Background: Leaf variegation is an intriguing phenomenon observed in many plant species. However, questions remain on its mechanisms causing patterns of different colours. In this study, we describe a tomato plant detected in an M₂ population of EMS mutagenised seeds, showing variegated leaves with sectors of dark green (DG), medium green (MG), light green (LG) hues, and white (WH). Cells and tissues of these classes, along with wild-type tomato plants, were studied by light, fluorescence, and transmission electron microscopy. We also measured chlorophyll a/b and carotene and quantified the variegation patterns with a machine-learning image analysis tool. We compared the genomes of pooled plants with wild-type-like and mutant phenotypes in a segregating F₂ population to reveal candidate genes responsible for the variegation. Results: A genetic test demonstrated a recessive nuclear mutation caused the variegated phenotype. Cross-sections displayed distinct anatomy of four-leaf phenotypes, suggesting a stepwise mesophyll degradation. DG sectors showed large spongy layers, MG presented intercellular spaces in palisade layers, and LG displayed deformed palisade cells. Electron photomicrographs of those mesophyll cells demonstrated a gradual breakdown of the chloroplasts. Chlorophyll a/b and carotene were proportionally reduced in the sectors with reduced green pigments, whereas white sectors have hardly any of these pigments. The colour segmentation system based on machine-learning image analysis was able to convert leaf variegation patterns into binary images for quantitative measurements. The bulk segregant analysis of pooled wild-type-like and variegated progeny enabled the identification of SNP and InDels via bioinformatic analysis. The mutation mapping bioinformatic pipeline revealed a region with three candidate genes in chromosome 4, of which the FtsH-like protein precursor (LOC100037730) carries an SNP that we consider the causal variegated phenotype mutation. Phylogenetic analysis shows the candidate is evolutionary closest to the Arabidopsis VAR1. The synonymous mutation created by the SNP generated a miRNA binding site, potentially disrupting the photoprotection mechanism and thylakoid development, resulting in leaf variegation. Conclusion: We described the histology, anatomy, physiology, and image analysis of four classes of cell layers and chloroplast degradation in a tomato plant with a variegated phenotype. The genomics and bioinformatics pipeline revealed a VAR1-related FtsH mutant, the first of its kind in tomato variegation phenotypes. The miRNA binding site of the mutated SNP opens the way to future studies on its epigenetic mechanism underlying the variegation.

Microsorum scolopendria is an important medicinal plant that belongs to the Polypodiaceae family. In this study, we analyzed the effects of foliar spraying of chitosan on growth promotion and 20-hydroxyecdysone (20E) production in M. scolopendria. Treatment with chitosan at a concentration of 50 mg/L in both young and mature sterile fronds induced the highest increase in the amount of accumulated 20E. Using RNA sequencing, we identified 3552 differentially expressed genes (DEGs) in response to chitosan treatment. The identified DEGs were associated with 236 metabolic pathways. We identified several DEGs involved in the terpenoid and steroid biosynthetic pathways that might be associated with secondary metabolite 20E biosynthesis. Eight upregulated genes involved in cholesterol and phytosterol biosynthetic pathway, five upregulated genes related to the methylerythritol 4-phosphate (MEP) and mevalonate (MVA) pathways, and several DEGs that are members of cytochrome P450s and ABC transporters were identified. Quantitative real-time RT-PCR confirmed the results of RNA-sequencing. Taken together, we showed that chitosan treatment increased plant dry weight and 20E accumulation in M. scolopendria. RNA-sequencing and DEG analyses revealed key enzymes that might be related to the production of the secondary metabolite 20E in M. scolopendria.

Durio zibethinus Murr., commonly known as durian or the “King of Fruits,” is prized for its strong aroma, spiny rind, and unique flavor. With global demand rising, it has become a key export, especially for Thailand, which led the market in 2024 with US$4.4 billion in revenue. However, breeding efforts are hindered by limited genetic diversity research, long generation times, and environmental sensitivity. These challenges are compounded by weak enforcement of intellectual property protections under Thailand’s Plant Variety Protection Act (PVP), which limits incentives for breeders. To address this, Thailand has turned to Geographical Indications (GIs) to protect and promote region-specific varieties. By 2024, 17 GI designations were granted across 16 provinces, including the notable Monthong durian from Pakchong in Nakhon Ratchasima. Although classified under the Monthong group, genetic similarity was observed, while notable phenotypic variation exists among varieties. These differences may be attributed to specific agronomic or genetic traits, warranting investigation into the cultivation characteristics that influence consumer-related qualities and preferences. Strengthening supply chain standards through good agricultural practices, GIs, genetic profiling, and international certification, combined with the adoption of modern molecular breeding tools including marker-assisted selection, genomic selection, and CRISPR/Cas9, would support sustainable innovation, improved farmer revenues, and long-term global competitiveness in the durian industry across Southeast Asia.

Durio zibethinus Murr., commonly known as durian or the "King of Fruits," is prized for its strong aroma, spiny rind, and unique flavor. With global demand rising, it has become a key export, especially for Thailand, which led the market in 2024 with US$4.4 billion in revenue. However, breeding efforts are hindered by limited genetic diversity research, long generation times, and environmental sensitivity. These challenges are compounded by weak enforcement of intellectual property protections under Thailand’s Plant Variety Protection Act (PVP), which limits incentives for breeders. To address this, Thailand has turned to Geographical Indications (GIs) to protect and promote region-specific varieties. By 2024, 17 GI designations were granted across 16 provinces, including the notable Monthong durian from Pakchong in Nakhon Ratchasima. Although classified under the Monthong group, genetic similarity was observed, while notable phenotypic variation exists among varieties. These differences may be attributed to specific agronomic or genetic traits, warranting investigation into the cultivation characteristics that influence consumer-related qualities and preferences. Strengthening supply chain standards through good agricultural practices, GIs, genetic profiling, and international certification would support sustainable economic growth, improved farmer revenues, and long-term global competitiveness in the durian industry.