Nitrogen (N) and phosphorus (P) are essential phytomacronutrients, and deficiencies in these two elements limit growth and yield in apple (Malus domestica Borkh.). The rootstock plays a key role in the nutrient uptake and environmental adaptation of apple. The objective of this study was to investigate the effects of N and/or P deficiency on hydroponically-grown dwarfing rootstock ‘M9-T337’ seedlings, particularly the roots, by performing an integrated physiological, transcriptomics-, and metabolomics-based analyses. Compared to N and P sufficiency, N and/or P deficiency inhibited aboveground growth, increased the partitioning of total N and total P in roots, enhanced the total number of tips, length, volume, and surface area of roots, and improved the root-to-shoot ratio. P and/or N deficiency inhibited NO3− influx into roots, and H⁺ pumps played a important role in the response to P and/or N deficiency. Conjoint analysis of differentially expressed genes and differentially accumulated metabolites in roots revealed that N and/or P deficiency altered the biosynthesis of cell wall components such as cellulose, hemicellulose, lignin, and pectin. The expression of MdEXPA4 and MdEXLB1, two cell wall expansin genes, were shown to be induced by N and/or P deficiency. Overexpression of MdEXPA4 enhanced root development and improved tolerance to N and/or P deficiency in transgenic Arabidopsis thaliana plants. In addition, overexpression of MdEXLB1 in transgenic Solanum lycopersicum seedlings increased the root surface area and promoted acquisition of N and P, thereby facilitating plant growth and adaptation to N and/or P deficiency. Collectively, these results provided a reference for improving root architecture in dwarfing rootstock and furthering our understanding of integration between N and P signaling pathways.

Apple trees grafted on different rootstock types, including vigorous rootstock (VR), dwarfing interstock (DIR), and dwarfing self-rootstock (DSR), are widely planted in production, but the molecular determinants of tree branch architecture growth regulation induced by rootstocks are still not well known. In this study, the branch growth phenotypes of three combinations of ‘Fuji’ apple trees grafted on different rootstocks (VR: Malus baccata; DIR: Malus baccata/T337; DSR: T337) were investigated. The VR trees presented the biggest branch architecture. The results showed that the sugar content, sugar metabolism-related enzyme activities, and hormone content all presented obvious differences in the tender leaves and buds of apple trees grafted on these rootstocks. Transcriptomic profiles of the tender leaves adjacent to the top buds allowed us to identify genes that were potentially involved in signaling pathways that mediate the regulatory mechanisms underlying growth differences. In total, 3610 differentially expressed genes (DEGs) were identified through pairwise comparisons. The screened data suggested that sugar metabolism-related genes and complex hormone regulatory networks involved the auxin (IAA), cytokinin (CK), abscisic acid (ABA) and gibberellic acid (GA) pathways, as well as several transcription factors, participated in the complicated growth induction process. Overall, this study provides a framework for analysis of the molecular mechanisms underlying differential tree branch growth of apple trees grafted on different rootstocks.

A quick method was developed for diagnosis of nitrogen (N) in apple trees based on multiple linear regressions to establish the relationship between near-infrared reflectance spectra (NIRS) and the N contents of fresh and dry tissue. Spectral pretreatment methods such as derivatives, smoothing, and normalization were used. The derivatives appeared to be the most effective. The best calibration for fresh leaf gave 0.842 for the correlation coefficient of validation (R_v), 1.119 g kg⁻¹ for the root mean square error of prediction (RMSEP), and 8.311 for the ratio of the range in reference data from the validation samples to the root mean square error of prediction (RER). The best calibration for dried ground samples was obtained with R_v = 0.952, RMSEP = 0.633 g kg⁻¹, the ratio performance deviation (RPD) = 3.27, and RER = 13.728. The results showed that calibrations of dry-apple leaf are robust enough for an accurate prediction of N.

Rootstocks largely determine the tree architecture of the grafted scions, significantly affects yield, suitability for mechanical harvesting, and planting pattern of apple orchards. It is thus important to reveal the mechanisms behind the rootstocks influence on the tree architecture of scions in apple trees. This study analyzed the grafting survival rate, the physiological parameters including plant growth, photosynthesis and nutrient accumulation in the apple variety ‘Harlikar’ with eight apple rootstocks. We also explored the mechanism of scion architecture formation using transcriptomics based on different scion/rootstock combinations. The results indicated that ‘Harlikar’ had the lowest grafting survival rate with rootstock ‘M26’, with less callus formed at the graft interface, foliage etiolation, and weak photosynthetic capacity. While ‘Harlikar’ had better affinities with ‘M9-T337’, ‘M9-Nic29’, ‘M9-Pajam2’, ‘B9’, ‘71-3-150’, ‘Qingzhen 2’, and ‘Malus baccata’. Among these, the highest plant height and the highest number of lateral branches were observed in ‘Harlikar’ with rootstock ‘Qingzhen 2’, they were 1.12-times and 2.0-times higher than ‘Harlikar’ with vigorous rootstock ‘M. baccata’, respectively. The highest accumulations of total nitrogen, total phosphorus, and total potassium in scions were observed in ‘Harlikar’/‘Qingzhen 2’, they were 2.22-times, 2.10-times, and 11.80-times higher than that in ‘Harlikar’/‘M. baccata’. The lowest plant height was observed in ‘Harlikar’/‘71-3-150’, only 50.47% of ‘Harlikar’/‘Qingzhen 2’ and 56.51% of ‘Harlikar’/‘M. baccata’, and the lowest internode length was observed in ‘Harlikar’/‘M9-Nic29’, only 60.76% of ‘Harlikar’/‘Qingzhen 2’ and 79.11% of ‘Harlikar’/‘M. baccata’. The transcriptome, weighted gene co-expression network and KEGG enrichment analyses revealed that, compared to ‘Harlikar’/‘M. baccata’, most differentially expressed genes screened from ‘Harlikar’/‘Qingzhen 2’, ‘Harlikar’/‘71-3-150’, and ‘Harlikar’/‘M9-Nic29’ were enriched in hormone signal transduction pathways. Specifically, auxin-repressed protein gene ARP, cytokinin synthesis related genes CKXs and CYP92A6, and brassinosteroid synthesis related gene CYP87A3 were involved in the dwarfing of ‘Harlikar’/‘71-3-150’ and ‘Harlikar’/‘M9-Nic29’. Cytokinin synthesis related gene ARR-A and abscisic acid-responsive element binding factor gene ABF were the key to increased branching in ‘Harlikar’/‘Qingzhen 2’. In addition, acid phosphatase genes ACPs, and serine/threonine-protein kinase genes PBLs were involved in the vegetative growth of scions in ‘Harlikar’/‘Qingzhen 2’ by affecting the absorption and utilization of nutrients. These results provide theoretical guidance for cultivating high-quality ‘Harlikar’ apple trees and elucidate the molecular mechanisms regulating plant height and lateral branch formation in apple.