The regulatory module MdBT2-MdMYB88/MdMYB124-MdNRTs regulates nitrogen usage in apple

Ubiquitin ligase VvPUB26 in grapevine promotes proanthocyanidin synthesis and resistance to powdery mildew

Proanthocyanidins (PAs) are an important group of flavonoids that contribute to astringency, color, and flavor in grapes (Vitis vinifera) and wines. They also play a crucial role in enhancing plant resistance to various stresses. However, the underlying regulatory mechanism governing PAs biosynthesis, particularly in relation to conferring resistance to powdery mildew, has not been extensively explored. This study focused on identifying a key player in PAs biosynthesis, namely the plant U-box (PUB) E3 ubiquitin ligase VvPUB26. We discovered that overexpression of VvPUB26 in grapes leads to a significant increase in PAs content, whereas interfering with VvPUB26 has the opposite effect. Additionally, our findings demonstrated that overexpression of VvPUB26 in transgenic grapevines enhances defense against powdery mildew while interfering with VvPUB26 results in increased susceptibility to the pathogen. Interestingly, we observed that VvPUB26 interacts with the WRKY transcription factor VvWRKY24, thereby facilitating ubiquitination and degradation processes. Through RNA-Seq analysis, we found that VvWRKY24 primarily participates in secondary metabolites biosynthesis, metabolic pathways, and plant-pathogen interaction. Notably, VvWRKY24 directly interacts with the promoters of dihydroflavonol-4-reductase (DFR) and leucoanthocyanidin reductase (LAR) to inhibit PAs biosynthesis. Meanwhile, VvWRKY24 also influences the expression of MYB transcription factor genes related to PAs synthesis. In conclusion, our results unveil a regulatory module involving VvPUB26-VvWRKY24-VvDFR/VvLAR that plays a fundamental role in governing PAs biosynthesis in grapevines. These findings enhance our understanding of the relationship between PAs biosynthesis and defense mechanisms against powdery mildew.

Genome-wide identification, structural and gene expression analysis of BTB gene family in soybean

BACKGROUND

The Bric-a-Brac/Tramtrack/Broad Complex (BTB) gene family plays essential roles in various biological processes in plants. These genes encode proteins that contain a conserved BTB domain, which is involved in protein-protein interactions and regulation of gene expression. However, there is no systematic reports on the BTB gene family in G.max.

RESULTS

In total, 122 soybean BTB genes were identified, which were classified into four groups based on the phylogenetic analysis. Gene structures analysis indicated that the number of exon-intron in GmBTBs ranges from 0 to18. Cis-element analysis revealed that most GmBTB genes contained cis-elements related to an abiotic stress response. In addition, qRT-PCR analyses indicated that most GmBTBs are significantly up-regulated under salinity, drought, and nitrate stresses. They suggested their potential for targeted improvement of soybean response to multiple abiotic stresses and nitrate availability.

CONCLUSION

These results provide valuable information for identifying the members of the GmBTB gene family in soybean and could provide a functional characterization of GmBTB genes in further research.

The BTB-BACK-TAZ domain protein MdBT2 reduces drought resistance by weakening the positive regulatory effect of MdHDZ27 on apple drought tolerance via ubiquitination

Drought stress is one of the dominating challenges to the growth and productivity in crop plants. Elucidating the molecular mechanisms of plants responses to drought stress is fundamental to improve fruit quality. However, such molecular mechanisms are poorly understood in apple (Malus domestica Borkh.). In this study, we explored that the BTB-BACK-TAZ protein, MdBT2, negatively modulates the drought tolerance of apple plantlets. Moreover, we identified a novel Homeodomain-leucine zipper (HD-Zip) transcription factor, MdHDZ27, using a yeast two-hybrid (Y2H) screen with MdBT2 as the bait. Overexpression of MdHDZ27 in apple plantlets, calli, and tomato plantlets enhanced their drought tolerance by promoting the expression of drought tolerance-related genes [responsive to dehydration 29A (MdRD29A) and MdRD29B]. Biochemical analyses demonstrated that MdHDZ27 directly binds to and activates the promoters of MdRD29A and MdRD29B. Furthermore, in vitro and in vivo assays indicate that MdBT2 interacts with and ubiquitinates MdHDZ27, via the ubiquitin/26S proteasome pathway. This ubiquitination results in the degradation of MdHDZ27 and weakens the transcriptional activation of MdHDZ27 on MdRD29A and MdRD29B. Finally, a series of transgenic analyses in apple plantlets further clarified the role of the relationship between MdBT2 and MdHDZ27, as well as the effect of their interaction on drought resistance in apple plantlets. Collectively, our findings reveal a novel mechanism by which the MdBT2-MdHDZ27 regulatory module controls drought tolerance, which is of great significance for enhancing the drought resistance of apple and other plants.

