From seed to spice: Scientists map the genetic life of chili peppers
image: Transcriptomics functions implemented in Transcriptome data of PFTVD 1.0. A The home page of the PFTVD 1.0. The banner menus show functions included in each tab. Most analyses in ‘Transcriptomics’ will provide the output shown in panels B–E: B transcriptome data; C mRNA expression; D gene network; and E biomarker transcripts.
Credit: Horticulture Research
What makes a chili pepper spicy, colorful, and full of flavor? Scientists have now decoded the genetic journey behind pepper development, using long-read sequencing to build the most comprehensive chili transcriptome to date. By profiling eight tissues across five developmental stages, they uncovered over 485,000 transcripts—most of them previously unknown—revealing how gene expression changes with time and tissue. Key pathways in pigment production, capsaicin biosynthesis, and fruit growth were mapped in detail. The researchers also launched a powerful online platform, the Pepper Full-Length Transcriptome Variation Database (PFTVD 1.0), to share this vast genomic resource with the global community.
Chili peppers (Capsicum annuum L.) are among the most widely cultivated spice crops, valued for their color, flavor, and fiery capsaicinoids. Over the past two decades, advances in genome sequencing have shed light on their evolutionary origins and metabolic complexity. However, existing datasets primarily focus on DNA-level variation, leaving a gap in our understanding of transcript-level changes—particularly those driving traits like fruit maturation and spiciness. Moreover, previous efforts using short-read sequencing fall short in resolving transcript diversity and alternative splicing. Due to these limitations, a high-resolution, transcriptome-wide analysis across tissues and developmental stages is urgently needed to better understand chili pepper biology.
In a study (DOI: 10.1093/hr/uhae198) published on July 24, 2024, in Horticulture Research, researchers from Hunan Agricultural University and collaborators performed full-length transcriptome sequencing on chili pepper tissues at five growth stages. Using Oxford Nanopore Technology, they generated over 1.2 billion high-quality reads and captured the expression profiles of genes across organs such as fruit, placenta, flower, and leaf. The study reveals how transcript diversity and gene regulation shape the fruit's growth, color, and pungency. A user-friendly online database—PFTVD 1.0—was also released, offering interactive tools for exploring tissue-specific expression and splicing events.
The team identified over 485,000 transcripts, of which 450,000 were novel, including long non-coding RNAs and protein-coding variants. Expression patterns varied significantly across tissues, with flowers showing the highest number of specific transcripts. Fruit development showed stage-specific clustering of genes involved in cell differentiation, cellulose biosynthesis, and sugar metabolism. As fruit matured, genes linked to carotenoid and pigment production became highly expressed—especially between 25 and 50 days after flowering. In the placenta, capsaicin content steadily rose alongside the expression of genes from the valine, leucine, and isoleucine degradation and citrate cycle pathways. Transcripts such as ilvE, BCKDHA, and DBT were strongly upregulated, offering new targets for breeding spicier varieties. Widespread alternative splicing events were also observed, with skipped exons being most common. To share these findings, the PFTVD 1.0 platform was created, allowing researchers to visualize and download gene expression data for any tissue or stage.
“This work represents a milestone in chili pepper research,” said Prof. Xuexiao Zou, one of the study’s senior authors. “By sequencing full-length transcripts and mapping their expression over time and space, we can now understand how a pepper builds its heat, color, and form. What’s more, the PFTVD 1.0 database makes this information accessible to researchers and breeders worldwide, empowering future discoveries in plant science and agriculture.”
The launch of PFTVD 1.0 offers a valuable tool for scientists aiming to improve chili pepper yield, nutrition, and flavor. With intuitive search, visualization, and analysis features, the database can support gene discovery, marker-assisted breeding, and functional studies. It enables researchers to pinpoint tissue-specific and developmental gene expression, especially in traits like capsaicin content and pigment accumulation. Beyond peppers, this approach sets a model for applying long-read transcriptomics to other horticultural crops. Ultimately, these insights may lead to the development of climate-resilient, high-quality varieties that meet consumer demand for both flavor and function.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhae198
Funding information
This work was financially supported by Natural Science Foundation of China (32130097, 32302574, 32320103011), and the Ministry of Finance and Ministry of Agriculture and Rural Affairs of China (CARS-24-A05).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.