochemical attributes and yield related traits. The highest values of the recorded traits were observed for 100% N with and without PGPR inoculation and 75% N with PGPR inoculation. The lowest values of the recorded traits were noted for 50% N without PGPR inoculation. The PGPR inoculation improved the measured traits compared to the traits recorded noted in same N dose without PGPR inoculation. Results revealed that PGPR had the potential to lower 25% N requirement for chili. Therefore, it is recommended that PGPR must be used in chili cultivation to lower N requirements.

Effect of biostimulants on the growth, yield and nutritional value of Capsicum annuum grown in an unheated plastic tunnel.

Recent years have witnessed an increased interest in the cultivation and consumption of peppers. Therefore, new solutions are being sought to provide pepper plants with the most favorable conditions for growth and development. In view of the above, the aim of this study was to evaluate the effect of selected biostimulants on the biometric parameters, yield and nutritional value of Capsicum annuum fruit. The research hypothesis postulates that biostimulants can increase the yield and improve the nutritional quality of pepper fruit. The experiment was conducted in an unheated plastic tunnel. The experimental materials comprised three sweet ('Solario F1', 'Turbine F1' and 'Whitney F1') and two hot ('Cyklon' and 'Palivec') cultivars of C. annuum. It was found that the combined application of environmentally-friendly microbial-based biostimulants (BB Soil, BB Foliar, Multical, MK5 and Biocin F) did not clearly improve the morphological traits of pepper fruit, yield or the concentrations of sugars and organic acids in fruit, therefore their use is not economically justified. Hot peppers had a higher content of dry matter, total sugars and L-ascorbic acid than sweet peppers. The analyzed biostimulants increased nitrate (V) concentrations in the fruit of both hot and sweet peppers. 'Turbine F1' and 'Solario F1' were particularly prone to nitrate (V) accumulation in fruit, therefore the use of biostimulants should be limited in their cultivation. Pepper fruits with the largest horizontal diameter and the thickest skin should be preferred because these traits are associated with high sugar content.

CaWRKY30 Positively Regulates Pepper Immunity by Targeting CaWRKY40 against Ralstonia solanacearum Inoculation through Modulating Defense-Related Genes.

The WRKY transcription factors (TFs) network is composed of WRKY TFs' subset, which performs a critical role in immunity regulation of plants. However, functions of WRKY TFs' network remain unclear, particularly in non-model plants such as pepper (Capsicum annuum L.). This study functionally characterized CaWRKY30-a member of group III Pepper WRKY protein-for immunity of pepper against Ralstonia solanacearum infection. The CaWRKY30 was detected in nucleus, and its transcriptional expression levels were significantly upregulated by R. solanacearum inoculation (RSI), and foliar application ethylene (ET), abscisic acid (ABA), and salicylic acid (SA). Virus induced gene silencing (VIGS) of CaWRKY30 amplified pepper's vulnerability to RSI. Additionally, the silencing of CaWRKY30 by VIGS compromised HR-like cell death triggered by RSI and downregulated defense-associated marker genes, like CaPR1, CaNPR1, CaDEF1, CaABR1, CaHIR1, and CaWRKY40. Conversely, transient over-expression of CaWRKY30 in pepper leaves instigated HR-like cell death and upregulated defense-related maker genes. Furthermore, transient over-expression of CaWRKY30 upregulated transcriptional levels of CaWRKY6, CaWRKY22, CaWRKY27, and CaWRKY40. On the other hand, transient over-expression of CaWRKY6, CaWRKY22, CaWRKY27, and CaWRKY40 upregulated transcriptional expression levels of CaWRKY30. The results recommend that newly characterized CaWRKY30 positively regulates pepper's immunity against Ralstonia attack, which is governed by synergistically mediated signaling by phytohormones like ET, ABA, and SA, and transcriptionally assimilating into WRKY TFs networks, consisting of CaWRKY6, CaWRKY22, CaWRKY27, and CaWRKY40. Collectively, our data will facilitate to explicate the underlying mechanism of crosstalk between pepper's immunity and response to RSI.

Morpho-physiological and biochemical attributes of Chili (Capsicum annum L.) genotypes grown under varying salinity levels.

