Stem strength is a key agronomic trait that influences planting adaptability and mechanical harvesting efficiency. Pepper is the most widely cultivated vegetable crop in China, and full mechanization of its production is crucial for enhancing quality and productivity. In the preliminary stage of this study, transcriptomic analysis was performed on pepper accessions exhibiting substantial differences in stem strength at various developmental stages. Through weighted gene co-expression network analysis focused on genes involved in cell wall biosynthesis and transport, a candidate gene potentially regulating stem strength, designated CaDUF642.01, was identified. The CaDUF642.01 protein contains two DUF642 domains and localizes to the cell wall, plasma membrane, and nucleus. Silencing CaDUF642.01 led to a 42.17% decrease in soluble pectin content, a 1.63% reduction in water content, a 43.18% shortening of internode length, and more compact cell arrangement. Furthermore, CaDUF642.01 was shown to directly interact with pectin methylesterase 2 (CaPME2), forming a protein complex that modulates pectin methylation levels via regulation of random PME demethylesterification, thereby influencing stem strength. Our results demonstrate that the CaDUF642.01-CaPME2 complex attenuates stem strength by altering pectin composition through PME activity, which also increases stem water content and promotes looser parenchyma cell packing. This study reveals a novel regulatory mechanism of stem strength in pepper, providing a theoretical basis for manipulating plant architecture and breeding mechanization-adapted pepper varieties.

Heterosis is a highly effective strategy for increasing yield and quality of pepper (Capsicum annuum L.). Although genic male sterile (GMS) lines offer advantages for seed production by avoiding the limitations associated with cytoplasmic male sterile lines, their use typically requires the labor-intensive removal of 50% of fertile plants during seed production. To address this challenge, we identified an anthocyanidin-absent (aa) mutant characterized by green hypocotyls at the seedling stage and yellow anthers. We identified dihydroflavonol 4-reductase (CaDFR) as a key gene regulating anthocyanin biosynthesis in pepper through fine mapping and virus-induced gene silencing. Genetic segregation analysis revealed that CaDFR and CaDYT1 (a GMS gene) were closely linked. Based on this finding, we developed an efficient hybrid seed production strategy for screening sterile plants at the seedling-stage by combining the green hypocotyl morphological marker from the aa mutant with the male sterile line gms1 (CaDYT1 locus). In conclusion, we successfully cloned CaDFR, a key gene controlling hypocotyl and anther color in pepper. In addition, we proposed an efficient seed propagation strategy to accelerate hybrid seed production and facilitate the utilization of heterosis. This study not only deepens our understanding of the genetic regulation of pepper pigmentation but also establishes a practical framework for optimizing hybrid breeding protocols, thereby simplifying the pepper breeding process.

The transcription factor BRASSINAZOLE-RESISTANT 1 (BZR1) plays a crucial role not only in plant responses to various biotic and abiotic stresses but also serves a critical function in plant growth and development. In this study, we analyzed the origin and evolution of the BZR family in plants. Then, we identified nine CaBZR1 genes from the pepper pan-genome and performed bioinformatics analyses. Through the integration of transcriptome data analysis with our prior bioinformatics findings, we have identified and selected a specific member of the CaBZR1 family, CaBZR1.2, for further comprehensive investigation. We systematically investigated the biological function of CaBZR1.2 in pepper through classical reverse genetics approaches and subsequently identified proteins that interact with CaBZR1.2. After inhibiting the expression of CaBZR1.2 via virus-induced gene silencing (VIGS), the growth of pepper lateral branches was significantly suppressed, whereas heterologous overexpression of CaBZR1.2 increased lateral branch number in tomato. This result confirms the key role of CaBZR1.2 in the development of pepper lateral branches. Furthermore, protein-protein interaction assays confirmed that the Sucrose Nonfermenting 1-Related Protein Kinase 1 β subunit 2 (CaSnRK1β2) protein interacts with CaBZR1.2, with subsequent analyses revealing that these two proteins modulate pepper lateral branch development through a mutually antagonistic regulatory mechanism. This study reveals a novel mechanism by which CaBZR1.2 and CaSnRK1β2 coordinately regulate lateral branch development in pepper, providing candidate genes and a theoretical basis for the molecular breeding for pepper plant architecture.

