Adventitious Root Formation Research Articles

Genome-wide association study (GWAS) analyses of early anatomical changes in rose adventitious root formation

Adventitious root (AR) formation is a genetically complex trait with high genotypic variability. Therefore, only a limited range of cultivars are currently propagated by cuttings in rose. In this study, we analysed the anatomy of in vitro shoots, the early formation of root primordia (RP) and the formation of ARs in a diverse set of 106 rose genotypes. Correlation analysis indicated that the growth in shoot diameter and the vasculature dimensions after 1 week of rooting contributed to successful AR formation. Using phenotypic data for genome-wide association studies (GWAS) analyses, nine significantly associated single nucleotide polymorphisms (SNPs) and genomic regions contributing to various RP and AR formation traits were identified. The contribution of genomic regions to trait variation was notably greater for traits associated with earlier processes than for traits associated with later developmental stages. The combination of RP and AR data allowed the detection of regions by GWAS that contain factors that potentially limit RP emergence. Homologues of 47 genes known to be involved in AR formation from the literature could be assigned to the identified peaks. Further studies are needed to investigate the suitability of SNPs exhibiting strong effects as allele-specific PCR markers for use in breeding.

Biochemical and physiological effects of propagule type and auxin concentration on adventitious root formation in novel Jasmine genotypes

Jasmine is primarily propagated through asexual methods, and bio-stimulants can improve soil fertility around plant roots. Some jasmine genotypes are mainly propagated through cuttings; however, the rooting process is slow and inconsistent. Specific jasmine genotypes are primarily propagated through cuttings, but the rooting process is slow and uneven. This study evaluated the regeneration potential of stem cuttings by investigating the effects of auxins and various propagule types on adventitious root formation, along with associated biochemical changes. A field experiment conducted by the Department of Floriculture and Landscaping at TNAU, Coimbatore, Tamil Nadu, from December 2023 to June 2024, during the winter monsoon, investigated the rooting of stem cuttings in three Jasminum genotypes using auxin. Stem cuttings of J. sambac Double Flower type (DF), J. grandiflorum White Flower type (WF) and a new cultivar of J. multiflorum CO.1 Winter Jasmine (CO.1 WJ) were treated with three Indole-3-Butyric Acid (IBA) concentrations (0.5, 1, 1.5 g L-1) and distilled water as control. Utilizing a Factorial, Completely Randomized Design for terminal and semi-hardwood cuttings, the study found that rooting hormone significantly enhanced root formation and stem and shoot growth. Semi-hardwood cuttings of J. sambac (DF) treated with 1g L-1 IBA had the highest rooting rate (88.60%), number of roots (9.34), root length (12.74 cm), shoot length (10.26 cm) and number of leaves (6.60). The highest rooting rate of 48.15% was obtained from the terminal cuttings of J. grandiflorum (WF) that had been treated with 1g L-1 IBA, in addition to other parameters such as number of roots (13.52), root length (12.03 cm), shoot length (14.30 cm), and number of leaves (13.48). On the other hand, J. multiflorum (CO.1 WJ) recorded the highest rooting rate of 72.23%, root number of 16.52, root length of 17.22 cm, shoot length of 14.14 cm and number of leaves, which was pegged at 31.70 when terminal cuttings were treated with 1g L-1 IBA. The current findings indicate that the application of auxins is crucial for promoting early root initiation and achieving higher rooting success, making it advantageous for vegetative propagation.

Breeding for water-logging tolerance in pigeonpea: current status and future prospects

AbstractPigeonpea is grown in semi-arid tropics where the annual precipitation ranges from 200 to 800 mm and soil orders comprising of Inceptisols, Entisols, Alfisols, Vertisols, Mixed soils, and Aridisols. During monsoons, the semi-arid tropics also receive up to 140–180 mm/day rainfall for a span of 5–10 days, highlighting the chances of waterlogging in an early vegetative stage of pigeonpea, causing 25–30% yield loss in the Indian subcontinent. Waterlogging is a state where soil reaches saturation at submergence, creating an anaerobic condition in the root zone of the plants. As a result, plant withering, leaf chlorosis, stunted growth, lowered photosynthetic rate and plant mortality is evidenced widely. In response to waterlogging, the formation of aerenchyma cells, lenticels and adventitious roots were noticed as morphological adaptations. Whereas, the production of proline, peroxidase, superoxide dismutase, ethylene and alcohol dehydrogenase (ADH) as biochemical modifications. The minimal breeding efforts for waterlogging tolerance in pigeonpea may be the reason for the susceptibility of current varieties to waterlogging stress. This review emphasized the importance of breeding for waterlogging tolerance in pigeonpea. It focused on the morphological, physiological and biochemical adaptations of a plant when subjected to waterlogging stress. It accentuated the need for a standard screening protocol for waterlogging tolerance. Breeding strategies inclusive of novel single pod descent method, marker-assisted selection and rapid generation advancement techniques are discussed in detail.

