High miR156 Expression Is Required for Auxin-Induced Adventitious Root Formation via MxSPL26 Independent of PINs and ARFs in Malus xiaojinensis

Adventitious rooting in response to long-term cold: a possible mechanism of clonal growth in alpine perennials

Arctic alpine species experience extended periods of cold and unpredictable conditions during flowering. Thus, often, alpine plants use both sexual and asexual means of reproduction to maximize fitness and ensure reproductive success. We used the arctic alpine perennial Arabis alpina to explore the role of prolonged cold exposure on adventitious rooting. We exposed plants to 4°C for different durations and scored the presence of adventitious roots on the main stem and axillary branches. Our physiological studies demonstrated the presence of adventitious roots after 21 weeks at 4°C saturating the effect of cold on this process. Notably, adventitious roots on the main stem developing in specific internodes allowed us to identify the gene regulatory network involved in the formation of adventitious roots in cold using transcriptomics. These data and histological studies indicated that adventitious roots in A. alpina stems initiate during cold exposure and emerge after plants experience growth promoting conditions. While the initiation of adventitious root was not associated with changes of DR5 auxin response and free endogenous auxin level in the stems, the emergence of the adventitious root primordia was. Using the transcriptomic data, we discerned the sequential hormone responses occurring in various stages of adventitious root formation and identified supplementary pathways putatively involved in adventitious root emergence, such as glucosinolate metabolism. Together, our results highlight the role of low temperature during clonal growth in alpine plants and provide insights on the molecular mechanisms involved at distinct stages of adventitious rooting.

Above and belowground phenotypic response to exogenous auxin across Arabidopsis thaliana mutants and natural accessions varies from seedling to reproductive maturity

Background

Plant hormones influence phenology, development, and function of above and belowground plant structures. In seedlings, auxin influences the initiation and development of lateral roots and root systems. How auxin-related genes influence root initiation at early life stages has been investigated from numerous perspectives. There is a gap in our understanding of how these genes influence root size through the life cycle and in mature plants. Across development, the influence of a particular gene on plant phenotypes is partly regulated by the addition of a poly-A tail to mRNA transcripts via alternative polyadenylation (APA). Auxin related genes have documented variation in APA, with auxin itself contributing to APA site switches. Studies of the influence of exogenous auxin on natural plant accessions and mutants of auxin pathway gene families exhibiting variation in APA are required for a more complete understanding of genotype by development by hormone interactions in whole plant and fitness traits.

Methods

We studied Arabidopsis thaliana homozygous mutant lines with inserts in auxin-related genes previously identified to exhibit variation in number of APA sites. Our growth chamber experiment included wildtype Col-0 controls, mutant lines, and natural accession phytometers. We applied exogenous auxin through the life cycle. We quantified belowground and aboveground phenotypes in 14 day old, 21 day old seedlings and plants at reproductive maturity. We contrasted root, rosette and flowering phenotypes across wildtype, auxin mutant, and natural accession lines, APA groups, hormone treatments, and life stages using general linear models.

Results

The root systems and rosettes of mutant lines in auxin related genes varied in response to auxin applications across life stages and varied between genotypes within life stages. In seedlings, exposure to auxin decreased size, but increased lateral root density, whereas at reproductive maturity, plants displayed greater aboveground mass and total root length. These differences may in part be due to a shift which delayed the reproductive stage when plants were treated with auxin. Root traits of auxin related mutants depended on the number of APA sites of mutant genes and the plant's developmental stage. Mutants with inserts in genes with many APA sites exhibited lower early seedling belowground biomass than those with few APA sites but only when exposed to exogenous auxin. As we observed different responses to exogenous auxin across the life cycle, we advocate for further studies of belowground traits and hormones at reproductive maturity. Studying phenotypic variation of genotypes across life stages and hormone environments will uncover additional shared patterns across traits, assisting efforts to potentially reach breeding targets and enhance our understanding of variation of genotypes in natural systems.

GWAS of adventitious root formation in roses identifies a putative phosphoinositide phosphatase (SAC9) for marker-assisted selection

Rose propagation by cuttings is limited by substantial genotypic differences in adventitious root formation. To identify possible genetic factors causing these differences and to develop a marker for marker-assisted selection for high rooting ability, we phenotyped 95 cut and 95 garden rose genotypes in a hydroponic rooting system over 6 weeks. Data on rooting percentage after 3 to 6 weeks, root number, and root fresh mass were highly variable among genotypes and used in association mappings performed on genotypic information from the WagRhSNP 68 K Axiom SNP array for roses. GWAS analyses revealed only one significantly associated SNP for rooting percentage after 3 weeks. Nevertheless, prominent genomic regions/peaks were observed and further analysed for rooting percentage after 6 weeks, root number and root fresh mass. Some of the SNPs in these peak regions were associated with large effects on adventitious root formation traits. Very prominent were ten SNPs, which were all located in a putative phosphoinositide phosphatase SAC9 on chromosome 2 and showed very high effects on rooting percentage after 6 weeks of more than 40% difference between nulliplex and quadruplex genotypes. SAC9 was reported to be involved in the regulation of endocytosis and in combination with other members of the SAC gene family to regulate the translocation of auxin-efflux PIN proteins via the dephosphorylation of phosphoinositides. For one SNP within SAC9, a KASP marker was successfully derived and used to select genotypes with a homozygous allele configuration. Phenotyping these homozygous genotypes for adventitious root formation verified the SNP allele dosage effect on rooting. Hence, the presented KASP derived from a SNP located in SAC9 can be used for marker-assisted selection in breeding programs for high rooting ability in the future.

DNA methylation variation is crucial to restore adventitious rooting ability during in vitro shoot culture-induced rejuvenation in apple rootstock

In vitro shoot culture has been widely used for restoring adventitious rooting ability in rooting recalcitrant woody perennial species for the past few decades, but its molecular mechanism is largely uncovered. DNA methylation is an essential epigenetic mark that participates in many biological processes. Recent reports suggested a role of DNA methylation in vitro culture in plants. In this study, we characterized the single-base resolution DNA methylome and transcriptome of adult and in vitro shoot culture-induced rejuvenation cuttings of apple rootstock M9T337. We found a global decrease in DNA methylation during rejuvenation, which may be correlated with increased expression of DNA demethylase genes and decreased expression of DNA methyltransferase genes. We additionally documented DNA hypomethylation in 'T337'_R in gene protomer associated with higher transcript levels of several adventitious rooting-related genes. The application of a DNA methylation inhibitor (5-azacytidine) enhanced the adventitious rooting ability and the expression level of adventitious rooting-related genes, such as, MdANT, MdMPK3, MdABCB21, MdCDC48, MdKIN8B, pri-MdMIR156a5 and pri-MdMIR156a12. Together, the DNA hypomethylation is critical for the rejuvenation-dependent adventitious rooting ability in apple rootstock. In addition, increased DNA methylation was also found in thousands of genes in 'T337'_R. We additionally documented that DNA hypermethylation is required for inhibition of adventitious rooting-repressed genes, such as MdGAD5a, encoding glutamate decarboxylase, which can catalyze glutamate decarboxylated to form γ-aminobutyric acid (GABA). Our results revealed that in vitro shoot culture-dependent DNA methylation variation plays important roles in adventitious rooting in apple rootstock.

