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Abstract Somatic variations can give rise to bud sports with advantageous traits, serving as the foundation for bud sport breeding in perennial plants. Here, we report a fully phased genome assembly of ‘Fuji’ apple, enabling comprehensive identification of somatic variants across 74 clonally propagated ‘Fuji’ varieties. Phylogenetic analysis indicates that spur-type and early-maturation traits in ‘Fuji’ sport varieties arise from multiple independent events. Several putative functional somatic variants have been identified, including a spur-type-specific deletion in the promoter of the TCP transcription factor gene MdTCP11. DNA methylation level of the deletion-associated miniature inverted-repeat transposable element is lower in spur-type varieties compared to standard-type varieties, while the expression of MdTCP11 is significantly higher. Overexpression of MdTCP11 in apple decreases plant height, highlighting its important role in the development of spur-type apple varieties. This study sheds light on the cloning history of ‘Fuji’ and provides valuable resources for apple breeding.

Adventitious root (AR) formation is the key to asexual reproduction; however, cytokinin (CK) hampers AR formation. But the mechanism by which CK inhibits it is still unknown. In this study, we used Malus prunifolia var. ringo apple stem cuttings that were treated with exogenous 6-benzyl adenine (6-BA) at 1 mg/L and lovastatin (CK biosynthesis inhibitor) at 1 mg/L to compare with control (untreated) cuttings. The results indicated that the control and 6-BA-treated cuttings failed to produce ARs; however, lovastatin-treated cuttings successfully produced a few ARs after 20 days (d) of treatments by increasing indole-3-acetic acid (IAA) and reducing zeatin riboside (ZR) content at several time points. The 6-BA treatment induced the expression of CK-related genes, such as MdARR3, MdARR5, MdARR5-2, MdAKH4, and MdCKX5, at most time points. However, lovastatin-treated cuttings reduced their expression, which favors AR formation. Furthermore, the expression of auxin-related genes, including MdIAA23, MdARF7, and MdARF19, was induced by lovastatin treatment. Like auxin-related genes, several root-development-related genes (MdWOX5, MdWOX11, MdLB29, and MdARRO1) were also promoted in response to lovastatin treatment that were repressed by 6-BA and control cuttings. In conclusion, lovastatin treatment supports AR formation by inhibiting CK biosynthesis inside the cuttings, as compared to the control and 6-BA-treated cuttings. This study laid the foundation for future studies on the relationship of CK biosynthesis inhibitors with adventitious rooting in apples and other crops.

Lateral roots (LRs) are critical for absorbing water, minerals, and nutrients. Nitrate is a vital signaling molecule for regulating LR growth. However, understanding how nitrate interacts with endogenous hormones and genes to coordinate LR development is a bottleneck. In this study, B9 apple rootstock nursery plants were cultured hydroponically and treated with different nitrate treatments (Control; T1, 2.25 mM L−1; T2, 9 mM L−1; T3, 18 mM L−1; T4, 36 mM L−1; and T5, 72 mM L−1), where T5 outperformed the other treatments. Nursery plants were subsequently treated with control and T5 to explore the underlying physiological and molecular mechanisms by which nitrate promoted LR growth. Plant height, stem diameter, root morphological parameters, endogenous hormones, and gene expression levels were measured. Results showed that T5 promoted LR growth by increasing the endogenous contents of indole-3-acetic acid (IAA) and gibberellic acid (GA), and by decreasing the contents of abscisic acid (ABA), jasmonic acid (JA), and zeatin riboside (ZR) at most time points. Furthermore, the relative expression levels of nitrate transporter genes were upregulated in the control group, and nitrate assimilation genes were upregulated in T5 nursery plants at various time points. In addition, the transcript abundances of auxin-related genes were higher in T5 nursery plants, which increased auxin contents. MdSHR, MdGATA1, and MdSCR1 expressions were induced, hence increasing LR growth. In contrast, higher auxin content raised MdWOX11 expression, which enhanced the MdLBD16 and MdLBD29 expression levels, thus prompting the transcripts of cell cycle-related genes: MdCYCD1;1 and MdCYCP4;1. Overall, the changes in hormonal content and gene expression levels followed superior LR growth by T5.

Abstract Background Melatonin (MT) is important for plant growth and development; however, it is not known whether MT is involved in apple adventitious root (AR) development. In this study, we treated Malus prunifolia (MP) at four different stages of AR development, and analyzed the level of the endogenous hormones MT, auxin (IAA), zeatin-riboside (ZR), abscisic acid (ABA), and gibberellins (GA1 + 3) in all four treatment groups and the untreated control group. The expression of MT, IAA biosynthesis, transport and signal transduction, the cell cycle, and root development related genes were quantified by RT-qPCR. The function of MdWOX11 was analyzed in transgenic apple plants. Results The promotion of AR development by MT was dependent on the stage of AR induction between 0 and 2 d in apple rootstocks. MT-treatment increased the level of IAA and crosstalk existed between MT and IAA during AR formation. The expression of MdWOX11 was induced by MT treatment and positively regulated AR formation in apple. Furthermore, transgenic lines that overexpressed MdWOX11 lines produced more ARs than ‘GL3’. Phenotypic analysis indicated that MdWOX11 overexpression lines were more sensitive to exogenous MT treatment than ‘GL3’, suggesting that MdWOX11 regulates AR formation in response to MT in apple rootstock. Conclusions MT promotes AR formation mainly during the AR induction stage by inducing IAA levels and upregulating MdWOX11.

