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Background The widely cultivated pepper ( Capsicum spp.) is one of the most diverse vegetables; however, little research has focused on characterizing the genetic diversity and relatedness of commercial varieties grown in China. In this study, a panel of 92 perfect single-nucleotide polymorphisms (SNPs) was identified using re-sequencing data from 35 different C. annuum lines. Based on this panel, a Target SNP-seq genotyping method was designed, which combined multiplex amplification of perfect SNPs with Illumina sequencing, to detect polymorphisms across 271 commercial pepper varieties. Results The perfect SNPs panel had a high discriminating capacity due to the average value of polymorphism information content, observed heterozygosity, expected heterozygosity, and minor allele frequency, which were 0.31, 0.28, 0.4, and 0.31, respectively. Notably, the studied pepper varieties were morphologically categorized based on fruit shape as blocky-, long horn-, short horn-, and linear-fruited. The long horn-fruited population exhibited the most genetic diversity followed by the short horn-, linear-, and blocky-fruited populations. A set of 35 core SNPs were then used as kompetitive allele-specific PCR (KASPar) markers, another robust genotyping technique for variety identification. Analysis of genetic relatedness using principal component analysis and phylogenetic tree construction indicated that the four fruit shape populations clustered separately with limited overlaps. Based on STRUCTURE clustering, it was possible to divide the varieties into five subpopulations, which correlated with fruit shape. Further, the subpopulations were statistically different according to a randomization test and F st statistics. Nine loci, located on chromosomes 1, 2, 3, 4, 6, and 12, were identified to be significantly associated with the fruit shape index ( p  < 0.0001). Conclusions Target SNP-seq developed in this study appears as an efficient power tool to detect the genetic diversity, population relatedness and molecular breeding in pepper. Moreover, this study demonstrates that the genetic structure of Chinese pepper varieties is significantly influenced by breeding programs focused on fruit shape.

Doil Choi and colleagues report the genome sequence of the hot pepper, Capsicum annuum , as well as the resequencing of two cultivated peppers and a wild species, Capsicum chinense . Comparative genomic analysis across Solanaceae provides insights into genome expansion, pungency, ripening and disease resistance in hot peppers. Hot pepper ( Capsicum annuum ), one of the oldest domesticated crops in the Americas, is the most widely grown spice crop in the world. We report whole-genome sequencing and assembly of the hot pepper (Mexican landrace of Capsicum annuum cv. CM334) at 186.6× coverage. We also report resequencing of two cultivated peppers and de novo sequencing of the wild species Capsicum chinense . The genome size of the hot pepper was approximately fourfold larger than that of its close relative tomato, and the genome showed an accumulation of Gypsy and Caulimoviridae family elements. Integrative genomic and transcriptomic analyses suggested that change in gene expression and neofunctionalization of capsaicin synthase have shaped capsaicinoid biosynthesis. We found differential molecular patterns of ripening regulators and ethylene synthesis in hot pepper and tomato. The reference genome will serve as a platform for improving the nutritional and medicinal values of Capsicum species.

This study evaluated the effectiveness of a commercially available Ascophyllum nodosum alkaline extract as a plant growth stimulant and defense elicitor against foliar diseases of tomato and sweet pepper caused by Xanthomonas campestris pv. vesicatoria and Alternaria solani in a tropical environment. Foliar applications of 0.5% A. nodosum extract (AN) at 10-day intervals resulted in significant (P < 0.05) increase in plant growth parameters, including plant height (40%), leaf number (50%), plant dry biomass (52%), root length (59%) and chlorophyll content (20%) compared to control. Treated plants also had a significantly higher number of flower clusters, flower numbers, fruits per cluster and total harvested fruit yield. The Ascophyllum extract significantly (P < 0.05) reduced disease incidence by the pathogens in both crops under greenhouse and field conditions. The combinatory treatment of seaweed extract and a minimum dose of contact fungicide in field trials, recorded the overall lowest disease levels (60% reduction) and highest yield (57% increase). Investigations into the mechanisms of disease suppression revealed the effects of the extract in inducing the activities of defense-related enzymes including phenylalanine ammonia lyase, peroxidase, polyphenol oxidase, chitinase and β-1,3-glucanase, as well as the levels of total phenolic compounds. The effect on SA, JA and ET-mediated signalling defense pathways was examined by quantifying expression levels of marker genes including PR1-a, PinII and ETR-1, for the above pathways respectively. Both crop plants treated with A. nodosum extract had significantly higher expression levels of the PinII and ETR-1 marker genes than controls. This was coupled with a marked increase in gene transcripts involved in auxin (IAA), gibberellin (Ga2Ox) and cytokinin (IPT) biosynthesis, which provides possible evidence for induced growth in plants treated with AN extract. Cross-talks between growth and defense responses as a result of seaweed extract application could evidently implicate the benefits of seaweed extract usage in sustainable crop production.

