Elucidation of fruit cracking mechanism in bael [Aegle marmelos (L.) Correa.] using physico-biochemical and de novo transcriptomic approaches

• This study presents the first integrated biochemical and transcriptomic analysis of bael fruit cracking, identifying key biochemical constituents, genes, and pathways involved. • Cracking-tolerant genotypes exhibited significantly higher Ca and B levels in the fruit skull and pulp, while genes related to Ca and B metabolism and transport were highly downregulated in cracking-susceptible genotypes. • Vanillic acid was found in the highest concentration across all cracking-susceptible genotypes. • Differentially expressed genes (DEGs) associated with proline biosynthesis were highly upregulated, while genes involved in phenolics and flavonoid biosynthesis were significantly downregulated in cracking-tolerant genotypes. Fruit cracking in Bael [ Aegle marmelos (L) Correa.] is a major physiological disorder which is influenced by factors like water stress, nutrient deficiency, and environmental conditions. This study aimed to identify key biochemical constituents, genes, and pathways affecting fruit cracking using physical, biochemical, and transcriptomic analyses. Bael genotypes were categorized into three groups based on cracking incidence as tolerant (0 % cracking), moderately tolerant (>0–30 % cracking), and susceptible (>30 % cracking). Three genotypes from each category were selected for further analysis. Biochemical profiling revealed that total flavonoids, antioxidants, vanillic acid and soluble carbohydrates were predominant in the cracking-susceptible genotypes, while calcium and boron levels were significantly lower in these genotypes. Transcriptomic analysis using susceptible (Pant Aparna) and tolerant genotypes (ICAR-RCER 8–5) identified differentially expressed genes (DEGs) associated with cell wall and polysaccharide metabolism, phenolics and flavonoid biosynthesis, plant hormone biosynthesis and signaling, nutrient transport. Interestingly, aquaporin-encoding genes were found significantly upregulated in the cracking stage, while genes involved in MAPK signaling showed higher expression in the susceptible genotype. These transcriptomic changes were corroborated by biochemical findings, reinforcing their role in bael fruit cracking susceptibility. The insights gained from this study provide a foundation for developing cracking-tolerant bael cultivars and formulating management strategies to mitigate fruit cracking in bael.