The MpNAC72/MpERF105-MpMYB10b module regulates anthocyanin biosynthesis in Malus 'Profusion' leaves infected with Gymnosporangium yamadae

Apple rust is a serious fungal disease affecting Malus plants worldwide. Infection with the rust pathogen Gymnosporangium yamadae induces the accumulation of anthocyanins in Malus to resist rust disease. However, the mechanism of anthocyanin biosynthesis regulation in Malus against apple rust is still unclear. Here, we show that MpERF105 and MpNAC72 are key regulators of anthocyanin biosynthesis via the ethylene-dependent pathway in M. 'Profusion' leaves under rust disease stress. Exogenous ethephon treatment promoted high expression of MpERF105 and MpNAC72 and anthocyanin accumulation in G. yamadae-infected M. 'Profusion' leaves. Overexpression of MpERF105 increased the total anthocyanin content of Malus plant material and acted by positively regulating its target gene, MpMYB10b. MpNAC72 physically interacted with MpERF105 in vitro and in planta, and the two form a protein complex. Coexpression of the two leads to higher transcript levels of MpMYB10b and higher anthocyanin accumulation. In addition, overexpression of MpERF105 or MpNAC72 enhanced the resistance of M. 'Profusion' leaves to apple rust. In conclusion, our results elucidate the mechanism by which MpERF105 and MpNAC72 are induced by ethylene in G. yamadae-infected M. 'Profusion' leaves and promote anthocyanin accumulation by mediating the positive regulation of MpMYB10b expression.

MdbZIP44-MdCPRF2-like-Mdα-GP2 regulate starch and sugar metabolism in apple under nitrogen supply

Nitrogen (N) is regarded as an essential macronutrient and is tightly associated with carbon (C) metabolism in plants. The transcriptome data obtained from this study showed that the expression level of the apple basic leucine zipper (bZIP) transcription factor (TF) MdbZIP44 was up-regulated in 'Oregon Spur Delicious' (Malus domestica Borkh.) apple fruits under nitrogen supply. MdbZIP44 bound to the promoter of Mdα-GP2 gene and inhibited its expression, thereby promoting starch accumulation and decreasing glucose content in apple and tomato fruits. Besides, overexpression of MdbZIP44 promoted sucrose accumulation by regulating the activities of sucrose metabolism-related enzymes and the expression of sugar metabolism-related genes in apple callus and tomato fruits. Furthermore, biochemical assays indicated that MdbZIP44 directly interacted with MdCPRF2-like, another bZIP gene in apple. Meanwhile, this study found that MdCPRF2-like, along with the MdbZIP44 and MdCPRF2-like complex, could activate the expression of Mdα-GP2, respectively. In conclusion, this study provides a new reference for potential mechanisms underlying that MdbZIP44-MdCPRF2-like-Mdα-GP2 regulates starch and sugar metabolism under nitrogen supply.