Since its introduction to China in the late 16th century, Capsicum has transitioned from an exotic crop into a cornerstone of Chinese agriculture. This review examines the industry’s historical dissemination and current landscape, which now spans over 2.25 million hectares and yields exceeding 64 million tons annually. This scale supports a vertically integrated value chain, ranging from germplasm breeding and regionalized cultivation to extensive primary and advanced processing. Furthermore, we analyze cultivation practices, consumption dynamics and socioeconomic implications, while offering a strategic outlook on the industry’s global competitiveness. These findings highlight the integral role of Capsicum in shaping China’s culinary traditions and its significance as a pivotal component of the national agricultural economy.

The full text of this preprint has been withdrawn by the authors due to author disagreement with the posting of the preprint. Therefore, the authors do not wish this work to be cited as a reference. Questions should be directed to the corresponding author.

This study evaluated the efficacy of two distinct Enzyme-Linked Immunosorbent Assay (ELISA) kits for quantifying total capsaicinoids in dried peppers, benchmarked against High-Performance Liquid Chromatography (HPLC) as the reference method. Our analysis revealed a high correlation between the results from the ELISA-1 kit and HPLC (R-2 = 0.9335, p < 0.0001), confirming its accuracy and reliability. In contrast, the ELISA-2 kit proved unsuitable, yielding inconsistent data. To maximize the utility of the more cost-effective ELISA-1 assay, we systematically optimized its extraction protocol. The optimal conditions were established as using 80-mesh sieved pericarp powder, 95 % ethanol as the extraction solvent, and an ultrasonic treatment of 15 min, which significantly enhanced capsaicinoid recovery. Consequently, this research establishes an optimized protocol, validated through its strong correlation with HPLC, that offers an efficient and economical workflow for capsaicinoid analysis. This provides a valuable tool for high-throughput screening in pepper breeding programs and for industrial quality control.

Extreme heat driven by climate change poses a catastrophic threat to global vegetable production, undermining nutritional security because of the heightened physiological sensitivity and succulent tissues of these crops. This review synthesizes the multistage impacts of heat stress across critical developmental phases-from germination to reproduction-emphasizing morphological impairments (such as leaf wilting and floral abortion) and physiological disruptions (including photosynthetic inhibition and oxidative damage). We systematically dissect thermotolerance mechanisms in vegetables, highlighting transcriptional reprogramming by HSFs, WRKY, and NAC transcription factors; chaperone-mediated proteostasis via HSPs; epigenetic remodeling; Ca2+-ROS signaling pathways; and the role of phase separation dynamics. Importantly, we propose six strategic pathways to develop heat-resilient vegetables: harnessing natural variation through pan-genome-driven allele mining; employing biotechnological interventions such as CRISPR-mediated editing and synthetic promoters; engineering multistress tolerance by targeting conserved 'core response' pathways; exploiting epigenetic memory to achieve transgenerational resilience; optimizing source-sink dynamics with ''Climate-Responsive Carbon Optimization; and applying plant growth regulators and nanotechnology to enhance thermotolerance. Together, these strategies chart a clear roadmap for climate-smart vegetable breeding and call for interdisciplinary collaboration to translate molecular discoveries into practical breeding approaches for sustainable food systems under escalating thermal extremes.

Pepper (Capsicum annuum L.), recognized as a globally preeminent vegetable, holds substantial economic and nutritional value. The BTB (broad-complex, tramtrack, and bric-a-brac) family of proteins, characterized by a highly conserved BTB domain, also denoted as the POZ domain, are intricately involved in a diverse array of biological processes. However, the existing corpus of research regarding pepper BTB genes remains relatively meager. In this study, a total of 72 CaBTB gene members were meticulously identified from the entire genome of pepper. Phylogenetic analysis illuminated the presence of conspicuous collinear relationships between the CaBTB genes and those of its closely affiliated species. Gene expression profiling and RT-qPCR analysis revealed that multiple CaBTB genes exhibited pronounced differential expression under diverse treatment regimens. Expression pattern analysis unveiled that CaBTB25 manifested a remarkably elevated abundance in leaves. Moreover, its promoters were replete with an abundance of light-responsive cis-elements. Our comprehensive and in-depth explorations into subcellular localization revealed that CaBTB25 was predominantly detected to localize within the nucleus and lacked transcriptional activation. This research provides a crucial theoretical edifice, enabling a more profound understanding of the biological functions of the BTB gene family in pepper, thereby underscoring its potential significance within the intricate network of gene-environment interactions.