Adventitious root (AR) formation is required for the vegetative propagation of economically important horticultural crops, such as apples. Asexual propagation is commonly utilized for breeding programs because of its short life cycle, true-to-typeness, and high efficiency. The lack of AR formation from stem segments is a barrier to segment survival. Therefore, understanding the AR regulatory mechanisms is vital for the prolonged and effective use of biological resources. Several studies have been undertaken to comprehend the molecular and physiological control of AR, which has greatly extended our knowledge regarding AR formation in apples and other crops. Auxin, a master controller of AR formation, is widely used for inducing AR formation in stem cutting. At the same time, cytokinins (CKs) are important for cell division and molecular reprograming, and other hormones, sugars, and nutrients interact with auxin to control excision-induced AR formation. In this review, we discuss the present understandings of ARs’ formation from physiological and molecular aspects and highlight the immediate advancements made in identifying underlying mechanisms involved in the regulation of ARs. Despite the progress made in the previous decades, many concerns about excision-induced AR formation remain unanswered. These focus on the specific functions and interactions of numerous hormonal, molecular, and metabolic components and the overall framework of the entire shoot cutting in a demanding environment.

Abstract Background Somatic embryogenesis receptor-like kinases (SERKs) are leucine-rich repeat receptor-like kinases associated with various signaling pathways. These kinases have a relationship with stress signals, and they are also believed to be important for regulating plant growth. However, information about this protein family in apple is limited. Results Twelve apple SERK genes distributed across eight chromosomes were identified. These genes clustered into three distinct groups in a phylogenetic analysis. All of the encoded proteins contained typical SERK domains. The chromosomal locations, gene/protein structures, synteny, promoter sequences, protein–protein interactions, and physicochemical characteristics of MdSERK genes were analyzed. Bioinformatics analyses demonstrated that gene duplications have likely contributed to the expansion and evolution of SERK genes in the apple genome. Six homologs of SERK genes were identified between apple and Arabidopsis. Quantitative real-time PCR analyses revealed that the MdSERK genes showed different expression patterns in various tissues. Eight MdSERK genes were responsive to stress signals, such as methyl jasmonate, salicylic acid, abscisic acid, and salt (NaCl). The application of exogenous brassinosteroid and auxin increased the growth and endogenous hormone contents of Malus hupehensis seedlings. The expression levels of seven MdSERK genes were significantly upregulated by brassinosteroid and auxin. In addition, several MdSERK genes showed higher expression levels in standard trees of ‘Nagafu 2’ (CF)/CF than in dwarf trees of CF/‘Malling 9’ (M.9), and in CF than in the spur-type bud mutation “Yanfu 6” (YF). Conclusion This study represents the first comprehensive investigation of the apple SERK gene family. These data indicate that apple SERKs may function in adaptation to adverse environmental conditions and may also play roles in controlling apple tree growth.

Background: The root architecture of grafted apple (Malus spp.) is affected by various characteristics of the scions. To provide information on the molecular mechanisms underlying this influence, we examined root transcriptomes of M. robusta rootstock grafted with scions of wild-type (WT) apple (M. spectabilis) and a more-branching (MB) mutant at the branching stage. Results: The growth rate of rootstock grafted MB was repressed significantly, especially the primary root length and diameter, and root weight. Biological function categories of differentially expressed genes were significantly enriched in processes associated with hormone signal transduction and intracellular activity, with processes related to the cell cycle especially down-regulated. Roots of rootstock grafted with MB scions displayed elevated auxin and cytokinin contents and reduced expression of MrPIN1, MrARF, MrAHP, most MrCRE1 genes, and cell growth-related genes MrGH3, MrSAUR and MrTCH4. Although auxin accumulation and transcription of MrPIN3, MrALF1 and MrALF4 tended to induce lateral root formation in MB-grafted rootstock, the number of lateral roots was not significantly changed. Sucrose, fructose and glucose contents were not decreased in MB-grafted roots compared with those bearing WT scions, but glycolysis and tricarboxylic acid cycle metabolic activities were repressed. Root resistance and nitrogen metabolism were reduced in MB-grafted roots as well. Conclusions: Our findings suggest that root growth and development of rootstock are mainly influenced by sugar metabolism and auxin and cytokinin signaling pathways. This study provides a basis that the characteristics of scions are related to root growth and development, resistance and activity of rootstocks. [ABSTRACT FROM AUTHOR]