The MdmiR156n Regulates Drought Tolerance and Flavonoid Synthesis in Apple Calli and Arabidopsis

Drought is the major abiotic stress that limits apple productivity and quality. To date, many important and divergent regulatory functions of miR156/SBP genes in plant growth and development have been well understood. However, little is known about the role of apple miR156 in response to abiotic stress. To better understand the functions of MdmiR156 in abiotic stress tolerance, we constructed the overexpression (OE) and short tandem target mimic (STTM) vector of MdmiR156n and performed its functional analysis through the characterization of transgenic apple calli and Arabidopsis thaliana plants. In this study, MdmiR156n overexpression significantly increased the length of primary roots and the number of lateral roots in transgenic Arabidopsis plants under drought stress. In addition, MdmiR156n transgenic Arabidopsis and apple calli had a lower electrolyte leakage rate and less cell membrane damage than WT and STTM156 after drought stress. Further studies showed that MdmiR156n overexpression promoted the accumulation of flavonoids and scavenging of reactive oxygen species (ROS) under drought conditions in transgenic apple calli and A. thaliana plants. Taken together, overexpression MdmiR156n enhances drought tolerance by regulating flavonoid synthesis and ROS signaling cascades in apple calli and A. thaliana.

MicroRNA156ab regulates apple plant growth and drought tolerance by targeting transcription factor MsSPL13

Drought stress substantially reduces the productivity of apple plants and severely restricts the development of the apple industry. Malus sieversii, a wild apple with excellent drought resistance, is a valuable wild resource for rootstock improvement of cultivated apple (Malus domestica). miRNAs and their targets play essential roles in plant growth and stress responses, but their roles in drought stress responses in apple are unknown. Here, we demonstrate that microRNA156ab is upregulated in M. sieversii in response to drought stress. Overexpressing msi-miR156ab promoted auxin accumulation, maintained the growth of apple plants, and increased plant resistance to osmotic stress. Antioxidant enzyme activities and proline contents were also increased in miR156ab-OE transgenic apple lines, which improved drought resistance. The SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factor MsSPL13 is the target of msi-miR156ab, as demonstrated by 5-RACE and dual luciferase assays. Heterologous expression of MsSPL13 decreased auxin contents and inhibited growth in Arabidopsis (Arabidopsis thaliana) under normal and stress conditions. The activities of antioxidant enzymes were also suppressed in MsSPL13-OE transgenic Arabidopsis, reducing drought resistance. We showed that MsSPL13 regulates the expression of the auxin-related genes MsYUCCA5, PIN-FORMED7 (MsPIN7), and Gretchen Hagen3-5 (MsGH3-5) by binding to the GTAC cis-elements in their promoters, thereby regulating auxin metabolism. Finally, we demonstrated that the miR156ab-SPL13 module is involved in mediating the difference in auxin metabolism and stress responses between the M. sieversii and M26 (M. domestica) rootstocks. Overall, these findings reveal that the miR156ab-SPL13 module enhances drought stress tolerance in apples by regulating auxin metabolism and antioxidant enzyme activities.

Strigolactone regulates adventitious root formation via the MdSMXL7-MdWRKY6-MdBRC1 signaling cascade in apple

Propagation through stem cuttings is a popular method worldwide for species such as fruit tree rootstocks and forest trees. Adventitious root (AR) formation from stem cuttings is crucial for effective and successful clonal propagation of apple rootstocks. Strigolactones (SLs) are newly identified hormones involved in AR formation. However, the regulatory mechanisms underpinning this process remain elusive. In the present study, weighted gene co-expression network analysis, as well as rooting assays using stable transgenic apple materials, revealed that MdBRC1 served as a key gene in the inhibition of AR formation by SLs. We have demonstrated that MdSMXL7 and MdWRKY6 synergistically regulated MdBRC1 expression, depending on the interactions of MdSMXL7 and MdWRKY6 at the protein level downstream of SLs as well as the direct promoter binding on MdBRC1 by MdWRKY6. Furthermore, biochemical studies and genetic analysis revealed that MdBRC1 inhibited AR formation by triggering the expression of MdGH3.1 in a transcriptional activation pathway. Finally, the present study not only proposes a component, MdWRKY6, that enables MdSMXL7 to regulate MdBRC1 during the process of SL-controlled AR formation in apple, but also provides prospective target genes to enhance AR formation capacity using CRISPR (i.e. clustered regularly interspaced short palindromic repeats) technology, particularly in woody plants.

Integrated transgene and transcriptome reveal the molecular basis of MdWRKY87 positively regulate adventitious rooting in apple rootstock

For most fruit and forest species vegetative propagated from elite genotypes, adventitious rooting is essential. The ability to form adventitious roots significantly decreased during the juvenile to adult phase change. Apart from the miR156-SPL pathway, whether there is another regulation mechanism controlling age-dependent adventitious rooting ability remained largely unknown. In the present study, we showed that MdWRKY87 expression level was positively correlation with adventitious rooting ability. In addition, over-expressing of MdWRKY87 in tobacco leads to enhanced adventitious rooting ability, more adventitious root number and accelerated adventitious rooting process. Comparative transcriptome profiling indicated that MdWRKY87 overexpression can activate the expression of adventitious rooting-induced genes, such as WOX11 and AIL. In addition, MdWRKY87 overexpression can inhibit the transcription of adventitious rooting-repressed genes, such as AUX/IAAs and type-B cytokinin RRs. Collectively, here we demonstrated that higher expression level of MdWRKY87 contributes to age-dependent adventitious rooting-competent in juvenile apple rootstock.

Biologically Oriented Hybrids of Indole and Hydantoin Derivatives

Indoles and hydantoins are important heterocycles scaffolds which present in numerous bioactive compounds which possess various biological activities. Moreover, they are essential building blocks in organic synthesis, particularly for the preparation of important hybrid molecules. The series of hybrid compounds containing indoles and imidazolidin-2-one moiety with direct C-C bond were synthesized using an amidoalkylation one-pot reaction. All compounds were investigated as a growth regulator for germination, growth and development of wheat seeds (Triticum aestivum L). Their effect on drought resistance at very low concentrations (4 × 10^-5 M) was evaluated. The study highlighted identified the leading compounds, 3a and 3e, with higher growth-regulating activity than the indole-auxin analogues.

Integrated multi-omics analysis uncovers roles of mdm-miR164b-MdORE1 in strigolactone-mediated inhibition of adventitious root formation in apple

Apple is one of the most important fruit crops in temperate regions and largely relies on cutting propagation. Adventitious root formation is crucial for the success of cutting propagation. Strigolactones have been reported to function in rooting of woody plants. In this study, we determined that strigolactones have inhibitory effects on adventitious root formation in apple. Transcriptome analysis identified 12 051 differentially expressed genes over the course of adventitious root initiation, with functions related to organogenesis, cell wall biogenesis or plant development. Further analysis indicated that strigolactones might inhibit adventitious root formation through repressing two core hub genes, MdLAC3 and MdORE1. Combining small RNA and degradome sequencing, as well as dual-luciferase sensor assays, we identified and validated three negatively correlated miRNA-mRNA pairs, including mdm-miR397-MdLAC3 and mdm-miR164a/b-MdORE1. Overexpression of mdm-miR164b and silencing MdORE1 exhibited enhanced adventitious root formation in tobacco and apple, respectively. Finally, we verified the role of mdm-miR164b-MdORE1 in strigolactone-mediated repression of rooting ability. Overall, the identified comprehensive regulatory network in apple not only provides insight into strigolactone-mediated adventitious root formation in other woody plants, but also points to a potential strategy for genetic improvement of rooting capacity in woody plants.