Chili pepper is an important spice and a model plant for fruit development studies. Large-scale omics information on chili pepper plant development continues to be gathered for understanding development as well as capsaicin biosynthesis. In this study, a full-spectrum transcriptome data of eight chili pepper tissues at five growth stages using the Oxford Nanopore long-read sequencing approach was generated. Of the 485 351 transcripts, 35 336 were recorded as reference transcripts (genes), while 450 015 were novel including coding, lnc, and other non-coding RNAs. These novel transcripts belonged to unknown/intergenic (347703), those retained introns (26336), and had multi-exons with at least one junction match (20333). In terms of alternative splicing, retained intron had the highest proportion (14795). The number of tissue-specific expressed transcripts ranged from 22 925 (stem) to 40 289 (flower). The expression changes during fruit and placenta development are discussed in detail. Integration of gene expression and capsaicin content quantification throughout the placental development clarifies that capsaicin biosynthesis in pepper is mainly derived from valine, leucin, and isoleucine degradation as well as citrate cycle and/or pyrimidine metabolism pathways. Most importantly, a user-friendly Pepper Full-Length Transcriptome Variation Database (PFTVD 1.0) (http://pepper-database.cn/) has been developed. PFTVD 1.0 provides transcriptomics and genomics information and allows users to analyse the data using various tools implemented. This work highlights the potential of long-read sequencing to discover novel genes and transcripts and their diversity in plant developmental biology.

Plant stems constitute the most abundant renewable resource on earth. The function of lysine (K)-2-hydroxyisobutyrylation (K-hib), a novel post-translational modification (PTM), has not yet been elucidated in plant stem development. Here, by assessing typical pepper genotypes with straight stem (SS) and prostrate stem (PS), we report the first large-scale proteomics analysis for protein K-hib to date. K-hib-modifications influenced central metabolic processes involved in stem development, such as glycolysis/gluconeogenesis and protein translation. The high K-hib level regulated gene expression and protein accumulation associated with cell wall formation in the pepper stem. Specially, we found that CaMYB61 knockdown lines that exhibited prostrate stem phenotypes had high K-hib levels. Most histone deacetylases (HDACs, e.g., switch-independent 3 associated polypeptide function related 1, AFR1) potentially function as the "erasing enzymes" involved in reversing K-hib level. CaMYB61 positively regulated CaAFR1 expression to erase K-hib and promote cellulose and hemicellulose accumulation in the stem. Therefore, we propose a bidirectional regulation hypothesis of "K-hib modifications" and "K-hib erasing" in stem development, and reveal a novel epigenetic regulatory network in which the CaMYB61-CaAFR1 molecular module participating in the regulation of K-hib levels and biosynthesis of cellulose and hemicellulose for the first time.

Chlorophylls and carotenoids are 2 pivotal photosynthetic pigments directly influencing the economic value of pepper (Capsicum annuum L.) fruits. However, the coordinated regulatory mechanisms governing the accumulation of both chlorophylls and carotenoids during pepper fruit development remain elusive. In this study, pepper B-box 10 (CaBBX10), a candidate hub transcription factor, was found to play dual roles in the early development of pepper fruit. CaBBX10 virus-induced gene silencing and overexpression experiments demonstrated that the encoded transcription factor promotes both chlorophyll and carotenoid accumulation in pepper fruit. Further comprehensive analyses showed that CaBBX10 directly binds to the promoter of magnesium chelatase subunit D subunit (CaCHLD) and phytoene synthase 1 (CaPSY1), thereby activating their expression in the chlorophyll and carotenoid biosynthesis pathways, respectively. Additionally, the photomorphogenic factor CaCOP1 was found to physically interact with CaBBX10 and lead to its degradation. Therefore, CaBBX10 may serve as a critical link connecting chlorophyll and carotenoid biosynthesis to light signaling. Altogether, our findings reveal a mechanism for the complex transcriptional regulation that simultaneously promotes chlorophyll and carotenoid accumulation in pepper fruit.