Climate change is causing soil salinization, resulting in huge crop losses throughout the world. Multiple physiological and biochemical pathways determine the ability of plants to tolerate salt stress. Chili (Capsicum annum L.) is a salt-susceptible crop; therefore, its growth and yield is negatively impacted by salinity. Irreversible damage at cell level and photo inhibition due to high production of reactive oxygen species (ROS) and less CO2 availability caused by water stress is directly linked with salinity. A pot experiment was conducted to determine the impact of five NaCl salinity levels, i.e., 0,1.5, 3.0, 5.0 and 7.0 dS m-1 on growth, biochemical attributes and yield of two chili genotypes ('Plahi' and 'A-120'). Salinity stress significantly reduced fresh and dry weight, relative water contents, water use efficiency, leaf osmotic potential, glycine betaine (GB) contents, photosynthetic rate (A), transpiration rate (E), stomatal conductance (Ci), and chlorophyll contents of tested genotypes. Salinity stress significantly enhanced malondialdehyde (MDA) contents and activities of the enzymatic antioxidants such as superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD). In addition, increasing salinity levels significantly reduced the tissue phosphorus and potassium concentrations, while enhanced the tissue sodium and chloride concentrations. Genotype 'Plahi' had better growth and biochemical attributes compared to 'A-120'. Therefore, 'Plahi' is recommended for saline areas to improve chili production.

Transcriptomic analysis of a wild and a cultivated varieties of Capsicum annuum over fruit development and ripening.

Chili pepper (Capsicum annuum) is one of the most important crops worldwide. Its fruits contain metabolites produced over the maturation process like capsaicinoids and carotenoids. This metabolic process produces internal changes in flavor, color, texture, and aroma in fruits to make them more attractive for seed dispersal organisms. The chiltepin (C. annuum L. var. glabriusculum) is a wild variety of the C. annuum L. species that is considered a source of genetic resources that could be used to improve the current chili crops. In this study, we performed a transcriptomic analysis on two fruit maturation stages: immature stage (green fruit) and mature stage (red fruit) of a wild and a cultivated pepper variety. We found 19,811 genes expressed, and 1,008 genes differentially expressed (DEGs) in at least one of the five contrast used; 730 DEGs were found only in one contrast, and most DEGs in all contrasts were downregulated. GO enrichment analysis showed that the majority of DEGs are related to stress responses. KEGG enrichment analysis detected differences in expression patterns in metabolic pathways related to phenylpropanoid biosynthesis, secondary metabolites, plant hormone signal transduction, carotenoid biosynthesis and sesquiterpenoid and triterpenoid biosynthesis. We selected 105 tomato fruit ripening-related genes, and found 53 pepper homologs differentially expressed related to shape, size, and secondary metabolite biosynthesis. According to the transcriptome analysis, the two peppers showed very similar gene expression patterns; differences in expression patterns of genes related to shape, size, ethylene and secondary metabolites biosynthesis suggest that changes produced by domestication of chilli pepper could be very specific to the expression of genes related to traits desired in commercial fruits.

Genome-Wide Identification and Transcriptional Expression Analysis of Annexin Genes in Capsicum annuum and Characterization of CaAnn9 in Salt Tolerance.

Annexin (Ann) is a polygenic, evolutionarily conserved, calcium-dependent and phospholipid-binding protein family, which plays key roles in plant growth, development, and stress response. However, a comprehensive understanding of CaAnn genes of pepper (Capsicum annuum) at the genome-wide level is limited. Based on the available pepper genomic information, we identified 15 members of the CaAnn gene family. Phylogenetic analysis showed that CaAnn proteins could be categorized into four different orthologous groups. Real time quantitative RT-PCR analysis showed that the CaAnn genes were tissue-specific and were widely expressed in pepper leaves after treatments with cold, salt, and drought, as well as exogenously applied MeJA and ABA. In addition, the function of CaAnn9 was further explored using the virus-induced gene silencing (VIGS) technique. CaAnn9-silenced pepper seedlings were more sensitive to salt stress, reflected by the degradation of chlorophyll, the accumulation of reactive oxygen species (ROS), and the decrease of antioxidant defense capacity. This study provides important information for further study of the role of pepper CaAnn genes and their coding proteins in growth, development, and environmental responses.