Calmodulin-like protein MdCML15 interacts with MdBT2 to modulate iron homeostasis in apple

BTB and TAZ domain proteins (BTs) function as specialized adaptors facilitating substrate recognition of the CUL3-RING ubiquitin ligase (CRL3) complex that targets proteins for ubiquitination in reaction to diverse pressures. Nonetheless, knowledge of the molecular mechanisms by which the apple scaffold protein MdBT2 responds to external and internal signals is limited. Here we demonstrate that a putative Ca 2+ sensor, calmodulin-like 15 (MdCML15), acts as an upstream regulator of MdBT2 to negatively modulate its functions in plasma membrane H+-ATPase regulation and iron deficiency tolerance. MdCML15 was identified to be substantially linked to MdBT2, and to result in the ubiquitination and degradation of the MdBT2 target protein MdbHLH104. Consequently, MdCML15 repressed the MdbHLH104 target, MdAHA8's expression, reducing levels of a specific membrane H+-ATPase. Finally, the phenotype of transgenic apple plantlets and calli demonstrated that MdCML15 modulates membrane H+-ATPase-produced rhizosphere pH lowering alongside iron homeostasis through an MdCML15-MdBT2-MdbHLH104-MdAHA8 pathway. Our results provide new insights into the relationship between Ca2+ signaling and iron homeostasis.

miR164-MhNAC1 regulates apple root nitrogen uptake under low nitrogen stress

Nitrogen is an essential nutrient for plant growth and serves as a signaling molecule to regulate gene expression inducing physiological, growth and developmental responses. An excess or deficiency of nitrogen may have adverse effects on plants. Studying nitrogen uptake will help us understand the molecular mechanisms of utilization for targeted molecular breeding. Here, we identified and functionally validated an NAC (NAM-ATAF1/2-CUC2) transcription factor based on the transcriptomes of two apple rootstocks with different nitrogen uptake efficiency. NAC1, a target gene of miR164, directly regulates the expression of the high-affinity nitrate transporter (MhNRT2.4) and citric acid transporter (MhMATE), affecting root nitrogen uptake. To examine the role of MhNAC1 in nitrogen uptake, we produced transgenic lines that overexpressed or silenced MhNAC1. Silencing MhNAC1 promoted nitrogen uptake and citric acid secretion in roots, and enhanced plant tolerance to low nitrogen conditions, while overexpression of MhNAC1 or silencing miR164 had the opposite effect. This study not only revealed the role of the miR164-MhNAC1 module in nitrogen uptake in apple rootstocks but also confirmed that citric acid secretion in roots affected nitrogen uptake, which provides a research basis for efficient nitrogen utilization and molecular breeding in apple.

Identification of candidate genes and residues for improving nitrogen use efficiency in the N-sensitive medicinal plant Panax notoginseng

BACKGROUND

Nitrogen (N) metabolism-related key genes and conserved amino acid sites in key enzymes play a crucial role in improving N use efficiency (NUE) under N stress. However, it is not clearly known about the molecular mechanism of N deficiency-induced improvement of NUE in the N-sensitive rhizomatous medicinal plant Panax notoginseng (Burk.) F. H. Chen. To explore the potential regulatory mechanism, the transcriptome and proteome were analyzed and the three-dimensional (3D) information and molecular docking models of key genes were compared in the roots of P. notoginseng grown under N regimes.

RESULTS

Total N uptake and the proportion of N distribution to roots were significantly reduced, but the NUE, N use efficiency in biomass production (NUEb), the recovery of N fertilizer (RNF) and the proportion of N distribution to shoot were increased in the N0-treated (without N addition) plants. The expression of N uptake- and transport-related genes NPF1.2, NRT2.4, NPF8.1, NPF4.6, AVP, proteins AMT and NRT2 were obviously up-regulated in the N0-grown plants. Meanwhile, the expression of CIPK23, PLC2, NLP6, TCP20, and BT1 related to the nitrate signal-sensing and transduction were up-regulated under the N0 condition. Glutamine synthetase (GS) activity was decreased in the N-deficient plants, while the activity of glutamate dehydrogenase (GDH) increased. The expression of genes GS1-1 and GDH1, and proteins GDH1 and GDH2 were up-regulated in the N0-grown plants, there was a significantly positive correlation between the expression of protein GDH1 and of gene GDH1. Glu192, Glu199 and Glu400 in PnGS1 and PnGDH1were the key amino acid residues that affect the NUE and lead to the differences in GDH enzyme activity. The 3D structure, docking model, and residues of Solanum tuberosum and P. notoginseng was similar.

