Nutrient patterns can significantly influence the growth and development of fruit trees, especially fruit quality. In order to clarify the appropriate ratio of inorganic and organic fertilizers, six treatments with different ratios of cow manure and chemical fertilizers were set up in this study to evaluate the effects of different treatments on fruit yield, appearance quality, intrinsic quality and volatile substances. The results showed that, after replacing some chemical fertilizers with cow manure, the content of sugar, titratable acid, organic acid and aroma substance in the fruit increased, the fruit yield and colour did not change significantly, and the fruit weight per fruit decreased. Among the treatments of cow manure with chemical fertilizer, the fruits of 50% chemical fertilizer with 50% cow manure treatment had higher titratable acid (0.4%), malic acid (4.15 mg/g), sorbitol (0.51%), glucose (1.30%), fructose (5.81%) content and total aroma substance content (1047.82 μg/g) than chemical fertilizer alone. Compared to the fertilizer treatment alone, the application of cow manure instead of 50% of the chemical fertilizer had a positive effect on fruit quality.

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.