Cytoplasmic male sterility (CMS) is pivotal in plant breeding and widely employed in various crop hybrids, including pepper. However, the functional validation of the restorer of fertility (Rf) gene in pepper has been lacking until now. This study identifies and characterizes CaRf, a single dominant locus crucial for restoring CMS in the pepper strong recovery inbred line Zhangshugang. The CaRf gene encodes a mitochondria-targeted pentatricopeptide repeat protein, validated through the induction of male sterility upon its silencing in hybrid F1 plants. To enhance pepper breeding efficiency, 176 important pepper breeding parent materials were resequenced, and a PepperSNP50K liquid-phase breeding chip was developed, comprising 51 172 markers. Integration of CaRf functional characterization and PepperSNP50K facilitated the development of a high-quality red pepper hybrid. These findings provide significant insights and practical strategies for advancing molecular-designed breeding in peppers.

Light quality and intensity can have a significant impact on plant health and crop productivity. Chlorophylls and carotenoids are classes of plant pigments that are responsible for harvesting light energy and protecting plants from the damaging effects of intense light. Our understanding of the role played by plant pigments in light sensitivity has been aided by light-sensitive mutants that change colors upon exposure to light of variable intensity. In this study, we conducted transcriptomic, metabolomic, and hormone analyses on a novel yellowing mutant of pepper (yl1) to shed light on the molecular mechanism that regulates the transition from green to yellow leaves in this mutant upon exposure to high-intensity light. Our results revealed greater accumulation of the carotenoid precursor phytoene and the carotenoids phytofluene, antheraxanthin, and zeaxanthin in yl1 compared with wild-type plants under high light intensity. A transcriptomic analysis confirmed that enzymes involved in zeaxanthin and antheraxanthin biosynthesis were upregulated in yl1 upon exposure to high-intensity light. We also identified a single basic helix-loop-helix (bHLH) transcription factor, bHLH71-like, that was differentially expressed and positively correlated with light intensity in yl1. Silencing of bHLH71-like in pepper plants suppressed the yellowing phenotype and led to reduced accumulation of zeaxanthin and antheraxanthin. We propose that the yellow phenotype of yl1 induced by high light intensity could be caused by an increase in yellow carotenoid pigments, concurrent with a decrease in chlorophyll accumulation. Our results also suggest that bHLH71-like functions as a positive regulator of carotenoid biosynthesis in pepper.

Capsaicinoids are naturally specialized metabolites in pepper and are the main reason that Capsicum fruits have a pungent smell. During the synthesis of capsaicin, MYB transcription factors play key regulatory roles. In particular, R2R3-MYB subfamily genes are the most important members of the MYB family and are critical candidate factors in capsaicinoid biosynthesis. The 108 R2R3-MYB genes in pepper were identified in this study and all are shown to have two highly conserved MYB binding domains. Phylogenetic and structural analyses clustered CaR2R3-MYB genes into seven groups. Interspecies collinearity analysis found that the R2R3-MYB family contains 16 duplicated gene pairs and the highest gene density is on chromosome 00 and 03. The expression levels of CaR2R3-MYB differentially expressed genes (DEGs) and capsaicinoid-biosynthetic genes (CBGs) in fruit development stages were obtained via RNA-seq and quantitative polymerase chain reaction (qRT-PCR). Co-expression analyses reveal that highly expressed CaR2R3-MYB genes are co-expressed with CBGs during early stages of pericarp and placenta development processes. It is speculated that six candidate CaR2R3-MYB genes are involved in regulating the synthesis of capsaicin and dihydrocapsaicin. This study is the first systematic analysis of the CaR2R3-MYB gene family and provided references for studying their molecular functions. At the same time, these results also laid the foundation for further research on the capsaicin characteristics of CaR2R3-MYB genes in pepper.

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.

在人类发展的过程中,有很多不起眼的小东西,它们却代表着文明的一段进程.辣椒起源于南美,但是新航路的开辟改变了这一切,现今辣椒已遍植于整个世界,是人类餐桌上流传最广的香料和常用蔬菜.湖南人性格具野性,且豪放,加之尚滋味,好辛香,故辣椒入湘,洗却香料的神秘,在瘴湿之地盛行,甚至融入湘人的性格,滋养出湘人无辣不欢、敢为人先的辣椒精神,成为湖湘文化中不可或缺的重要元素,对中国社会产生了深远影响.从辣椒的起源与种类、辣椒入湘简史、辣椒与湖湘人文精神、辣椒与湖湘饮食风尚等方面进行了阐述,并对辣椒与湖湘文化的融合、传承及创新进行了提炼与诠释,彰显了浓郁的地域文化特色.湘人自强坚韧,注重经世致用,讲究社会责任感和使命感,有着桀骜骁勇的精神品性和宏阔志向,而辣椒所具备的热辣奔放气息则成为湖湘文化革故鼎新的精神图腾和创造精神驱动的典范.