CONCLUSIONS

N deficiency might promote the expression of key genes for N uptake (genes NPF8.1, NPF4.6, AMT, AVP and NRT2), transport (NPF1.2 and NRT2.4), assimilation (proteins GS1 and GDH1), signaling and transduction (genes CIPK23, PLC2, NLP6, TCP20, and BT1) to enhance NUE in the rhizomatous species. N deficiency might induce Glu192, Glu199 and Glu400 to improve the biological activity of GS1 and GDH, this has been hypothesized to be the main reason for the enhanced ability of N assimilation in N-deficient rhizomatous species. The key genes and residues involved in improving NUE provide excellent candidates for the breeding of medicinal plants.

Melatonin confers tolerance to nitrogen deficiency through regulating MdHY5 in apple plants

Nitrogen (N) is an essential nutrient for crop growth and development, significantly influencing both yield and quality. Melatonin (MT), a known enhancer of abiotic stress tolerance, has been extensively studied. However, its relationship with nutrient stress, particularly N deficiency, and the underlying regulatory mechanisms of MT on N absorption remain unclear. In this study, exogenous MT treatment was found to improve the tolerance of apple plants to N deficiency. Apple plants overexpressing the MT biosynthetic gene N-acetylserotonin methyltransferase 9 (MdASMT9) were used to further investigate the effects of endogenous MT on low-N stress. Overexpression of MdASMT9 improved the light harvesting and heat transfer capability of apple plants, thereby mitigating the detrimental effects of N deficiency on the photosynthetic system. Proteomic and physiological data analyses indicated that MdASMT9 overexpression enhanced the trichloroacetic acid cycle and positively modulated amino acid metabolism to counteract N-deficiency stress. Additionally, both exogenous and endogenous MT promoted the transcription of MdHY5, which in turn bound to the MdNRT2.1 and MdNRT2.4 promoters and activated their expression. Notably, MT-mediated promotion of MdNRT2.1 and MdNRT2.4 expression through regulating MdHY5, ultimately enhancing N absorption. Taken together, these findings shed light on the association between MdASMT9-mediated MT biosynthesis and N absorption in apple plants under N-deficiency conditions.

MdHB7-like positively modulates apple salt tolerance by promoting autophagic activity and Na+ efflux

Salt stress adversely affects the yield and quality of crops and limits their geographical distribution. Studying the functions and regulatory mechanisms of key genes in the salt stress response is important for breeding crops with enhanced stress resistance. Autophagy plays an important role in modulating the tolerance of plants to various types of abiotic stressors. However, the mechanisms underlying salt-induced autophagy are largely unknown. Cation/Ca2+ exchanger proteins enhance apple salt tolerance by inhibiting Na+ accumulation but the mechanism underlying the response to salt stress remains unclear. Here, we show that the autophagy-related gene MdATG18a modulated apple salt tolerance. Under salt stress, the autophagic activity, proline content, and antioxidant enzyme activities were higher and Na+ accumulation was lower in MdATG18a-overexpressing transgenic plants than in control plants. The use of an autophagy inhibitor during the salt treatment demonstrated that the regulatory function of MdATG18a depended on autophagy. The yeast-one-hybrid assay revealed that the homeodomain-leucine zipper (HD-Zip) transcription factor MdHB7-like directly bound to the MdATG18a promoter. Transcriptional regulation and genetic analyses showed that MdHB7-like enhanced salt-induced autophagic activity by promoting MdATG18a expression. The analysis of Na+ efflux rate in transgenic yeast indicated that MdCCX1 expression significantly promoted Na+ efflux. Promoter binding, transcriptional regulation, and genetic analyses showed that MdHB7-like promoted Na+ efflux and apple salt tolerance by directly promoting MdCCX1 expression, which was independent of the autophagy pathway. Overall, our findings provide insight into the mechanism underlying MdHB7-like-mediated salt tolerance in apple through the MdHB7-like-MdATG18a and MdHB7-like-MdCCX1 modules. These results will aid future studies on the mechanisms underlying stress-induced autophagy and the regulation of stress tolerance in plants.