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.

Drought stress can have negative impacts on crop productivity. It triggers the accumulation of reactive oxygen species, which causes oxidative stress. Limited water and nutrient uptake under drought stress also decreases plant growth. Using cobalt and fulvic acid with biochar in such scenarios can effectively promote plant growth. Cobalt (Co) is a component of various enzymes and co-enzymes. It can increase the concentration of flavonoids, total phenols, antioxidant enzymes (peroxidase, catalase, and polyphenol oxidase) and proline. Fulvic acid (FA), a constituent of soil organic matter, increases the accessibility of nutrients to plants. Biochar (BC) can enhance soil moisture retention, nutrient uptake, and plant productivity during drought stress. That’s why the current study explored the influence of Co, FA and BC on chili plants under drought stress. This study involved 8 treatments, i.e., control, 4 g/L fulvic acid (4FA), 20 mg/L cobalt sulfate (20CoSO 4 ), 4FA + 20CoSO 4 , 0.50%MFWBC (0.50 MFWBC), 4FA + 0.50MFWBC, 20CoSO 4  + 0.50MFWBC, 4FA + 20CoSO 4  + 0.50MFWBC. Results showed that 4 g/L FA + 20CoSO 4 with 0.50MFWBC caused an increase in chili plant height (23.29%), plant dry weight (28.85%), fruit length (20.17%), fruit girth (21.41%) and fruit yield (25.13%) compared to control. The effectiveness of 4 g/L FA + 20CoSO 4 with 0.50MFWBC was also confirmed by a significant increase in total chlorophyll contents, as well as nitrogen (N), phosphorus (P), and potassium (K) in leaves over control. In conclusion4g/L, FA + 20CoSO 4 with 0.50MFWBC can potentially improve the growth of chili cultivated in drought stress. It is suggested that 4 g/L FA + 20CoSO 4 with 0.50MFWBC be used to alleviate drought stress in chili plants.

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.

Despite decades of research, the effects of spectral quality on plant growth, and development are not well understood. Much of our current understanding comes from studies with daily integrated light levels that are less than 10% of summer sunlight thus making it difficult to characterize interactions between light quality and quantity. Several studies have reported that growth is increased under fluorescent lamps compared to mixtures of wavelengths from LEDs. Conclusions regarding the effect of green light fraction range from detrimental to beneficial. Here we report the effects of eight blue and green light fractions at two photosynthetic photon fluxes (PPF; 200 and 500 μmol m-2 s-1; with a daily light integral of 11.5 and 29 mol m-2 d-1) on growth (dry mass), leaf expansion, stem and petiole elongation, and whole-plant net assimilation of seven diverse plant species. The treatments included cool, neutral, and warm white LEDs, and combinations of blue, green and/or red LEDs. At the higher PPF (500), increasing blue light in increments from 11 to 28% reduced growth in tomato, cucumber, and pepper by 22, 26, and 14% respectively, but there was no statistically significant effect on radish, soybean, lettuce or wheat. At the lower PPF (200), increasing blue light reduced growth only in tomato (41%). The effects of blue light on growth were mediated by changes in leaf area and radiation capture, with minimal effects on whole-plant net-assimilation. In contrast to the significant effects of blue light, increasing green light in increments from 0 to 30% had a relatively small effect on growth, leaf area and net assimilation at either low or high PPF. Surprisingly, growth of three of the seven species was not reduced by a treatment with 93% green light compared to the broad spectrum treatments. Collectively, these results are consistent with a shade avoidance response associated with either low blue or high green light fractions.

Salinity is a significant environmental stress impacting plant growth and metabolism in irrigated areas of arid and semi-arid regions; the use of biostimulants is an effective alternative to enhance plant productivity under saline conditions. This study examined the effects of salinity stress by applying various electrical conductivities (0.5, 1.5, 2.5, 3.5, and 4.5 dS m − 1 ) of irrigation water combined with foliar application of the in combination with foliar application of biostimulant VIUSID Agro (0, 0.3, and 0.6 mL L − 1 ) on the growth, productivity, physiological, and biochemical responses of bell pepper plants in a greenhouse. Conducted in a factorial design with a completely randomized layout and five replications, and the results indicated that salinity caused a significant reduction in growth, decreased chlorophyll levels, and increased malondialdehyde levels, osmoregulators, and antioxidant enzyme activity. Plants treated with biostimulant demonstrated relatively superior growth parameters, such as plant height, dry matter, leaf area and number of leaves, as well as fruit quality, such as fruit size, firmness, ascorbic acid and soluble solids. Both doses of the biostimulant effectively mitigated the effects of salt stress by maintaining higher chlorophyll levels (15% increase), enhancing photosynthetic performance (20% increase), and improving fruit size and quality, as well as leaf water status, ultimately leading to better crop performance. The biochemical mechanisms through which these effects occur include enhanced osmoregulation and increased antioxidant activity. The foliar application of the biostimulant was an effective strategy to enhance the tolerance of bell pepper plants under salt stress conditions and can serve as a sustainable solution for agricultural production in saline irrigation water.