An analysis of genome-wide gene expression profiles during floral organ development can provide important clues about the molecular basis of gene functions and developmental processes. In this study, we analyzed the transcriptome data of 36 samples obtained during floral organ development from pepper ‘6421’ and detected 30 016 genes that were expressed in at least one sample. K-means clustering analysis was used to classify the data into 16 clusters based on the similarities between the dynamic expression profiles of genes. Of these, 15 clusters exhibited notable up-regulation or down-regulation trends in different developmental stages or tissues of floral organs. We identified transcription factors expressed at the early, medium, and late stages of bud development (F1, F5, F9). Transcription factor families such as AP2-ERF, MADS-box, MYB, bHLH, and NAC showed significant levels of enrichment. In comparison with genes expressed in vegetative tissues at different stages, certain genes were specifically up-regulated during flower development; among these, the number of genes specifically up-regulated during the stamen (Sta10) and bud tetrad development (F4) stages was the highest. Through extensive studies of the ABCDE model of flower development in Arabidopsis, we identified 17 ABCDE model candidate genes in pepper, most of which were up-regulated at specific stages of flower bud development. The expression data provided in this study is the most comprehensive dataset available for pepper to date and will serve as a resource for identifying the functions of many specific genes involved in flower development in pepper and other Solanaceae plants.

Chili pepper is an important economic vegetable worldwide. MYB family gene members play an important role in the metabolic processes in plant growth and development. In this study, 103 pepper MYB-related members were identified and grouped into nine subfamilies according to phylogenetic relationships. Additionally, a total of 80, 20, and 37 collinear gene pairs were identified between pepper and tomato, pepper and Arabidopsis, and tomato and Arabidopsis, respectively. We performed promoter cis-element analysis and showed that CaMYB-related members may be involved in multiple biological processes such as growth and development, secondary metabolism, and circadian rhythm regulation. Expression pattern analysis indicated that CaMYB37 is significantly more enriched in fruit placenta, suggesting that this gene may be involved in capsaicin biosynthesis. Through VIGS, we confirmed that CaMYB37 is critical for the biosynthesis of capsaicin in placenta. Our subcellular localization studies revealed that CaMYB37 localized in the nucleus. On the basis of yeast one-hybrid and dual-luciferase reporter assays, we found that CaMYB37 directly binds to the promoter of capsaicin biosynthesis gene AT3 and activates its transcription, thereby regulating capsaicin biosynthesis. In summary, we systematically identified members of the CaMYB-related family, predicted their possible biological functions, and revealed that CaMYB37 is critical for the transcriptional regulation of capsaicin biosynthesis. This work provides a foundation for further studies of the CaMYB-related family in pepper growth and development.

The mechanism of resistance of plants to cold temperatures is very complicated, and the molecular mechanism and related gene network in pepper are largely unknown. Here, during cold treatment, we used cluster analysis (k-means) to classify all expressed genes into 15 clusters, 3,680 and 2,405 differentially expressed genes (DEGs) were observed in the leaf and root, respectively. The DEGs associated with certain important basic metabolic processes, oxidoreductase activity, and overall membrane compositions were most significantly enriched. In addition, based on the homologous sequence alignment of Arabidopsis genes, we identified 14 positive and negative regulators of the ICE-CBF-COR module in pepper, including CBF and ICE, and compared their levels in different data sets. The correlation matrix constructed based on the expression patterns of whole pepper genes in leaves and roots after exposure to cold stress showed the correlation between 14 ICE-CBF-COR signaling module genes, and provided insight into the relationship between these genes in pepper. These findings not only provide valuable resources for research on cold tolerance, but also lay the foundation for the genetic modification of cold stress regulators, which would help us achieve improved crop tolerance. To our knowledge, this is the first study to demonstrate the relationship between positive and negative regulators related to the ICE-CBF-COR module, which is of great significance to the study of low-temperature adaptive mechanisms in plants.