Engineering the Crop Microbiota Through Host Genetics

The microbiota populating the plant-soil continuum defines an untapped resource for sustainable crop production. The host plant is a driver for the taxonomic composition and function of these microbial communities. In this review, we illustrate how the host genetic determinants of the microbiota have been shaped by plant domestication and crop diversification. We discuss how the heritable component of microbiota recruitment may represent, at least partially, a selection for microbial functions underpinning the growth, development, and health of their host plants and how the magnitude of this heritability is influenced by the environment. We illustrate how host-microbiota interactions can be treated as an external quantitative trait and review recent studies associating crop genetics with microbiota-based quantitative traits. We also explore the results of reductionist approaches, including synthetic microbial communities, to establish causal relationships between microbiota and plant phenotypes. Lastly, we propose strategies to integrate microbiota manipulation into crop selection programs. Although a detailed understanding of when and how heritability for microbiota composition can be deployed for breeding purposes is still lacking, we argue that advances in crop genomics are likely to accelerate wider applications of plant-microbiota interactions in agriculture.

Insights into the molecular mechanisms underlying responses of apple trees to abiotic stresses

Apple (Malus[Formula: see text]domestica) is a popular temperate fruit crop worldwide. However, its growth, productivity, and quality are often adversely affected by abiotic stresses such as drought, extreme temperature, and high salinity. Due to the long juvenile phase and highly heterozygous genome, the conventional breeding approaches for stress-tolerant cultivars are time-consuming and resource-intensive. These issues may be resolved by feasible molecular breeding techniques for apples, such as gene editing and marker-assisted selection. Therefore, it is necessary to acquire a more comprehensive comprehension of the molecular mechanisms underpinning apples' response to abiotic stress. In this review, we summarize the latest research progress in the molecular response of apples to abiotic stressors, including the gene expression regulation, protein modifications, and epigenetic modifications. We also provide updates on new approaches for improving apple abiotic stress tolerance, while discussing current challenges and future perspectives for apple molecular breeding.

VqWRKY56 interacts with VqbZIPC22 in grapevine to promote proanthocyanidin biosynthesis and increase resistance to powdery mildew

Powdery mildew (PM) is a severe fungal disease of cultivated grapevine world-wide. Proanthocyanidins (PAs) play an important role in resistance to fungal pathogens; however, little is known about PA-mediated PM resistance in grapevine. We identified a WRKY transcription factor, VqWRKY56, from Vitis quinquangularis, the expression of which was significantly induced by PM. Overexpression (OE) of VqWRKY56 in Vitis vinifera increased PA content and reduced susceptibility to PM. Furthermore, the transgenic plants showed more cell death and increased accumulation of salicylic acid and reactive oxygen species. Transient silencing of VqWRKY56 in V. quinquangularis and V. vinifera reduced PA accumulation and increased the susceptibility to PM. VqWRKY56 interacted with VqbZIPC22 in vitro and in planta. The protein VqWRKY56 can bind to VvCHS3, VvLAR1, and VvANR promoters, and VqbZIPC22 can bind to VvANR promoter. Co-expression of VqWRKY56 and VqbZIPC22 significantly increased the transcript level of VvCHS3, VvLAR1, and VvANR genes. Finally, transient OE of VqbZIPC22 in V. vinifera promoted PA accumulation and improved resistance to PM, while transient silencing in V. quinquangularis had the opposite effect. Our study provides new insights into the mechanism of PA regulation by VqWRKY56 in grapevine and provides a basis for further metabolic engineering of PA biosynthesis to improve PM resistance.

PuHox52 promotes coordinated uptake of nitrate, phosphate, and iron under nitrogen deficiency in Populus ussuriensis

