Transposable elements (TEs) exert significant influence on plant genomic structure and gene expression. Here, we explored TE-related aspects across 14 Rosaceae genomes, investigating genomic distribution, transposition activity, expression patterns, and nearby differentially expressed genes (DEGs). Analyses unveiled distinct long terminal repeat retrotransposon (LTR–RT) evolutionary patterns, reflecting varied genome size changes among nine species over the past million years. In the past 2.5 million years, Rubus idaeus showed a transposition rate twice as fast as Fragaria vesca, while Pyrus bretschneideri displayed significantly faster transposition compared with Crataegus pinnatifida. Genes adjacent to recent TE insertions were linked to adversity resistance, while those near previous insertions were functionally enriched in morphogenesis, enzyme activity, and metabolic processes. Expression analysis revealed diverse responses of LTR–RTs to internal or external conditions. Furthermore, we identified 3695 pairs of syntenic DEGs proximal to TEs in Malus domestica cv. ‘Gala’ and M. domestica (GDDH13), suggesting TE insertions may contribute to varietal trait differences in these apple varieties. Our study across representative Rosaceae species underscores the pivotal role of TEs in plant genome evolution within this diverse family. It elucidates how these elements regulate syntenic DEGs on a genome-wide scale, offering insights into Rosaceae-specific genomic evolution.

(1) Background and Aims: Manure is an important source of nutrients for plants, and organic substrate, as an effective soil amendment substrate, is a common material for maintaining soil health in the context of agricultural intensification. The use of organic fertilizers to meet the nutrient requirements of crops and to improve soil structure is a natural choice for sustainable agriculture. The high cost of chemical fertilizers and their overuse can lead to agricultural pollution, so farmers’ awareness of organic farming is increasing, which is helping to drive agriculture in a more environmentally friendly and sustainable direction. (2) Methods: In a fertilization experiment conducted on 38-year-old ‘Changfu No.2’ apple trees, four different fertilization treatments were designed to assess their effects on soil fertility, fruit quality, and apple yield. These treatments included no fertilizer as a control (CK); chemical fertilizer combined with organic substrate (NPK + O); chemical fertilizer combined with sheep manure (NPK + SM); and a combination of chemical fertilizer, organic substrate, and sheep manure (NPK + O + SM). Principal component analysis (PCA) was used to comprehensively evaluate soil fertility, apple yield, and quality under these treatments. (3) Results: The NPK + O + SM treatment significantly improved soil fertility and apple yield compared to the other treatments. It provided comprehensive nutrition, meeting the diverse needs of plant growth. The slow-release properties of the organic substrate combined with the immediate nutrient supply from the sheep manure ensured stable nutrition throughout the growing season. This mixed fertilizer also improved soil biological activity. (4) Conclusion: The fertilization strategy combining organic substrate and sheep manure (NPK + O + SM) is highly effective in improving soil fertility, fruit quality, and apple yield, thus supporting sustainable agricultural practices.

Iron (Fe) plays an important role in cellular respiration and catalytic reactions of metalloproteins in plants and animals. Plants maintain iron homeostasis through absorption, translocation, storage, and compartmentalization of iron via a cooperative regulative network. Here, we showed different physiological characteristics in the leaves and roots of Malus baccata under Fe sufficiency and Fe deficiency conditions and propose that MbHY5 (elongated hypocotyl 5), an important transcription factor for its function in photomorphogenesis, participated in Fe deficiency response in both the leaves and roots of M. baccata. The gene co-expression network showed that MbHY5 was involved in the regulation of chlorophyll synthesis and Fe transport pathway under Fe-limiting conditions. Specifically, we found that Fe deficiency induced the expression of MbYSL7 in root, which was positively regulated by MbHY5. Overexpressing or silencing MbYSL7 influenced the expression of MbHY5 in M. baccata.

Hail, known as an agricultural meteorological disaster, can substantially constrain the growth of the apple industry. Presently, apple orchards use a variety of colored (photo-selective) hail nets as a preventative measure. However, it is unclear which color proves most effective for apple orchards. This study provides a systematic investigation of the impact of four photo-selective colored hail nets (white, blue, black, and green; with white being the control) on the microenvironment of apple orchards, fruit tree development, fruit quality, and yield over a two-year period (2020–2021). Different photo-selective nets do not evidently alter the intensity of light, although the nets’ shading effects decrease in the order from black to green to blue. Among them, blue nets increased the proportion of blue light, while green nets enhanced the proportion of green light. On the other hand, black, green, and blue nets diminished the proportion of red and far-red light. Such photo-selective nets effectively lowered soil temperature but did not have an impact on relative humidity and air temperature. Encasing apple trees with blue nets promoted growth, increasing shoot length, thickness, leaf area, and water content, while simultaneously decreasing leaf thickness. Black nets had comparable effects, although the impacts of green nets were inconsistent. Different photo-selective nets did not significantly influence the leaf shape index or overall chlorophyll content. However, black and green nets reduced the chlorophyll a/b ratio, while blue nets slightly boosted this ratio. Additionally, blue nets proved beneficial for apple trees’ photosynthesis. With the employment of a principal component analysis and comprehensive evaluation, this study concludes that blue nets offer the most favorable environmental conditions for apple growth while protecting apple orchards against hail, compared to black, white, and green nets.

The optimal load capacity provides sustainable production and high quality in 'Fuji' apple production. Determining optimal crop loads with simple and affordable thinning methods is critical for apple. We set different load capacities on different apple tree rootstocks and evaluated their effects on tree development, fruit yield and quality. The optimal load capacity for vigorous stock, dwarfing rootstock, and dwarfing interstock were 240, 90, and 100 for apples above 80 mm in diameter, respectively. To explore the optimal strategies of diverse fruit thinning agents (carbaryl, 6-BA, NAA, and Metamitron) used in the 'Fuji' apple tree, we assess from thinning agents' types, varying spraying concentrations, and application time in the most widely used dwarfing interstock. The results showed that the best use of fruit thinning agents is 2,000 mg/L carbaryl at 10 d after flowering could significantly reduce fruit set rate and improve the fruit quality in the dwarfing interstock. During the research, only the fruit thinner NAA treatment suppresses fruit development. Thus, we performed the transcriptome analysis on the NAA-treated and control fruits at 60 (FS1), 90 (FS2), 120 (FS3), and 150 (FS4) days after flowering stages to investigate the potential transcriptional regulations of NAA on fruit development and ripening. Transcriptome results showed that genes related to fruit expansion (expansin A15, expansin B3), phytohormone-related genes (HVA22C, PRE1, AHP1, etc.), fruit coloring-related genes (PAL), and many ripening-related transcription factors (EIN3, ERF, ARF, etc.) might be regulated by exogenous NAA. Our results provide an important reference for the sustainable production and optimal use of fruit thinning agents.