Transcription Factor IAA27 Positively Regulates P Uptake through Promoted Adventitious Root Development in Apple Plants

Phosphate (P) deficiency severely limits the growth and production of plants. Adventitious root development plays an essential role in responding to low phosphorus stress for apple plants. However, the molecular mechanisms regulating adventitious root growth and development in response to low phosphorus stress have remained elusive. In this study, a mutation (C-T) in the coding region of the apple AUXIN/INDOLE-3-ACETIC ACID 27 (IAA27) gene was identified. MdIAA27T-overexpressing transgenic apple improved the tolerance to phosphorus deficiency, which grew longer and denser adventitious roots and presented higher phosphorous content than the control plants under low phosphorus conditions, while the overexpression of MdIAA27C displayed the opposite trend. Moreover, the heterologous overexpression of MdIAA27 in tobacco yielded the same results, supporting the aforementioned findings. In vitro and in vivo assays showed that MdIAA27 directly interacted with AUXIN RESPONSE FACTOR (ARF8), ARF26 and ARF27, which regulated Small Auxin-Up RNA 76 (MdSAUR76) and lateral organ boundaries domain 16 (MdLBD16) transcription. The mutation in IAA27 resulted in altered interaction modes, which in turn promoted the release of positive ARFs to upregulate SAUR76 and LBD16 expression in low phosphorus conditions. Altogether, our studies provide insights into how the allelic variation of IAA27 affects adventitious root development in response to low phosphorus stress.

Roles of Auxin in the Growth, Development, and Stress Tolerance of Horticultural Plants

Auxin, a plant hormone, regulates virtually every aspect of plant growth and development. Many current studies on auxin focus on the model plant Arabidopsis thaliana, or on field crops, such as rice and wheat. There are relatively few studies on what role auxin plays in various physiological processes of a range of horticultural plants. In this paper, recent studies on the role of auxin in horticultural plant growth, development, and stress response are reviewed to provide novel insights for horticultural researchers and cultivators to improve the quality and application of horticultural crops.

MdWOX4-2 modulated MdLBD41 functioning in adventitious shoot of apple (Malus domestica)

Apple (Malus domestica Borkh.) is not only an important fruit crop distributed worldwide, but also a common model plant. However, the lack of efficient genetic transformation procedures for apples limits the in-depth studies of their gene functions. Although leaf-regenerated adventitious shoots (LRAS) are a prerequisite for successful genetic transformation of apple, little is known about the underlying molecular mechanism of LRAS. Here, we identified the WUSCHEL-related homeobox (WOX) transcription factor in apple, MdWOX4-2, which was a transcriptional activator. Gene expression as well as morphological and histological observations revealed that MdWOX4-2 is involved in the development of LRAS. Overexpression of MdWOX4-2 conferred higher regenerative capacity in transgenic tobacco (Nicotiana tabacum) as compared to the wild type (WT). The combined results of the yeast one-hybrid (Y1H), electrophoretic mobility shift assay (EMSA), dual luciferase assays, and transient transactivation assay, revealed that MdWOX4-2 directly bound to and activated the MdLBD41 promoter. Moreover, transgenic experiments further demonstrated that MdLBD41 could significantly enhance the formation of adventitious shoot in transgenic tobacco. Collectively, our findings demonstrate that MdWOX4-2 is important for regulating the LRAS development by activating MdLBD41.

Key regulatory pathways, microRNAs, and target genes participate in adventitious root formation of Acer rubrum L

Red maple (Acer rubrum L.) is a type of colorful ornamental tree with great economic value. Because this tree is difficult to root under natural conditions and the seedling survival rate is low, vegetative propagation methods are often used. Because the formation of adventitious roots (ARs) is essential for the asexual propagation of A. rubrum, it is necessary to investigate the molecular regulatory mechanisms of AR formation in A. rubrum. To address this knowledge gap, we sequenced the transcriptome and small RNAs (sRNAs) of the A. rubrum variety ‘Autumn Fantasy’ using high-throughput sequencing and explored changes in gene and microRNA (miRNA) expression in response to exogenous auxin treatment. We identified 82,468 differentially expressed genes (DEGs) between the treated and untreated ARs, as well as 48 known and 95 novel miRNAs. We also identified 172 target genes of the known miRNAs using degradome sequencing. Two key regulatory pathways (ubiquitin mediated proteolysis and plant hormone signal transduction), Ar-miR160a and the target gene auxin response factor 10 (ArARF10) were selected based on KEGG pathway and cluster analyses. We further investigated the expression patterns and regulatory roles of ArARF10 through subcellular localization, transcriptional activation, plant transformation, qRT-PCR analysis, and GUS staining. Experiments overexpressing ArARF10 and Ar-miR160a, indicated that ArARF10 promoted AR formation, while Ar-miR160a inhibited AR formation. Transcription factors (TFs) and miRNAs related to auxin regulation that promote AR formation in A. rubrum were identified. Differential expression patterns indicated the Ar-miR160a-ArARF10 interaction might play a significant role in the regulation of AR formation in A. rubrum. Our study provided new insights into mechanisms underlying the regulation of AR formation in A. rubrum.

The BTB protein MdBT2 recruits auxin signaling components to regulate adventitious root formation in apple

Ubiquitination is an important post-translational protein modification. Although BROAD-COMPLEX, TRAMTRACK AND BRIC A BRAC and TRANSCRIPTION ADAPTOR PUTATIVE ZINC FINGER domain protein 2 (BT2) is involved in many biological processes, its role in apple (Malus domestic) root formation remains unclear. Here, we revealed that MdBT2 inhibits adventitious root (AR) formation through interacting with AUXIN RESPONSE FACTOR8 (MdARF8) and INDOLE-3-ACETIC ACID INDUCIBLE3 (MdIAA3). MdBT2 facilitated MdARF8 ubiquitination and degradation through the 26S proteasome pathway and negatively regulated GRETCHEN HAGEN 3.1 (MdGH3.1) and MdGH3.6 expression. MdARF8 regulates AR formation through inducing transcription of MdGH3s (MdGH3.1, MdGH3.2, MdGH3.5, and MdGH3.6). In addition, MdBT2 facilitated MdIAA3 stability and slightly promoted its interaction with MdARF8. MdIAA3 inhibited AR formation by forming heterodimers with MdARF8 as well as other MdARFs (MdARF5, MdARF6, MdARF7, and MdARF19). Our findings reveal that MdBT2 acts as a negative regulator of AR formation in apple.

Transcriptome analysis reveals that cytokinins inhibit adventitious root formation through the MdRR12-MdCRF8 module in apple rootstock

Adventitious root (AR) formation is great significance for apple rootstock breeding. Transcriptome analyses were performed with cytokinins (CTKs) signal treatments to analyze the mechanism of AR formation. The results showed that 6-benzyadenine (6-BA) treatment inhibited AR formation. Histological analysis also observed that AR primordium cell formation was significantly suppressed by 6-BA treatment; the ratio of auxin/cytokinins exhibited the lowest values at 1 and 3 day (d) in the 6-BA treatment group. Furthermore, the differentially expressed genes were divided into five categories, including auxin, cytokinins, other hormones, cell cycle, and carbohydrate metabolism pathways. Due to the study of cytokinins signal treatment, it is important to understand the particular module mediated by the cytokinins pathway. The expression level of MdRR12 (a family member of B-type cytokinins-responsive factors) was significantly upregulated at 3 d by 6-BA treatment. Compared to the wild type, the 35S::MdRR12 transgenic tobaccos suppressed AR formation. The promoter sequence of MdCRF8 contains AGATT motif elements that respond to MdRR12. RNA-seq and RT-qPCR assays predicted cytokinins response factor (MdCRF8) to be a downstream gene regulated by MdRR12. The activity of the pro-MdCRF8-GUS promoter was obviously induced by 6-BA treatment and inhibited by lovastatin (Lov) treatment. Yeast one-hybrid, dual-luciferase reporter, and GUS coexpression assays revealed that MdRR12 could directly bind to the MdCRF8 promoter. Additionally, 35S::MdCRF8 transgenic tobaccos also blocked AR growth. Compared to the wild type, 35S::MdRR12 and 35S::MdCRF8 transgenic tobaccos enhanced sensitivity to cytokinins. Thus, we describe that MdRR12 and MdCRF8 function as integrators of cytokinins signals that affect cell cycle- and carbohydrate metabolism-related genes to regulate cell fate transition during AR formation. On the basis of these results, we concluded that the MdRR12-MdCRF8 module is involved in the negative regulation of AR formation in apple rootstock and can potentially be applied in agriculture using genetic approaches.