Bell pepper ( Capsicum annuum L.) is a commercially important and nutritionally rich vegetable crop in the Solanaceae family. Alkaline stress (AS) can disrupt growth, metabolism, and, particularly, nutritional quality. This study aims to evaluate the role of iron oxide nanoparticles (FeNP) in mitigating AS and enhancing plant growth and metabolic functions by conducting experiments under controlled greenhouse conditions with four main treatments: AS (irrigating plants with alkaline salts mixture solution); FeNP (foliar application of Fe 3 O 4 nanoparticles at 100 mg L − ¹); AS + FeNP (integrated treatment of AS and FeNP); and CK (control). The results clearly demonstrated that the AS treatment negatively affects plant biomass, photosynthetic attributes, membrane integrity, carbohydrate metabolism, and the balance of the antioxidant system. Additionally, key phenolic and flavonoid compounds decreased under the AS, indicating a detrimental effect on the plant’s secondary metabolites. In contrast, the application of FeNP under the AS not only improved growth and photosynthetic attributes but also enhanced membrane integrity and restored antioxidant balance. This restoration was driven by the accumulation of sugars (glucose, fructose, sucrose) and starch, along with key carbohydrate metabolism enzymes—sucrose phosphate synthase (SPS), sucrose synthase (SuSy), neutral invertase (NI), and vacuolar invertase (VI)—and their associated gene expression. The correlation analysis further revealed a tight regulation of carbohydrate metabolism at both enzymatic and transcript levels in all tissue types, except for SPS in the roots. Furthermore, the AS + FeNP treatment resulted in increased levels of key phenolics (dihydrocapsaicin, capsaicin, p-coumaric acid, sinapic acid, p-OH benzoic acid, p-OH benzaldehyde, and ferulic acid) and flavonoid compounds (dihydroquercetin, naringenin, kaempferol, dihydrokaempferol, and quercetin) compared to the AS treatment, thus suggesting that these secondary metabolites likely contribute to the stabilization of cellular structures and membranes, ultimately supporting improved physiological functions and resilience under stress. In conclusion, the application of FeNP demonstrate potential in enhancing the resilience of bell pepper plants against the AS by improving growth, carbohydrate metabolism, and the levels of secondary metabolites.

Pepper (Capsicum annuum, Solanaceae) fruits are consumed worldwide and are of great economic importance. In most species ripening is characterized by important visual and metabolic changes, the latter including emission of volatile organic compounds associated with respiration, destruction of chlorophylls, synthesis of new pigments (red/yellow carotenoids plus xanthophylls and anthocyanins), formation of pectins and protein synthesis. The involvement of nitric oxide (NO) in fruit ripening has been established, but more work is needed to detail the metabolic networks involving NO and other reactive nitrogen species (RNS) in the process. It has been reported that RNS can mediate post-translational modifications of proteins, which can modulate physiological processes through mechanisms of cellular signalling. This study therefore examined the potential role of NO in nitration of tyrosine during the ripening of California sweet pepper. The NO content of green and red pepper fruit was determined spectrofluorometrically. Fruits at the breaking point between green and red coloration were incubated in the presence of NO for 1 h and then left to ripen for 3 d. Profiles of nitrated proteins were determined using an antibody against nitro-tyrosine (NO2-Tyr), and profiles of nitrosothiols were determined by confocal laser scanning microscopy. Nitrated proteins were identified by 2-D electrophoresis and MALDI-TOF/TOF analysis. Treatment with NO delayed the ripening of fruit. An enhancement of nitrosothiols and nitroproteins was observed in fruit during ripening, and this was reversed by the addition of exogenous NO gas. Six nitrated proteins were identified and were characterized as being involved in redox, protein, carbohydrate and oxidative metabolism, and in glutamate biosynthesis. Catalase was the most abundant nitrated protein found in both green and red fruit. The RNS profile reported here indicates that ripening of pepper fruit is characterized by an enhancement of S-nitrosothiols and protein tyrosine nitration. The nitrated proteins identified have important functions in photosynthesis, generation of NADPH, proteolysis, amino acid biosynthesis and oxidative metabolism. The decrease of catalase in red fruit implies a lower capacity to scavenge H2O2, which would promote lipid peroxidation, as has already been reported in ripe pepper fruit.