Global range expansion history of pepper (Capsicum spp.) revealed by over 10,000 genebank accessions.

Genebanks collect and preserve vast collections of plants and detailed passport information, with the aim of preserving genetic diversity for conservation and breeding. Genetic characterization of such collections has the potential to elucidate the genetic histories of important crops, use marker-trait associations to identify loci controlling traits of interest, search for loci undergoing selection, and contribute to genebank management by identifying taxonomic misassignments and duplicates. We conducted a genomic scan with genotyping by sequencing (GBS) derived single nucleotide polymorphisms (SNPs) of 10,038 pepper (Capsicum spp.) accessions from worldwide genebanks and investigated the recent history of this iconic staple. Genomic data detected up to 1,618 duplicate accessions within and between genebanks and showed that taxonomic ambiguity and misclassification often involve interspecific hybrids that are difficult to classify morphologically. We deeply interrogated the genetic diversity of the commonly consumed Capsicum annuum to investigate its history, finding that the kinds of peppers collected in broad regions across the globe overlap considerably. The method ReMIXTURE-using genetic data to quantify the similarity between the complement of peppers from a focal region and those from other regions-was developed to supplement traditional population genetic analyses. The results reflect a vision of pepper as a highly desirable and tradable cultural commodity, spreading rapidly throughout the globe along major maritime and terrestrial trade routes. Marker associations and possible selective sweeps affecting traits such as pungency were observed, and these traits were shown to be distributed nonuniformly across the globe, suggesting that human preferences exerted a primary influence over domesticated pepper genetic structure.

The flavin monooxygenase Bs3 triggers cell death in plants, impairs growth in yeast and produces H2O2 in vitro.

The pepper resistance gene Bs3 triggers a hypersensitive response (HR) upon transcriptional activation by the corresponding effector protein AvrBs3 from the bacterial pathogen Xanthomonas. Expression of Bs3 in yeast inhibited proliferation, demonstrating that Bs3 function is not restricted to the plant kingdom. The Bs3 sequence shows striking similarity to flavin monooxygenases (FMOs), an FAD- and NADPH-containing enzyme class that is known for the oxygenation of a wide range of substrates and their potential to produce H2O2. Since H2O2 is a hallmark metabolite in plant immunity, we analyzed the role of H2O2 during Bs3 HR. We purified recombinant Bs3 protein from E. coli and confirmed the FMO function of Bs3 with FAD binding and NADPH oxidase activity in vitro. Translational fusion of Bs3 to the redox reporter roGFP2 indicated that the Bs3-dependent HR induces an increase of the intracellular oxidation state in planta. To test if the NADPH oxidation and putative H2O2 production of Bs3 is sufficient to induce HR, we adapted previous studies which have uncovered mutations in the NADPH binding site of FMOs that result in higher NADPH oxidase activity. In vitro studies demonstrated that recombinant Bs3S211A protein has twofold higher NADPH oxidase activity than wildtype Bs3. Translational fusions to roGFP2 showed that Bs3S211A also increased the intracellular oxidation state in planta. Interestingly, while the mutant derivative Bs3S211A had an increase in NADPH oxidase capacity, it did not trigger HR in planta, ultimately revealing that H2O2 produced by Bs3 on its own is not sufficient to trigger HR.

An Efficient Anther Culture on Double-Layered Media to Produce Doubled Haploid Plants of Pepper (Capsicum annuum).

An efficient anther culture on double-layered media to produce doubled haploid (DH) plants in pepper (Capsicum annuum) was clearly shown to outperformed other techniques such as anther culture on solid medium and direct isolated microspore culture on liquid medium. It was even used for DH production in a cayenne type of hot pepper which was previously known as less responsive or even more recalcitrant to androgenesis than sweet bell pepper. Indeed, anther culture on double-layered media has been routinely used to produce DH plants on broad genotypes of C. annuum as parental candidates to develop hybrid varieties. The step-by-step protocol of pepper anther culture on double-layered media, we hereby present in detail, includes the growth of donor plants, the use of flower buds as anther source, flower bud disinfection, anther isolation, anther culture and incubation processes, embryo germination and plant acclimatization process, and transplanting of plants to the soil-compost medium in pots.