Insights into Factors Controlling Adventitious Root Formation in Apples

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.

Plant Growth Regulators in Tree Rooting

Trees are long-lived organisms with complex life cycles that provide enormous benefits both in natural and cultivated stands [...]

The positive feedback regulatory loop of miR160-Auxin Response Factor 17-HYPONASTIC LEAVES 1 mediates drought tolerance in apple trees

Drought stress tolerance is a complex trait regulated by multiple factors. Here, we demonstrate that the miRNA160-Auxin Response Factor 17 (ARF17)-HYPONASTIC LEAVES 1 module is crucial for apple (Malus domestica) drought tolerance. Using stable transgenic plants, we found that drought tolerance was improved by higher levels of Mdm-miR160 or MdHYL1 and by decreased levels of MdARF17, whereas reductions in MdHYL1 or increases in MdARF17 led to greater drought sensitivity. Further study revealed that modulation of drought tolerance was achieved through regulation of drought-responsive miRNA levels by MdARF17 and MdHYL1; MdARF17 interacted with MdHYL1 and bound to the promoter of MdHYL1. Genetic analysis further suggested that MdHYL1 is a direct downstream target of MdARF17. Importantly, MdARF17 and MdHYL1 regulated the abundance of Mdm-miR160. In addition, the Mdm-miR160-MdARF17-MdHYL1 module regulated adventitious root development. We also found that Mdm-miR160 can move from the scion to the rootstock in apple and tomato (Solanum lycopersicum), thereby improving root development and drought tolerance of the rootstock. Our study revealed the mechanisms by which the positive feedback loop of Mdm-miR160-MdARF17-MdHYL1 influences apple drought tolerance.

Shaping the root system: the interplay between miRNA regulatory hubs and phytohormones

The root system commonly lies underground, where it provides anchorage for the aerial organs, as well as nutrients and water. Both endogenous and environmental cues contribute to the establishment of the root system. Among the endogenous cues, microRNAs (miRNAs), transcription factors, and phytohormones modulate root architecture. miRNAs belong to a subset of endogenous hairpin-derived small RNAs that post-transcriptionally control target gene expression, mostly transcription factors, comprising the miRNA regulatory hubs. Phytohormones are signaling molecules involved in most developmental processes. Some miRNAs and targets participate in more than one hormonal pathway, thereby providing new bridges in plant hormonal crosstalk. Unraveling the intricate network of molecular mechanisms underlying the establishment of root systems is a central aspect in the development of novel strategies for plant breeding to increase yield and optimize agricultural land use. In this review, we summarize recent findings describing the molecular mechanisms associated with the interplay between miRNA regulatory hubs and phytohormones to ensure the establishment of a proper root system. We focus on post-embryonic growth and development of primary, lateral, and adventitious roots. In addition, we discuss novel insights for future research on the interaction between miRNAs and phytohormones in root architecture.

An HD-ZIP transcription factor, MxHB13, integrates auxin-regulated and juvenility-determined control of adventitious rooting in Malus xiaojinensis

Adventitious root (AR) formation is a critical factor in the vegetative propagation of forestry and horticultural plants. Competence for AR formation declines in many species during the miR156/SPL-mediated vegetative phase change. Auxin also plays a regulatory role in AR formation. In apple rootstock, both high miR156 expression and exogenous auxin application are prerequisites for AR formation. However, the mechanism by which the miR156/SPL module interacts with auxin in controlling AR formation is unclear. In this paper, leafy cuttings of juvenile (Mx-J) and adult (Mx-A) phase Malus xiaojinensis were used in an RNA-sequencing experiment. The results revealed that numerous genes involved in phytohormone signaling, carbohydrate metabolism, cell dedifferentiation, and reactivation were downregulated in Mx-A cuttings in response to indole butyric acid treatment. Among the differentially expressed genes, an HD-ZIP transcription factor gene, MxHB13, was found to be under negative regulation of MdSPL26 by directly binding to MxHB13 promoter. MxTIFY9 interacts with MxSPL26 and may play a role in co-repressing the expression of MxHB13. The expression of MxTIFY9 was induced by exogenous indole butyric acid. MxHB13 binds to the promoter of MxABCB19-2 and positively affects the expression. A model is proposed in which MxHB13 links juvenility-limited and auxin-limited AR recalcitrance mechanisms in Mx-A.

Mdm-MIR393b-mediated adventitious root formation by targeted regulation of MdTIR1A expression and weakened sensitivity to auxin in apple rootstock

Adventitious root (AR) formation is of great significance for apple rootstock breeding. It is widely accepted that miR393 influences AR formation in many plant species; however, the molecular mechanism by which factors regulate AR formation remains insufficient. In this study, the evolutionary relationship of mdm-miR393 and candidate target genes MdTIR1/AFB was systematically identified, and the expression patterns were analysed. Multisequence alignment analysis of miR393 family members suggests that miR393 conservatively evolved between different species. The evolutionary relationship of the TIR1/AFBs can be divided into G1, G2 and G3 subgroups. During AR formation, the expression level of mdm-miR393a/b/c was significantly upregulated at 1 d and 7 d by exogenous auxin treatment. Furthermore, the expression levels of MdTIR1A, MdTIR1D, MdAFB1, MdAFB2, MdAFB3, MdAFB4 and MdAFB8 also appeared to be significantly changed by exogenous auxin induction. Subsequently, tissue-specific expression analysis showed that the expression levels of mdm-miR393 and MdTIR1/AFBs in different tissues exhibited significant differences. The promoter of mdm-miR393 contains multiple elements that respond to ABA, adversity and light signals; auxin treatment can activate the mdm-MIR393b promoter but is obviously inhibited by NPA treatment. The targeting relationship between mdm-MIR393b and MdTIR1A was verified by expression patterns, degradation group data, transient tobacco conversion results, and genes functions experiments. Heterologous overexpression of mdm-MIR393b (35S::mdm-MIR393b) decreased the number of ARs in the phenotype and reduced the expression level of the target gene NtTIR1 in tobacco. Compared to the wild type, the 35S::mdm-MIR393b transgenic plants demonstrated insensitivity to auxin. Furthermore, tir1 mutant exhibited reduced root system structure relative to the control. The above results illustrated that mdm-MIR393b is involved in mediating AR formation by targeted regulation of MdTIR1A expression in apple rootstock.

Reinvigoration/Rejuvenation Induced through Micrografting of Tree Species: Signaling through Graft Union

Trees have a distinctive and generally long juvenile period during which vegetative growth rate is rapid and floral organs do not differentiate. Among trees, the juvenile period can range from 1 year to 15–20 years, although with some forest tree species, it can be longer. Vegetative propagation of trees is usually much easier during the juvenile phase than with mature phase materials. Therefore, reversal of maturity is often necessary in order to obtain materials in which rooting ability has been restored. Micrografting has been developed for trees to address reinvigoration/rejuvenation of elite selections to facilitate vegetative propagation. Generally, shoots obtained after serial grafting have increased rooting competence and develop juvenile traits; in some cases, graft-derived shoots show enhanced in vitro proliferation. Recent advances in graft signaling have shown that several factors, e.g., plant hormones, proteins, and different types of RNA, could be responsible for changes in the scion. The focus of this review includes (1) a discussion of the differences between the juvenile and mature growth phases in trees, (2) successful restoration of juvenile traits through micrografting, and (3) the nature of the different signals passing through the graft union.

