During transgenic plant production, tissue culture often carries epigenetic, and genetic changes that underlie somaclonal variations, leading to unpredictable phenotypes. Additionally, specific treatments for rice (Oryza sativa) transformation processes may individually or jointly contribute to somaclonal variations, but their specific impacts on rice epigenomes toward transcriptional variations remain unknown. Here, the impact of individual transformation treatments on genome-wide DNA methylation and the transcriptome were examined. In addition to activating stress-responsive genes, individual transformation components targeted different gene expression modules that were enriched in specific functional categories. The transformation treatments strongly impacted DNA methylation and expression; 75% were independent of tissue culture. Furthermore, our genome-wide analysis showed that the transformation treatments consistently resulted in global hypo-CHH methylation enriched at promoters highly associated with downregulation, particularly when the promoters were colocalized with miniature inverted-repeat transposable elements. Our results clearly highlight the specificity of impacts triggered by individual transformation treatments during rice transformation with the potential association between DNA methylation and gene expression. These changes in gene expression and DNA methylation resulting from rice transformation treatments explain a significant portion of somaclonal variations, that is, way beyond the tissue culture effect.

Plant factories offer a promising opportunity for fresh food production due to their minimal land requirements. Among the adjustable factors in the production system of plant factories, light serves as a critical element, significantly influencing both crop yield and quality. Cilantro, a prevalent culinary herb and a traditional flavoring agent, plays a crucial role in Taiwanese gastronomy. This research investigated cilantro plants grown under nine different light treatments with varying red to far-red ratios and green light percentages over a 49-day period. Results demonstrate that maximum fresh and dry biomass accumulation in both shoot and root tissues occurred under treatments with red to far-red ratios of approximately of 1.8 combined with medium green light intensity. Conversely, medium far-red ratios negatively affected lutein and carotenoid concentrations in foliar tissues. Carotenoid biosynthesis exhibited an inverse relationship with green light intensity, with lower green light percentages corresponding to significantly higher carotenoid concentrations. In terms of energy efficiency, a red to far-red ratio of approximately 1.8 yielded the highest energy yield (g kWh⁻¹) and photon yield (g mol⁻¹), indicating optimal energy conversion efficiency under this spectral composition. In conclusion, this study demonstrates that cilantro cultivation under R53G05B13FR29 spectral composition (53% red, 5% green, 13% blue, 29% far-red) with a 49-day production cycle maximizes biomass while optimizing energy utilization efficiency.

Over the last decades, world agriculture has suffered from soil salinity problems such as nutrient deficiency and salt toxicity. The use of plant growth-promoting bacteria (PGPR) has been widely reported to alleviate salt stress and promote plant growth via various mechanisms including the decrease in ethylene levels and the increase of bioavailability of nutrients. We have tested 39 bacteria stains for their plant growth-promoting traits such as 1-aminocylopropane-1-carboxylate (ACC) deaminase, indole acetic acid (IAA) production as well as phosphate solubilization. The results showed that 33 isolates produced ACC deaminase, ranging from 0.3 to 35.0 µmol -KA/mg/h and 27 isolates produced IAA from 1.4-59.9 µg/mL. Sixteen isolates showed the ability to solubilize bio-unavailable phosphate, resulting in halo-zones in the size of 1.5 to 13.3 mm, with 7 isolates of phosphate solubilization index above 2.0. To conclude, isolates with great potential for plant growth promotion have been isolated. The application of these isolates can be an option to replace chemicals used in current agriculture practices and help the development of sustainable agriculture.

Early discrimination of haploid seedlings is an important step in doubled haploid (DH) breeding of sweet corn because putative haploids occur within a much larger population of predominantly diploid progeny. However, the combined discriminatory value of early seedling phenotypes across diverse sweet corn breeding materials remains insufficiently characterized. This study evaluated integrated seedling phenotyping for the preliminary discrimination of sweet corn seedlings routinely classified as haploid or diploid. Seedlings derived from controlled donor × inducer crosses were evaluated for shoot growth, leaf development, root architecture, chlorophyll content, and stomatal characteristics. Principal component analysis (PCA), Pearson correlation analysis, Random Forest, and linear discriminant analysis (LDA) were used to characterize multivariate phenotypic patterns and identify informative traits associated with the routine classification. Seedlings routinely classified as haploid generally exhibited lower plant height, shorter and narrower leaves, reduced root development, smaller guard cells, and higher stomatal number than routinely classified diploid seedlings. Multivariate analyses showed coordinated variation among shoot growth, root development, and stomatal traits. Random Forest identified leaf length, plant height, stomatal number, and leaf width as the most informative variables. A reduced four-trait LDA model achieved complete agreement with the routine classification in the evaluated dataset. Because chromosome number was not independently validated, the results should be interpreted as phenotypic discrimination relative to the routine classification rather than definitive confirmation of ploidy. These findings demonstrate that integrated early seedling phenotyping may support preliminary and complementary screening of putative haploids in sweet corn DH breeding.

The heavy reliance of the mushroom industry on sawdust substrates is putting increasing pressure on already limited forest resources, forcing researchers to seek alternative materials. This study investigated the feasibility of using post-harvest djulis (Chenopodium formosanum Koidz.) stems, waste from this indigenous crop in Taiwan, to partially replace sawdust for Pleurotus sajor-caju cultivation. Initial screening with 0–100% djulis replacement revealed growth inhibition above 50% incorporation levels. Refined experiments focusing on 0–30% djulis ratios demonstrated that strain PT exhibited superior adaptation to djulis-containing substrates. Commercial scale grow bag trials showed that among djulis treatments, 25% djulis incorporation achieved the fastest mycelial colonization rate (1.0 cm/day), while 15% incorporation yielded the highest biological efficiency (76.17%), comparable to commercial controls (76.80%). Three-flush harvest cycles confirmed stable productivity across treatments, with total yields ranging from 286 to 320 g/bag. Nutritional analysis showed no major changes in amino acids and antioxidants, with djulis incorporation maintaining protein quality while some enhancement in total free amino acid content and reducing power at 25% incorporation. These findings demonstrate that 15–25% djulis stem substitution sustained commercial production parameters while contributing to sustainable agricultural waste management and reducing forest resource dependence.