It is of great importance to better understand how trees regulate nitrogen (N) uptake under N deficiency conditions which severely challenge afforestation practices, yet the underlying molecular mechanisms have not been well elucidated. Here, we functionally characterized PuHox52, a Populus ussuriensis HD-ZIP transcription factor, whose overexpression greatly enhanced nutrient uptake and plant growth under N deficiency. We first conducted an RNA sequencing experiment to obtain root transcriptome using PuHox52-overexpression lines of P. ussuriensis under low N treatment. We then performed multiple genetic and phenotypic analyses to identify key target genes of PuHox52 and validated how they acted against N deficiency under PuHox52 regulation. PuHox52 was specifically induced in roots by N deficiency, and overexpression of PuHox52 promoted N uptake, plant growth, and root development. We demonstrated that several nitrate-responsive genes (PuNRT1.1, PuNRT2.4, PuCLC-b, PuNIA2, PuNIR1, and PuNLP1), phosphate-responsive genes (PuPHL1A and PuPHL1B), and an iron transporter gene (PuIRT1) were substantiated to be direct targets of PuHox52. Among them, PuNRT1.1, PuPHL1A/B, and PuIRT1 were upregulated to relatively higher levels during PuHox52-mediated responses against N deficiency in PuHox52-overexpression lines compared to WT. Our study revealed a novel regulatory mechanism underlying root adaption to N deficiency where PuHox52 modulated a coordinated uptake of nitrate, phosphate, and iron through 'PuHox52-PuNRT1.1', 'PuHox52-PuPHL1A/PuPHL1B', and 'PuHox52-PuIRT1' regulatory relationships in poplar roots.

Comparative transcriptome and genome analysis unravels the response of Tatary buckwheat root to nitrogen deficiency

Tartary buckwheat (Fagopyrum tataricum Garetn.), a dicotyledonous herbaceous crop, has good adaptation to low nitrogen (LN) condition. The plasticity of roots drives the adaption of Tartary buckwheat under LN, but the detailed mechanism behind the response of TB roots to LN remains unclear. In this study, the molecular mechanism of two Tartary buckwheat genotypes' roots with contrasting sensitivity in response to LN was investigated by integrating physiological, transcriptome and whole-genome re-sequencing analysis. LN improved primary and lateral root growth of LN-sensitive genotype, whereas the roots of LN-insensitive genotype showed no response to LN. 2, 661 LN-responsive differentially expressed genes (DEGs) were identified by transcriptome analysis. Of these genes, 17 N transport and assimilation-related and 29 hormone biosynthesis and signaling genes showed response to LN, and they may play important role in Tartary buckwheat root development under LN. The flavonoid biosynthetic genes' expression was improved by LN, and their transcriptional regulations mediated by MYB and bHLH were analyzed. 78 transcription factors, 124 small secreted peptides and 38 receptor-like protein kinases encoding genes involved in LN response. 438 genes were differentially expressed between LN-sensitive and LN-insensitive genotypes by comparing their transcriptome, including 176 LN-responsive DEGs. Furthermore, nine key LN-responsive genes with sequence variation were identified, including FtNRT2.4, FtNPF2.6 and FtMYB1R1. This paper provided useful information on the response and adaptation of Tartary buckwheat root to LN, and the candidate genes for breeding Tartary buckwheat with high N use efficiency were identified.

Effects of Magnesium on nitrate uptake and sorbitol synthesis and translocation in apple seedlings

Both magnesium (Mg) and nitrogen (N) play many important roles in plant physiological and biochemical processes. Plants usually exhibit low nitrogen utilization efficiency (NUE) under Mg deficiency conditions, but the mechanisms by which Mg regulates NUE are not well understood. Herein, we investigated biomass, nutrient uptake, sorbitol and sucrose transport, and relative gene expression in apple seedlings under various concentrations of Mg and N treatments in hydroponic cultures. We first observed that low Mg supply significantly limited plant growth and N, Mg concentrations. Increasing the supply of N, but not Mg, partially alleviated the inhibition of plant growth under low Mg stress, which indicated that Mg deficiency had a negative impact on plant growth because it inhibits N absorption. Moreover, we found that the expression of nitrate transporter genes MdNRT2.1 and MdNRT2.4 was significantly downregulated by low Mg stress, and sufficient Mg significantly promoted sucrose and sorbitol synthesis and transport from leaves to roots by regulating relevant enzyme activity and genes expression. Further experiments showed that exogenous sorbitol could rapidly restore MdNRT2.1/2.4 expression and nitrate uptake under low Mg availability without increasing internal Mg level, suggesting that Mg may regulate MdNRT2.1/2.4 expression by regulating more sorbitol transport to roots, the effect of Mg on N was indirect, sorbitol played a key role during this process. Taken together, Mg promoted sorbitol synthesis and transport into roots, thus upregulating the expression of MdNRT2.1/2.4 and increasing the absorption of nitrate.