Bracing for sustainable agriculture: the development and function of brace roots in members of Poaceae

Optimization of crop production requires root systems to function in water uptake, nutrient use, and anchorage. In maize, two types of nodal roots-subterranean crown and aerial brace roots function in anchorage and water uptake and preferentially express multiple water and nutrient transporters. Brace root development shares genetic control with juvenile-to-adult phase change and flowering time. We present a comprehensive list of the genes known to alter brace roots and explore these as candidates for QTL studies in maize and sorghum. Brace root development and function may be conserved in other members of Poaceae, however research is limited. This work highlights the critical knowledge gap of aerial nodal root development and function and suggests new focus areas for breeding resilient crops.

Phylogenetic Analysis of the SQUAMOSA Promoter-Binding Protein-Like Genes in Four Ipomoea Species and Expression Profiling of the IbSPLs During Storage Root Development in Sweet Potato (Ipomoea batatas)

As a major plant-specific transcription factor family, SPL genes play a crucial role in plant growth, development, and stress tolerance. The SPL transcription factor family has been widely studied in various plant species; however, systematic studies on SPL genes in the genus Ipomoea are lacking. Here, we identified a total of 29, 27, 26, and 23 SPLs in Ipomoea batatas, Ipomoea trifida, Ipomoea triloba, and Ipomoea nil, respectively. Based on the phylogenetic analysis of SPL proteins from model plants, the Ipomoea SPLs were classified into eight clades, which included conserved gene structures, domain organizations and motif compositions. Moreover, segmental duplication, which is derived from the Ipomoea lineage-specific whole-genome triplication event, was speculated to have a predominant role in Ipomoea SPL expansion. Particularly, tandem duplication was primarily responsible for the expansion of SPL subclades IV-b and IV-c. Furthermore, 25 interspecific orthologous groups were identified in Ipomoea, rice, Arabidopsis, and tomato. These findings support the expansion of SPLs in Ipomoea genus, with most of the SPLs being evolutionarily conserved. Of the 105 Ipomoea SPLs, 69 were predicted to be the targets of miR156, with seven IbSPLs being further verified as targets using degradome-seq data. Using transcriptomic data from aboveground and underground sweet potato tissues, IbSPLs showed diverse expression patterns, including seven highly expressed IbSPLs in the underground tissues. Furthermore, the expression of 11 IbSPLs was validated using qRT-PCR, and two (IbSPL17/IbSPL28) showed significantly increased expression during root development. Additionally, the qRT-PCR analysis revealed that six IbSPLs were strongly induced in the roots under phytohormone treatments, particularly zeatin and abscisic acid. Finally, the transcriptomic data of storage roots from 88 sweet potato accessions were used for weighted gene co-expression network analysis, which revealed four IbSPLs (IbSPL16/IbSPL17/IbSPL21/IbSPL28) clusters with genes involved in "regulation of root morphogenesis," "cell division," "cytoskeleton organization," and "plant-type cell wall organization or biogenesis," indicating their potential role in storage root development. This study not only provides novel insights into the evolutionary and functional divergence of the SPLs in the genus Ipomoea but also lays a foundation for further elucidation of the potential functional roles of IbSPLs on storage root development.

Molecular Bases for the Regulation of Adventitious Root Generation in Plants

The formation of adventitious roots (ARs) is an ecologically and economically important developmental process in plants. The evolution of AR systems is an important way for plants to cope with various environmental stresses. This review focuses on identified genes that have known to regulate the induction and initiation of ARs and offers an analysis of this process at the molecular level. The critical genes involved in adventitious rooting are the auxin signaling-responsive genes, including the AUXIN RESPONSE FACTOR (ARF) and the LATERAL ORGAN BOUNDARIES-DOMAIN (LOB) gene families, and genes associated with auxin transport and homeostasis, the quiescent center (QC) maintenance, and the root apical meristem (RAM) initiation. Several genes involved in cell wall modulation are also known to be involved in the regulation of adventitious rooting. Furthermore, the molecular processes that play roles in the ethylene, cytokinin, and jasmonic acid signaling pathways and their crosstalk modulate the generation of ARs. The crosstalk and interaction among many molecular processes generates complex networks that regulate AR generation.

Intricate genetic variation networks control the adventitious root growth angle in apple

Background

The root growth angle (RGA) typically determines plant rooting depth, which is significant for plant anchorage and abiotic stress tolerance. Several quantitative trait loci (QTLs) for RGA have been identified in crops. However, the underlying mechanisms of the RGA remain poorly understood, especially in apple rootstocks. The objective of this study was to identify QTLs, validate genetic variation networks, and develop molecular markers for the RGA in apple rootstock.

Results

Bulked segregant analysis by sequencing (BSA-seq) identified 25 QTLs for RGA using 1955 hybrids of the apple rootstock cultivars ‘Baleng Crab’ (Malus robusta Rehd., large RGA) and ‘M9’ (M. pumila Mill., small RGA). With RNA sequencing (RNA-seq) and parental resequencing, six major functional genes were identified and constituted two genetic variation networks for the RGA. Two single nucleotide polymorphisms (SNPs) of the MdLAZY1 promoter damaged the binding sites of MdDREB2A and MdHSFB3, while one SNP of MdDREB2A and MdIAA1 affected the interactions of MdDREB2A/MdHSFB3 and MdIAA1/MdLAZY1, respectively. A SNP within the MdNPR5 promoter damaged the interaction between MdNPR5 and MdLBD41, while one SNP of MdLBD41 interrupted the MdLBD41/MdbHLH48 interaction that affected the binding ability of MdLBD41 on the MdNPR5 promoter. Twenty six SNP markers were designed on candidate genes in each QTL interval, and the marker effects varied from 0.22°-26.11°.

Conclusions

Six diagnostic markers, SNP592, G122, b13, Z312, S1272, and S1288, were used to identify two intricate genetic variation networks that control the RGA and may provide new insights into the accuracy of the molecular markers. The QTLs and SNP markers can potentially be used to select deep-rooted apple rootstocks.

Genome-wide identification and characterization of Respiratory Burst Oxidase Homolog genes in six Rosaceae species and an analysis of their effects on adventitious rooting in apple

Adventitious root formation is essential for plant propagation, development, and response to various stresses. Reactive oxygen species (ROS) are essential for adventitious root formation. However, information on Respiratory Burst Oxidase Homolog (RBOH), a key enzyme that catalyzes the production ROS, remains limited in woody plants. Here, a total of 44 RBOH genes were identified from six Rosaceae species (Malus domestica, Prunus avium, Prunus dulcis 'Texas’, Rubus occidentalis, Fragaria vesca and Rosa chinensis), including ten from M. domestica. Their phylogenetic relationships, conserved motifs and gene structures were analyzed. Exogenous treatment with the RBOH protein inhibitor diphenyleneiodonium (DPI) completely inhibited adventitious root formation, whereas exogenous H₂O₂ treatment enhanced adventitious root formation. In addition, we found that ROS accumulated during adventitious root primordium inducing process. The expression levels of MdRBOH-H, MdRBOH-J, MdRBOH-A, MdRBOH-E1 and MdRBOH-K increased more than two-fold at days 3 or 9 after auxin treatment. In addition, cis-acting element analysis revealed that the MdRBOH-E1 promoter contained an auxin-responsive element and the MdRBOH-K promoter contained a meristem expression element. Based on the combined results from exogenous DPI and H₂O₂ treatment, spatiotemporal expression profiling, and cis-element analysis, MdRBOH-E1 and MdRBOH-K appear to be candidates for the control of adventitious rooting in apple.

