The study used untargeted metabolomics and QTL mapping in a tomato recombinant inbred line population to characterize root exudate composition and identify genetic loci controlling specific metabolites. It reveals domestication-driven changes in exudate profiles and links metabolic QTLs with previously reported microbial QTLs, suggesting a genetic basis for shaping the root microbiome.

The study identifies the serine/arginine-rich splicing factor RS2Z36 as a key regulator of ovary patterning and early fruit morphology in tomato, with loss‑of‑function mutants producing smaller, ellipsoid fruits and elongated pericarp cells. RNA‑seq and proteomic analyses reveal widespread alternative splicing and altered protein abundance, including novel splice‑variant peptides, while mutant pericarps show increased deposition of LM6‑detected arabinan and AGP epitopes.

The study functionally characterizes a conserved structured RNA motif (45ABC) in Arabidopsis RBP45 pre‑mRNAs, showing that its sequence and pairing elements mediate a negative auto‑ and cross‑regulatory feedback loop through alternative splicing that produces unproductive isoforms and reduces RBP45 expression. Transcriptome‑wide splicing analysis and phenotypic assessment of rbp45 mutants reveal that RBP45B plays a dominant role and that proper regulation of this motif is essential for root growth and flowering time.

The study investigates the molecular basis of heat‑tolerant pollen tube growth in tomato (Solanum lycopersicum) by comparing thermotolerant and sensitive cultivars. Using live imaging, transcriptomics, proteomics, and genetics, the authors identified the Rapid Alkalinization Factor (RALF) signaling pathway as a key regulator of pollen tube integrity under high temperature, with loss of a specific RALF peptide enhancing tube integrity in a thermotolerant cultivar.

A large-scale proteomic study in Arabidopsis thaliana identified over 32,000 isoform-specific peptides, confirming that alternative splicing, particularly intron retention, produces translated protein isoforms. Integrated proteogenomic analysis, SUPPA classification, and AlphaFold modeling revealed structural impacts and a non-linear regulation of transcript and protein abundance, with mutant phenotypes linking splicing to growth, chlorophyll content, and anthocyanin accumulation.

The study applied limited proteolysis‑coupled mass spectrometry (LiP‑MS) to map JA‑protein interactions, validating known JA binders and uncovering novel candidates, including several UDP‑glucuronosyltransferases (UGTs). Functional omics, biochemical, enzymatic, and structural analyses demonstrated that two tomato UGTs glucosylate jasmonic acid, revealing a previously missing step in JA catabolism.

The study assessed the impact of adding mammalian growth factors and cytokines to transformation media on CRISPR‑Cas9–mediated genome editing in six tomato (Solanum lycopersicum) accessions with varying regeneration capacities. Over three years, supplementation with these factors significantly increased regeneration rates and the production of stable secondary transgenic lines, especially in recalcitrant genotypes.

The researchers created tomato lines overexpressing the autophagy gene SlATG8f and evaluated their performance under high-temperature stress. qRT‑PCR and physiological measurements revealed that SlATG8f overexpression enhances expression of autophagy‑related and heat‑shock protein genes, accelerates fruit ripening, and improves fruit quality under heat stress.

Proteomic comparison of mock‑ and potato spindle tuber viroid‑infected tomato revealed a broad down‑regulation of nucleoporins and nuclear transport receptors, leading to impaired nuclear import of the immune regulator NPR1. Overexpression of NPR1 or treatment with a salicylic‑acid analog restored defense and reduced PSTVd infection, highlighting nuclear transport repression as a key vulnerability in plant immunity against viroids.

The study isolated an endophytic Pseudomonas aeruginosa strain (SPT08) from tomato cotyledon seedlings that suppressed the wilt pathogen Ralstonia pseudosolanacearum and promoted plant growth, increasing height by 20% and root biomass by 60%. GFP labeling confirmed endophytic colonization, and genomic analysis revealed multiple secretion systems and secondary‑metabolite gene clusters associated with biocontrol and growth‑promoting traits.