The study evaluated whether integrating genomic, transcriptomic, and drone-derived phenomic data improves prediction of 129 maize traits across nine environments, using both linear (rrBLUP) and nonlinear (SVR) models. Multi-omics models consistently outperformed single-omics models, with transcriptomic data especially enhancing cross‑environment predictions and capturing genotype‑by‑environment interactions. The results highlight the added value of combining transcriptomics and phenomics with genotypes for more accurate and generalizable trait prediction in maize.

Phytoplasma infection in sesame (Sesamum indicum) triggers tissue-specific alterations in gene expression and metabolite composition, with floral organs adopting leaf-like traits and distinct changes in porphyrin, brassinosteroid, and phenylpropanoid pathways. Integrated transcriptomic and metabolomic analyses, supported by biochemical, histological, and qRT-PCR assays, reveal differential stress and secondary metabolite responses between infected leaves and flowers.

The study introduces the Botanical Spectrum Analyzer (BSA), a GUI that incorporates a modified U‑Net deep neural network for accurate segmentation of plant images from RGB and hyperspectral (VNIR and SWIR) data. BSA was tested on wheat, barley, and Arabidopsis datasets, achieving >99% accuracy and F1‑scores above 98%, and markedly outperformed commercial tools on root segmentation tasks.

The study examined how prior light‑acclimation influences the fitness and rapid photoprotective reprogramming of Chlamydomonas during transitions between low and high diurnal light intensities. While high‑light‑acclimated cells struggled to grow and complete the cell cycle after shifting to low light, low‑light‑acclimated cells quickly remodeled thylakoid ultrastructure, enhanced photoprotective quenching, and altered photosystem protein levels, recovering chloroplast function within a single day. Transcriptomic and proteomic profiling revealed swift induction of stress‑response genes, indicating high flexibility in diurnal light acclimation.

The study demonstrates that the chromatin remodeler DDM1 is essential for biomass heterosis in Arabidopsis thaliana hybrids, as loss of DDM1 function leads to reduced rosette growth and extensive genotype‑specific transcriptomic and DNA methylation changes. Whole‑genome bisulfite sequencing revealed widespread hypomethylation in ddm1 mutants, while salicylic acid levels were found unrelated to heterosis, indicating that epigenetic divergence, rather than SA signaling, underpins hybrid vigor.

The study examined how soil phosphorus and nitrogen availability influence wheat root-associated arbuscular mycorrhizal fungal (AMF) communities and the expression of mycorrhizal nutrient transporters. Field sampling across two years combined with controlled pot experiments showed that P and N jointly affect AMF colonisation, community composition (with Funneliformis dominance under high P), and regulation of phosphate, ammonium, and nitrate transporters. Integrating metabarcoding and RT‑qPCR provides a framework to assess AMF contributions to crop nutrition.

Using a controlled field experiment on clonal 35‑year‑old Norway spruce trees, the study examined molecular defense responses to Ips typographus attacks. A multi‑omics approach revealed rapid local increases in jasmonic acid and other phytohormones, leading to differential expression of up to 1,900 genes and corresponding proteomic and metabolomic changes that elevated deterrent compounds such as phenolic aglycones, diterpene resin acids, terpenes, and lignin.

The study applied a progressive, sublethal drought treatment to Arabidopsis thaliana, collecting time‑resolved phenotypic and transcriptomic data. Machine‑learning analysis revealed distinct drought stages driven by multiple overlapping transcriptional programs that intersect with plant aging, and identified high‑explanatory‑power transcripts as biomarkers rather than causal agents.

Salt stress strongly suppresses root growth in Festuca rubra while sparing shoot development. Transcriptome profiling identified over 68,000 differentially expressed genes, with up‑regulated genes enriched in methionine, melatonin, and suberin biosynthesis and down‑regulated genes involved in gibberellin, ABA, and sugar signaling, indicating extensive hormonal and metabolic reprogramming. Paradoxical regulation of gibberellin and ethylene pathways suggests a finely tuned balance between growth and stress responses.

The study presents a high-quality genome assembly for the nickel hyperaccumulator Noccaea caerulescens and uses it as a reference for comparative transcriptomic analyses across different N. caerulescens accessions and the non‑accumulating relative Microthlaspi perfoliatum. It identifies a limited set of metal transporters (NcHMA3, NcHMA4, NcIREG2, and NcIRT1) whose elevated expression correlates with hyperaccumulation, and demonstrates that frameshift mutations in NcIRT1 can abolish the trait, indicating an ancient, transporter‑driven origin of nickel hyperaccumulation.