Overexpression of MsGH3.5 inhibits shoot and root development through the auxin and cytokinin pathways in apple plants

Phytohormonal interactions are crucial for plant development. Auxin and cytokinin (CK) both play critical roles in regulating plant growth and development; however, the interaction between these two phytohormones is complex and not fully understood. Here, we isolated a wild apple (Malus sieversii Roem) GRETCHEN HAGEN3 (GH3) gene, MsGH3.5, encoding an indole-3-acetic acid (IAA)-amido synthetase. Overexpression of MsGH3.5 significantly reduced the free IAA content and increased the content of some IAA-amino acid conjugates, and MsGH3.5-overexpressing lines were dwarfed and produced fewer adventitious roots (ARs) than the control. This phenotype is consistent with the role of GH3 in conjugating excess free active IAA to amino acids in auxin homeostasis. Surprisingly, overexpression of MsGH3.5 significantly increased CK concentrations in the whole plant, and altered the expression of genes involved in CK biosynthesis, metabolism and signaling. Furthermore, exogenous CK application induced MsGH3.5 expression through the activity of the CK type-B response regulator, MsRR1a, which mediates the CK primary response. MsRR1a activated MsGH3.5 expression by directly binding to its promoter, linking auxin and CK signaling. Plants overexpressing MsRR1a also displayed fewer ARs, in agreement with the regulation of MsGH3.5 expression by MsRR1a. Taken together, we reveal that MsGH3.5 affects apple growth and development by modulating auxin and CK levels and signaling pathways. These findings provide insight into the interaction between the auxin and CK pathways, and might have substantial implications for efforts to improve apple architecture.

The role of miR156 in rejuvenation in Arabidopsis thaliana

Rejuvenation refers to the process enabling plants to regain physiological and molecular characteristics lost after entering the adult phase. The underlying molecular mechanism is poorly understood. Previous studies have revealed that microRNA156 (miR156) is highly accumulated at juvenile stage and maintains juvenile traits by repressing a group of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors. Here, we found that induction of miR156 expression in adult leaves can only restore some aspects of juvenile traits, such as loss of epidermal leaf hairs on the lower side of leaves and absence of serration at the leaf edges, but is incapable of delaying flowering and promoting adventitious root production.

Auxin perception in Agave is dependent on the species' Auxin Response Factors

Auxins are one of the most important and studied phytohormones in nature. Auxin signaling and perception take place in the cytosol, where the auxin is sensed. Then, in the nucleus, the auxin response factors (ARF) promote the expression of early-response genes. It is well known that not all plants respond to the same amount and type of auxins and that the response can be very different even among plants of the same species, as we present here. Here we investigate the behavior of ARF in response to various auxins in Agave angustifolia Haw., A. fourcroydes Lem. and A. tequilana Weber var. Azul. By screening the available database of A. tequilana genes, we have identified 32 ARF genes with high sequence identity in the conserved domains, grouped into three main clades. A phylogenetic tree was inferred from alignments of the 32 Agave ARF protein sequences and the evolutionary relationship with other species was analyzed. AteqARF 4, 15, 21, and 29 were selected as a representative diverse sample coming from each of the different subclades that comprise the two main clades of the inferred phylogenetic reconstruction. These ARFs showed differential species-specific expression patterns in the presence of indole-3-acetic acid (IAA) and 2,4-dichlorophenoxyacetic acid (2,4-D). Interestingly, A. angustifolia showed different phenotypes in the presence and absence of auxins. In the absence of auxin, A. angustifolia produces roots, while shoots are developed in the presence of IAA. However, in the presence of 2,4-D, the plant meristem converts into callus. According to our results, it is likely that AteqARF15 participates in this outcome.

miR156-targeted SPL10 controls Arabidopsis root meristem activity and root-derived de novo shoot regeneration via cytokinin responses

Root growth is modulated by different factors, including phytohormones, transcription factors, and microRNAs (miRNAs). MicroRNA156 and its targets, the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes, define an age-dependent pathway that controls several developmental processes, including lateral root emergence. However, it remains unclear whether miR156-regulated SPLs control root meristem activity and root-derived de novo shoot regeneration. Here, we show that MIR156 and SPL genes have opposing expression patterns during the progression of primary root (PR) growth in Arabidopsis, suggesting that age cues may modulate root development. Plants with high miR156 levels display reduced meristem size, resulting in shorter primary root (PRs). Conversely, plants with reduced miR156 levels show higher meristem activity. Importantly, loss of function of SPL10 decreases meristem activity, while SPL10 de-repression increases it. Meristem activity is regulated by SPL10 probably through the reduction of cytokinin responses, via the modulation of type-B ARABIDOPSIS RESPONSE REGULATOR1(ARR1) expression. We also show that SPL10 de-repression in the PRs abolishes de novo shoot regenerative capacity by attenuating cytokinin responses. Our results reveal a cooperative regulation of root meristem activity and root-derived de novo shoot regeneration by integrating age cues with cytokinin responses via miR156-targeted SPL10.

AP2/ERF Transcription Factors Integrate Age and Wound Signals for Root Regeneration

Age and wounding are two major determinants for regeneration. In plants, the root regeneration is triggered by wound-induced auxin biosynthesis. As plants age, the root regenerative capacity gradually decreases. How wounding leads to the auxin burst and how age and wound signals collaboratively regulate root regenerative capacity are poorly understood. Here, we show that the increased levels of three closely-related miR156-targeted Arabidopsis (Arabidopsis thaliana) SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors, SPL2, SPL10, and SPL11, suppress root regeneration with age by inhibiting wound-induced auxin biosynthesis. Mechanistically, we find that a subset of APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) transcription factors including ABSCISIC ACID REPRESSOR1 and ERF109 is rapidly induced by wounding and serves as a proxy for wound signal to induce auxin biosynthesis. In older plants, SPL2/10/11 directly bind to the promoters of AP2/ERFs and attenuates their induction, thereby dampening auxin accumulation at the wound. Our results thus identify AP2/ERFs as a hub for integration of age and wound signal for root regeneration.

The Artificial Promoter rMdAG2I Confers Flower-specific Activity in Malus

Genetic modifications of floral organs are important in the breeding of Malus species. Flower-specific promoters can be used to improve floral organs specifically, without affecting vegetative organs, and therefore developing such promoters is highly desirable. Here, we characterized two paralogs of the Arabidopsis thaliana gene AGAMOUS (AG) from Malus domestica (apple): MdAG1 and MdAG2. We then isolated the second-intron sequences for both genes, and created four artificial promoters by fusing each intron sequence to a minimal 35S promoter sequence in both the forward and reverse directions. When transferred into tobacco (Nicotiana benthamiana) by Agrobacterium tumefaciens-mediated stable transformation, one promoter, rMdAG2I, exhibited activity specifically in flowers, whereas the other three also showed detectable activity in vegetative organs. A test of the four promoters’ activities in the ornamental species Malus micromalus by Agrobacterium-mediated transient transformation showed that, as in tobacco, only rMdAG2I exhibited a flower-specific expression pattern. Through particle bombardment transformation, we demonstrated that rMdAG2I also had flower-specific activity in the apple cultivar ‘Golden Delicious’. The flower-specific promoter rMdAG2I, derived from M. domestica, thus has great potential for use in improving the floral characteristics of ornamental plants, especially the Malus species.

