Tomato (Solanum lycopersicum) is undeniably one of the most globally cultivated and consumed vegetable crops, cherished not only for its vivid red hue and broad culinary applications but also for its rich nutritional profile. However, despite its popularity and widespread use, the characteristic aroma of tomato fruits, a critical factor in flavor perception and consumer preference, has historically been compromised throughout the history of domestication and selective breeding. Many commercial cultivars today lack the sensory complexity and fragrance that wild-type or heirloom varieties once naturally possessed. This deficiency in aroma has driven scientists to explore innovative genetic avenues to reintroduce desirable flavor traits without sacrificing yield or agronomic performance.
Among the volatile organic compounds (VOCs) responsible for aroma in many edible plants, 2-acetyl-1-pyrroline (2-AP) stands out for its distinctive “popcorn-like” scent. In crops such as fragrant rice, the presence of 2-AP significantly enhances consumer appeal, underscoring the potential of this compound to elevate flavor profiles in other economically important species. The biosynthesis of 2-AP is linked to the disruption of the betaine aldehyde dehydrogenase 2 (BADH2) gene. In fragrant rice varieties, loss-of-function mutations in BADH2 lead to the accumulation of gamma-aminobutyraldehyde (GABald), which is then converted enzymatically into 2-AP. This biochemical pathway, however, had not been naturally exploited in tomato cultivars, and until recently, no popcorn-like fragrant tomato genotype had been identified.
In a novel and groundbreaking study, researchers from China and Australia embarked on a pioneering effort to bioengineer tomatoes with enhanced aromatic qualities by targeting homologous genes implicated in 2-AP biosynthesis. Their investigation centered on SlBADH1 and SlBADH2 — two putative homologs of the BADH2 gene identified through comprehensive genome screening in tomato. Utilizing the precision and efficiency afforded by the CRISPR/Cas9 gene editing platform, the team simultaneously disrupted both SlBADH1 and SlBADH2 genes in the popular tomato cultivar Alisa Craig (AC), thereby generating mutant lines with targeted knockouts.
The experimental design included the generation of single mutants for SlBADH1 and SlBADH2 as well as double mutants disrupting both genes. Analytical quantification of 2-AP content revealed a striking increase in fragrance-related compounds. Tomato plants harboring the slbadh2 mutation alone accumulated significantly higher levels of 2-AP compared to wild-type controls, corroborating the predominant role of SlBADH2 in aroma biosynthesis. More remarkably, the double mutants exhibited 2-AP concentrations in fruit and leaf tissues exceeding those of slbadh2 single mutants by more than fourfold, providing compelling evidence that SlBADH1, although secondary, contributes materially to the regulation of 2-AP accumulation. These findings indicate a synergistic influence of both gene loci on the aromatic phenotype in tomato.
Importantly, the genetic modifications introduced did not exert any detrimental effects on central agronomic traits. Measurements including flowering time, plant height, fruit weight, and biochemical markers such as soluble sugars (glucose, fructose, sucrose), organic acids (citric and malic), and vitamin C content remained statistically indistinguishable from wild-type plants. This achievement exemplifies a landmark breakthrough in flavor biofortification: the generation of aromatic tomato lines that maintain optimal yield and quality, dispelling longstanding trade-offs between flavor and productivity.
The generation of fragrant tomato plants via CRISPR/Cas9 technology opens the door for transforming the tomato market by reintroducing complex sensory characteristics that resonate with consumer desires. Traditionally, the erosion of flavor traits in commercial tomatoes was considered an unavoidable consequence of breeding for yield, disease resistance, and uniformity. This study overturns that paradigm by demonstrating that precise genome editing can recuperate and even amplify desirable volatile profiles without compromising core agronomic performance. Potential downstream applications include introgression of these traits into elite commercial cultivars to elevate flavor complexity, much like the success story of fragrant rice varieties.
At the molecular level, the study sheds light on the enzymatic pathways controlling aroma synthesis in Solanum lycopersicum. The SlBADH family encodes enzymes that catalyze the oxidation of betaine aldehyde to betaine, a critical step in secondary metabolite pathways. Loss-of-function mutations in these genes cause a buildup of intermediate aldehydes, shifting metabolic flux toward the synthesis of aroma-enhancing volatiles such as 2-AP. This nuanced understanding of metabolic control and gene regulation enables more targeted manipulations and the potential to fine-tune aroma profiles tailored to consumer preferences or environmental conditions.
The researchers emphasize that ongoing efforts aim to expand the scope of this innovation by applying the CRISPR/Cas9-mediated strategy to commercially relevant tomato cultivars with broader geographic distribution and market presence. The scalability of gene editing, combined with regulatory acceptance of genome-edited crops in various regions, paves the way for rapid translation from proof-of-concept to commercial implementation. This strategy aligns with contemporary consumer trends favoring natural flavor enhancement and minimal processing, positioning the fragrant tomato as a valuable commodity in fresh produce markets and gastronomy.
Beyond immediate agricultural and economic implications, this work exemplifies the versatility and power of CRISPR/Cas9 in plant metabolic engineering. It reinforces the paradigm that precise genetic interventions can resurrect lost traits and engineer novel phenotypes that merge agronomic excellence with consumer-centric quality attributes. Moreover, this approach serves as a blueprint for future endeavors aiming to enhance flavor, nutritional content, or stress resilience in other horticultural crops, fostering sustainable food systems and diversified crop portfolios.
Stepping back, the success of this research underscores the importance of integrating genomics, metabolomics, and advanced gene editing technologies to tackle longstanding challenges in crop improvement. It highlights how a detailed mechanistic understanding of biosynthetic pathways can inform targeted modifications that improve multiple phenotypic layers harmoniously. These findings inspire renewed optimism for breeding programs that aim to reconcile yield, flavor, and nutrition without compromise, thereby enhancing food quality and security.
In conclusion, the pioneering creation of popcorn-like fragrant tomatoes through CRISPR/Cas9-mediated disruption of SlBADH1 and SlBADH2 heralds a new chapter in tomato breeding and flavor improvement. By achieving significant elevation of 2-AP levels without adverse effects on yield or fruit quality, this breakthrough represents a critical milestone with far-reaching implications for food innovation, crop genetics, and consumer satisfaction worldwide.
Subject of Research: Cells
Article Title: Generating popcorn-like fragrant tomato using CRISPR/Cas9-mediated gene editing
Web References: http://dx.doi.org/10.1016/j.jia.2026.01.033
Image Credits: Zheng P, et al.
Keywords: Agriculture, Cell biology, Plant sciences, Molecular biology