Nitrate transporter MdNRT2.4 interacts with rhizosphere bacteria to enhance nitrate uptake in apple rootstocks

Plants have developed complex mechanisms to adapt to changing nitrate (NO3-) concentrations and can recruit microbes to boost nitrogen absorption. However, little is known about the relationship between functional genes and the rhizosphere microbiome in NO3- uptake of apple rootstocks. Here, we found that variation in Malus domestica NO3- transporter (MdNRT2.4) expression contributes to nitrate uptake divergence between two apple rootstocks. Overexpression of MdNRT2.4 in apple seedlings significantly improved tolerance to low nitrogen via increasing net NO3- influx at the root surface. However, inhibiting the root plasma membrane H+-ATPase activity abolished NO3- uptake and led to NO3- release, suggesting that MdNRT2.4 encodes an H+-coupled nitrate transporter. Surprisingly, the nitrogen concentration of MdNRT2.4-overexpressing apple seedlings in unsterilized nitrogen-poor soil was higher than that in sterilized nitrogen-poor soil. Using 16S ribosomal RNA gene profiling to characterize the rhizosphere microbiota, we found that MdNRT2.4-overexpressing apple seedlings recruited more bacterial taxa with nitrogen metabolic functions, especially Rhizobiaceae. We isolated a bacterial isolate ARR11 from the apple rhizosphere soil and identified it as Rhizobium. Inoculation with ARR11 improved apple seedling growth in nitrogen-poor soils, compared with uninoculated seedlings. Together, our results highlight the interaction of host plant genes with the rhizosphere microbiota for host plant nutrient uptake.

The apple BTB protein MdBT2 positively regulates MdCOP1 abundance to repress anthocyanin biosynthesis

The ubiquitin ligase CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) plays a central role in light-induced anthocyanin biosynthesis. However, the upstream regulatory factors of COP1 remain poorly understood, particularly in horticultural plants. Here, we identified an MdCOP1-interacting protein, BROAD-COMPLEX, TRAMTRACK AND BRIC A BRAC2 (MdBT2), in apple (Malus domestica). MdBT2 is a BTB protein that directly interacts with and stabilizes MdCOP1 by inhibiting self-ubiquitination. Fluorescence observation and cell fractionation assays showed that MdBT2 increased the abundance of MdCOP1 in the nucleus. Moreover, a series of phenotypic analyses indicated that MdBT2 promoted MdCOP1-mediated ubiquitination and degradation of the MdMYB1 transcription factor, inhibiting the expression of anthocyanin biosynthesis genes and anthocyanin accumulation. Overall, our findings reveal a molecular mechanism by which MdBT2 positively regulates MdCOP1, providing insight into MdCOP1-mediated anthocyanin biosynthesis.

MdFLP enhances drought tolerance by regulating MdNAC019 in self-rooted apple stocks

Self-rooted apple stocks are widely used for the production of apples worldwide. However, self-rooted apple stocks are weak due to shallow roots and poor grounding, resulting in poor drought resistance. Therefore, it is essential to understand the molecular mechanisms to develop self-rooted apple stock cultivars with drought resistance. We reported that MdFLP, an R2R3-MYB transcription factor, directly binds to the promoter of MdNAC019, activating its transcription and consequently enhancing drought tolerance in self-rooted apple stocks. In addition, MdFLP indirectly activates the transcriptional expression of abiotic stress-related genes, namely, MdERF6 and MdZAT10. The plants overexpressing MdFLP displayed stronger drought tolerance, whereas MdFLP-RNAi plants showed weak drought tolerance compared with non-transgenic "Gala" plants, indicating that MdFLP regulates drought tolerance in self-rooted apple stocks. Altogether, we believe that our findings provide novel insights into the functions of MdFLP in the regulation of drought tolerance in self-rooted apple stocks.