The grain yield modulator miR156 regulates seed dormancy through the gibberellin pathway in rice

The widespread agricultural problem of pre-harvest sprouting (PHS) could potentially be overcome by improving seed dormancy. Here, we report that miR156, an important grain yield regulator, also controls seed dormancy in rice. We found that mutations in one MIR156 subfamily enhance seed dormancy and suppress PHS with negligible effects on shoot architecture and grain size, whereas mutations in another MIR156 subfamily modify shoot architecture and increase grain size but have minimal effects on seed dormancy. Mechanistically, mir156 mutations enhance seed dormancy by suppressing the gibberellin (GA) pathway through de-represssion of the miR156 target gene Ideal Plant Architecture 1 (IPA1), which directly regulates multiple genes in the GA pathway. These results provide an effective method to suppress PHS without compromising productivity, and will facilitate breeding elite crop varieties with ideal plant architectures.

Pre-harvest sprouting reduces the yield of agriculturally important crops such as rice. Here, the authors show that mutating specific members of the MIR156 gene family can suppress pre-harvest sprouting in rice without negative effects on plant architecture, suggesting a practical route to elite crop varieties.

miRNAs associated with auxin signaling, stress response, and cellular activities mediate adventitious root formation in apple rootstocks

Adventitious root (AR) formation is essential for the vegetative propagation of apple rootstocks. miRNAs play a significant role in regulating AR development, however, large-scale transcriptomic data on miRNA mediated AR formation in apple rootstocks is lacking. Therefore, in order to identify the molecular mechanisms underlying AR formation in 'M9-T337' apple rootstocks, transcriptomic changes occurring during key time points of AR formation (0, 3, and 16 days) were analyzed using high-throughput sequencing with a focus on miRNAs. A total of 84 known miRNAs and 56 novel miRNAs have differentially expressed were identified. Additionally, a total of 88 target genes of known miRNAs and 76 target genes of novel miRNAs were identified by degradome sequencing. The expression levels of the miRNAs and target genes were quantified by RT-qPCR. Results indicate that miRNAs and their target genes are associated with auxin signal-related (miR160 and miR390), stress response-related (miR398, miR395 and miR408), cell fate transformation-, proliferation- and enlargement-related (miR171, miR156, miR166, miR319 and miR396). These all involve pathways that participate in AR formation in 'M9-T337' apple rootstock. In addition, hormones (AUX, CTK, GA3, BR, JA, and ABA) are also involved in regulating AR formation. The candidate genes belonging to pathways associated with AR formation exhibited significantly higher expression levels, providing evidence that they may be involved in the regulation of AR development. The collective results of the present study indicate that the developmental process associated with AR formation in apple rootstock is extremely complex. The known and novel miRNAs and target genes that were identified by high-throughput and degradome sequencing, respectively, provide a framework for the future analysis of miRNAs associated with AR development in apple rootstocks, and provide new information that can be used to better understand AR development in woody plants.

OsSPL3, an SBP-Domain Protein, Regulates Crown Root Development in Rice

The major root system of cereals consists of crown roots (or adventitious roots), which are important for anchoring plants in the soil and for water and nutrient uptake. However, the molecular basis of crown root formation is largely unknown. Here, we isolated a rice (Oryza sativa) mutant with fewer crown roots, named lower crown root number1 (lcrn1). Map-based cloning revealed that lcrn1 is caused by a mutation of a putative transcription factor-coding gene, O. sativa SQUAMOSA PROMOTER BINDING PROTEIN-LIKE3 (OsSPL3). We demonstrate that the point mutation in lcrn1 perturbs theO. sativa microRNA156 (OsmiR156)-directed cleavage of OsSPL3 transcripts, resulting in the mutant phenotype. Chromatin immunoprecipitation sequencing assays of OsSPL3 binding sites and RNA sequencing of differentially expressed transcripts in lcrn1 further identified potential direct targets of OsSPL3 in basal nodes, including a MADS-box transcription factor, OsMADS50. OsMADS50-overexpressing plants produced fewer crown roots, phenocopying lcrn1, while knocking out OsMADS50 in the lcrn1 background reversed this phenotype. We also show that OsSPL12, another OsmiR156 target gene, regulates OsMADS50 and crown root development. Taken together, our findings suggest a novel regulatory pathway in which the OsmiR156-OsSPL3/OsSPL12 module directly activates OsMADS50 in the node to regulate crown root development in rice.

Methane Control of Adventitious Rooting Requires γ-Glutamyl Cysteine Synthetase-Mediated Glutathione Homeostasis

Although the key role of methane (CH4) in the induction of cucumber adventitious rooting has been observed previously, the target molecules downstream of the CH4 action are yet to be fully elucidated. Here, we reported that exogenous glutathione (GSH) induced cucumber adventitious root formation; while l-buthionine-sulfoximine (BSO) treatment inhibited it. BSO is a known inhibitor of γ-glutamyl cysteine synthetase (γ-ECS), an enzyme involved in GSH biosynthesis. Further investigations showed that endogenous GSH content was rapidly increased by CH4 application, which was correlated with the increased CsGSH1 transcript and γ-ECS activity. Mimicking the responses of GSH, CH4 could upregulate cell cycle regulatory genes (CsCDC6, CsCDPK1, CsCDPK5 and CsDNAJ-1) and auxin-response genes (CsAux22D-like and CsAux22B-like). Meanwhile, adventitious rooting-related CsmiR160 and CsmiR167 were increased or decreased, respectively, and contrasting tendencies were observed in the changes of their target genes, that included CsARF17 and CsARF8. The responses above were impaired by the removal of endogenous GSH with BSO, indicating that CH4-triggered adventitious rooting was GSH-dependent. Genetic evidence revealed that in the presence of CH4, Arabidopsis mutants cad2 (a γ-ECS-defective mutant) exhibited, not only the decreased GSH content in vivo, but also the defects in adventitious root formation, both of which were rescued by GSH administration other than CH4. Together, it can be concluded that γ-ECS-dependent GSH homeostasis might be required for CH4-induced adventitious root formation.

Novel and Conserved miRNAs Among Brazilian Pine and Other Gymnosperms

The knowledge about plant miRNAs has increased exponentially, with thousands of miRNAs been reported in different plant taxa using high throughput sequencing technologies and bioinformatic tools. Nevertheless, several groups of plants remain unexplored, and the gap of knowledge about conifer miRNAs is considerable. There is no sequence or functional information available on miRNAs in Araucariaceae. This group is represented in Brazil by only one species, Araucaria angustifolia, an endangered species known as Brazilian pine. In the present study, Brazilian pine has its transcriptome explored with respect to small RNAs, representing the first description in a member of the Araucariaceae family. The screening for conserved miRNAs in Brazilian pine revealed 115 sequences of 30 miRNA families. A total of 106 precursors sequences were predicted. Forty one comprised conserved miRNAs from 16 families, whereas 65 were annotated as novel miRNAs. The comparison of Brazilian pine precursors with sRNA libraries of other five conifer species indicates that 9 out 65 novel miRNAs are conserved among gymnosperms, while 56 seems to be specific for Brazilian pine or restricted to Araucariaceae family. Analysis comparing novel Brazilian pine miRNAs precursors and Araucaria cunninghamii RNA-seq data identified seven orthologs between both species. Mature miRNA identified by bioinformatics predictions were validated using stem-loop RT-qPCR assays. The expression pattern of conserved and novel miRNAs was analyzed in five different tissues of 3-month-old Araucaria seedlings. The present study provides insights about the nature and composition of miRNAs in an Araucariaceae species, with valuable information on miRNAs diversity and conservation in this taxon.

Natural variation in cytokinin maintenance improves salt tolerance in apple rootstocks

Plants experiencing salt-induced stress often reduce cytokinin levels during the early phases of stress-response. Interestingly, we found that the cytokinin content in the apple rootstock "robusta" was maintained at a high level under salt stress. Through screening genes involved in cytokinin biosynthesis and catabolism, we found that the high expression levels of IPT5b in robusta roots were involved in maintaining the high cytokinin content. We identified a 42 bp deletion in the promoter region of IPT5b, which elevated IPT5b expression levels, and this deletion was linked to salt tolerance in robusta×M.9 segregating population. The 42 bp deletion resulted in the deletion of a Proline Response Element (ProRE), and our results suggest that ProRE negatively regulates IPT5b expression in response to proline. Under salt stress, the robusta cultivar maintains high cytokinin levels as IPT5b expression cannot be inhibited by proline due to the deletion of ProRE, leading to improve salt tolerance.

The auxin receptor TIR1 homolog (PagFBL 1) regulates adventitious rooting through interactions with Aux/IAA28 in Populus

Adventitious roots occur naturally in many species and can also be induced from explants of some tree species including Populus, providing an important means of clonal propagation. Auxin has been identified as playing a crucial role in adventitious root formation, but the associated molecular regulatory mechanisms need to be elucidated. In this study, we examined the role of PagFBL1, the hybrid poplar (Populus alba × P. glandulosa clone 84K) homolog of Arabidopsis auxin receptor TIR1, in adventitious root formation in poplar. Similar to the distribution pattern of auxin during initiation of adventitious roots, PagFBL1 expression was concentrated in the cambium and secondary phloem in stems during adventitious root induction and initiation phases, but decreased in emerging adventitious root primordia. Overexpressing PagFBL1 stimulated adventitious root formation and increased root biomass, while knock-down of PagFBL1 transcript levels delayed adventitious root formation and decreased root biomass. Transcriptome analyses of PagFBL1 overexpressing lines indicated that an extensive remodelling of gene expression was stimulated by auxin signalling pathway during early adventitious root formation. In addition, PagIAA28 was identified as downstream targets of PagFBL1. We propose that the PagFBL1-PagIAA28 module promotes adventitious rooting and could be targeted to improve Populus propagation by cuttings.

Plant Cellular and Molecular Biotechnology: Following Mariotti's Steps

This review is dedicated to the memory of Prof. Domenico Mariotti, who significantly contributed to establishing the Italian research community in Agricultural Genetics and carried out the first experiments of Agrobacterium-mediated plant genetic transformation and regeneration in Italy during the 1980s. Following his scientific interests as guiding principles, this review summarizes the recent advances obtained in plant biotechnology and fundamental research aiming to: (i) Exploit in vitro plant cell and tissue cultures to induce genetic variability and to produce useful metabolites; (ii) gain new insights into the biochemical function of Agrobacterium rhizogenes rol genes and their application to metabolite production, fruit tree transformation, and reverse genetics; (iii) improve genetic transformation in legume species, most of them recalcitrant to regeneration; (iv) untangle the potential of KNOTTED1-like homeobox (KNOX) transcription factors in plant morphogenesis as key regulators of hormonal homeostasis; and (v) elucidate the molecular mechanisms of the transition from juvenility to the adult phase in Prunus tree species.

MdGGT1 Impacts Apple miR156 Precursor Levels via Ontogenetic Changes in Subcellular Glutathione Homeostasis

The vegetative phase change in flowering plants is controlled by microRNA156 (miR156) under transcriptional regulation. However, the developmental signals upstream of miR156 are not well understood. The glutathione/glutathione disulfide (GSH/GSSG) ratios and GSH levels decline significantly during phase change, which is consistent with miR156 expression in apple (Malus domestica Borkh.). Here, we found that the content of protein conjugated glutathione was remarkably higher in chloroplasts and nuclei of adult than juvenile phase apple hybrids. The decrease in miR156 expression was most relevant to the activities of serine acetyltransferase (SAT) and soluble γ-glutamyl transpeptidase (GGT), and the expressions of MdGGT1 or MdSATs. Transgenic apples over-expressing MdMIR156 or miR156-mimetic (MIM156) did not alter MdGGT1 expression or the soluble GGT activity. Inhibition of GGT activity with serine-borate complex or acivicin led to significant reduction in GSH content, the GSH/GSSG ratio, and the expressions of MdMIR156a5, MdMIR156a12, and miR156. Depletion of GSH with diethyl maleate without altering GGT activity caused a dramatic decrease in the expression of MdMIR156a5, MdMIR156a12, and miR156. Manipulating GGT activity and GSH homeostasis by transgenic over-expressing or RNAi MdGGT1 increased or decreased MdMIR156a5 and MdMIR156a12 levels, respectively. These data provided novel evidence that MdGGT1 participates in transcriptional level of transcription regulation of miR156 precursors during ontogenesis.

HIGHLIGHTS

- MdGGT1 affects thiol redox status and indirectly participates in the regulation of miR156 expression during vegetative phase change.

Apple fruit acidity is genetically diversified by natural variations in three hierarchical epistatic genes: MdSAUR37, MdPP2CH and MdALMTII

Many efforts have been made to map quantitative trait loci (QTLs) to facilitate practical marker-assisted selection (MAS) in plants. In the present study, using MapQTL and BSA-seq (bulk segregant analysis using next generation sequencing) with two independent pedigree-based populations, we identified four major genome-wide QTLs responsible for apple fruit acidity. Candidate genes were screened in major QTL regions, and three functional gene markers, including a non-synonymous A/G single-nucleotide polymorphism (SNP) in the coding region of MdPP2CH, a 36-bp insertion in the promoter of MdSAUR37 and a previously reported SNP in MdALMTII, were validated to influence the malate content of apple fruits. In addition, MdPP2CH inactivated three vacuolar H⁺ -ATPases (MdVHA-A3, MdVHA-B2 and MdVHA-D2) and one aluminium-activated malate transporter (MdALMTII) via dephosphorylation and negatively influenced fruit malate accumulation. The dephosphotase activity of MdPP2CH was suppressed by MdSAUR37, which implied a higher hierarchy of genetic interaction. Therefore, the MdSAUR37/MdPP2CH/MdALMTII chain cascaded hierarchical epistatic genetic effects to precisely determine apple fruit malate content. An A/G SNP (-1010) on the MdMYB44 promoter region from a major QTL (qtl08.1) was closely associated with fruit malate content. The predicted phenotype values (PPVs) were estimated using the tentative genotype values of the gene markers, and the PPVs were significantly correlated with the observed phenotype values. Our findings provide an insight into plant genome-based selection in apples and will aid in conducting research to understand the fundamental physiological basis of quantitative genetics.

miR156 switches on vegetative phase change under the regulation of redox signals in apple seedlings

In higher plants, miR156 regulates the vegetative phase change via the target SBP/SPL genes. The regulation of miR156 during ontogenetic processes is not fully understood. In the apple genome, of 31 putative MdMIR156 genes that encode pre-miR156, seven were dominantly expressed. However, the transcript levels of only MdMIR156a5 and MdMIR156a12 decreased significantly during the vegetative phase change, which was consistent with the mature miR156 level, indicating that miR156 is under transcriptional regulation. Leaf H₂O₂ content was higher in the adult phase than in the juvenile phase because of excess H₂O₂ accumulation in chloroplasts. When in vitro shoots were treated with menadione, diphenyleneiodonium, L-2-oxothiazolidine-4-carboxylic acid or buthionine sulphoximine, the expressions of MdMIR156a5, MdMIR156a12, and as well miR156 were coordinated with reduced glutathione (GSH) contents and glutathione/glutathione disulfide ratio but not H₂O₂ contents. Alteration of miR156 expression level by MdMIR156a6-overexpressing or miR156-mimetic transgenic Nicotiana benthamiana did not cause a corresponding change in reactive oxygen species or GSH status. Collectively, the results indicate that the vegetative phase change in apple is controlled by the MdMIR156a5 and MdMIR156a12 transcriptional regulatory network in response to the plastid–nucleus redox signals, such as GSH.