Engineering drought-tolerant apple by knocking down six GH3 genes and potential application of transgenic apple as a rootstock

Drought poses a major threat to apple fruit production and quality. Because of the apple's long juvenile phase, developing varieties with improved drought tolerance using biotechnology approaches is needed. Here, we used the RNAi approach to knock down six GH3 genes in the apple. Under prolonged drought stress, the MdGH3 RNAi plants performed better than wild-type plants and had stronger root systems, higher root-to-shoot ratio, greater hydraulic conductivity, increased photosynthetic capacity, and increased water use efficiency. Moreover, MdGH3 RNAi plants promoted the drought tolerance of the scion when they were used as rootstock, compared with wild-type and M9-T337 rootstocks. Scions grafted onto MdGH3 RNAi plants showed increased plant height, stem diameter, photosynthetic capacity, specific leaf weight, and water use efficiency. The use of MdGH3 RNAi plants as rootstocks can also increase the C/N ratio of the scion and achieve the same effect as the M9-T337 rootstock in promoting the flowering and fruiting of the scion. Notably, using MdGH3 RNAi plants as rootstocks did not reduce fruit weight and scion quality compared with using M9-T337 rootstock. Our research provides candidate genes and demonstrates a general approach that could be used to improve the drought tolerance of fruit trees without sacrificing the yield and quality of scion fruits.

AP2/ERF transcription factor GmDREB1 confers drought tolerance in transgenic soybean by interacting with GmERFs

Soybean is the main economic crop, and also the main source of oil and protein for human consumption. Drought stress has a great influence on the growth and yield of soybean crops. Therefore, improving the drought resistance of soybean, especially drought resistance in the field, is important to increase soybean yield. AP2/ERF (APETALA2/ethylene responsive factor) transcription factors are one of the largest families of transcription factors in plants. However, there has been little research on the value of applying DREB (dehydration-responsive element-binding)-like genes in improving the drought resistance of soybean. Here, we further study the value of the application of GmDREB1 in soybean. The results of drought resistance identification in the field and greenhouse showed that the overexpression of GmDREB1 could significantly enhance the drought resistance of transgenic soybean, and the yield was clearly higher than that of the wild type. GmDREB1 has transcriptional activity and is located in the nucleus. For mechanism analysis of GmDREB1 in soybean, two ERF-like transcription factors, GmERF008 and GmERF106, were shown to interact with GmDREB1 using yeast two-hybrid (Y2H) and bimolecular fluorescence complementary (BiFC) experiments. qRT-PCR (quantitative real-time PCR) results showed that the expression of many stress-related genes in GmDREB1 transgenic soybean were significantly up-regulated compared with the WT under a drought environment. In conclusion, GmDREB1 can regulate the expression of downstream stress-related genes by forming a heterodimer with ERF-like transcription factors, which can improve the drought resistance of transgenic soybean.

MdATG5a induces drought tolerance by improving the antioxidant defenses and promoting starch degradation in apple

Drought occurrence seriously affects the productivity and quality of apple crop worldwide. Autophagy, a conserved process for the degradation and recycling of unwanted cellular components, is considered to positively regulate the tolerance of various abiotic stresses in plants. In the current study, we isolated two ATG5 homologs genes, namely, MdATG5a and MdATG5b, from apple, demonstrating their responsiveness to drought and oxidative stresses. In addition to having the same cellular localization in the nucleus and cytoplasm, both MdATG5a and MdATG5b could interact with MdATG12. Transgenic apple plants overexpressing MdATG5a exhibited an improved drought tolerance, as indicated by less drought-related damage and higher photosynthetic capacities compared to wild-type (WT) plants under drought stress. The overexpression of MdATG5a improved antioxidant defenses in apple when exposed to drought via elevating both antioxidant enzyme activities and the levels of beneficial antioxidants. Furthermore, under drought stress, the overexpression of MdATG5a promoted the mobilization of starch to accumulate greater levels of soluble sugars, contributing to osmotic adjustments and supporting carbon skeletons for proline synthesis. Such changes in physiological responses may be associated with increased autophagic activities in the transgenic plants upon exposure to drought. Our results demonstrate that MdATG5a-mediated autophagy enhances drought tolerance of apple plants via improving antioxidant defenses and metabolic adjustments.