Laser wounding pattern in relation to vascular tissue development for the stimulation of adventitious root formation in rose cuttings

The stimulation of adventitious root formation from laser-wounded rose cuttings in our previous study suggests that exposing the phloem proximities is one of the most relevant aspects for a positive effect on rooting response. But, the specific dimensions that wound patterns must fulfill to optimize rooting promotion remain unknown. This study analyzed the effect of wounded area and wound perimeter of laser marking patterns on the development of phloem, xylem, and callus using cross sections of single-leaf cuttings of Rosa canina 'Pfänder'. Four distinct laser patterns were designed and marked along the cutting base. Among these, three patterns were based on longitudinal strips, while one pattern was characterized by small squares, resulting in two distinct wound area levels and four wound perimeter levels. Periodic evaluations of stem sections showed that the development of phloem and xylem was significantly influenced by the pattern's geometry. Larger dimensions of xylem were associated with patterns of greater area and a smaller perimeter, while an increase in phloem was related to patterns of longer perimeter distributed in smaller areas. The maximum rooting success in wounded cuttings reached 44% in contrast to 9% observed in the control group in the absence of additional wounds. The development of vascular tissue was significantly correlated with adventitious rooting, with phloem being more closely linked with a Pearson coefficient of 0.92 compared to 0.30 for xylem. Additionally, a negative Pearson coefficient of −0.92 between the ratio area: perimeter and adventitious root formation showed that laser patterns with large wounded area with less borders led to a reduced rooting response. The results provide evidence of how wounded tissue contributes to the intrinsic development of adventitious roots and reveal the importance of proper wound dimensions.

Physiological Age of Stock Plants Determines Phytohormonal Changes in Leafy Cuttings of Prunus subhirtella 'Autumnalis'

AbstractThe aim of this study was to investigate adventitious root formation in cuttings obtained from physiologically different old stock material. The ornamental cherry Prunus subhirtella ´Autumnalis´ was used for the experiment. We examined three stock plants, namely a physiologically mature stock plant (about 60 years old) and physiologically juvenile plants (21 years old), which were previously propagated by cuttings, semi-mature stock material and in vitro juvenile stock material. We also investigated the role of phytohormones in the induction phase of adventitious root (AR) formation depending on the physiological age of the stock plant and the time after cutting. High performance liquid chromatography coupled with mass spectrometry (HPLC–MS/MS) was used to identify and quantify the phytohormones. The difference in rooting and quality of the developed AR is observed between semi-mature stock and mature stock material. Cuttings from semi-mature plants rooted in 95.00% of cases, while cuttings from mature stock plants only rooted in 68.33%. The high concentration of strigolactones and jasmonic acid (JA) immediately after severance had an inhibitory effect on the development of adventitious roots, especially in cuttings of mature origin. The development of AR is positively influenced by the increase in indole-3-acetic acid (IAA) 4 h after cutting from the stock plant. Our results show that the formation of adventitious root formation depends on the concentration and ratio between different phytohormones.

Genome-wide analysis of the WOX gene family and function exploration of RhWOX331 in rose (R. 'The Fairy').

WOXs are a class of plant-specific transcription factors that play key roles in plant growth and stress responses. However, the mechanism by which WOXs influence adventitious root development in Rosa hybrida remains unclear. In this study, RcWOX gene family in rose was identified and phylogenetically analyzed using bioinformatics analysis. A total of 381 RcWOX gene members were localized on seven chromosomes except of nine members. The main cis-acting elements involved in hormonal, light, developmental, and abiotic stress responses were identified in the promoters of RcWOX genes, suggesting their regulation by these signals. Nine RhWOX genes had significant different expression during rooting process of rose. RhWOX331, RhWOX308, RhWOX318 were positive with the formation of rose roots. RhWOX331 was positively involved in the formation of adventitious root primordia, which gene coding a transcription factor localized in the nucleus. The HOX conserved domain in the protein contributed to the self-activating activity of RhWOX331. We obtained genetically modified Arabidopsis to validate the function of RhWOX331. Overexpression of RhWOX331 gene alleviated the inhibition of root length of A. thaliana primary roots by high concentration of IBA and NPA, and significantly increased the number of lateral roots on the primary roots, as well as the height of A. thaliana plants. Additionally, RhWOX331 promoted adventitious root formation in A. thaliana and mitigated hormonal inhibition by exogenous 6-BA, NPA, and GA3. The RhWOX331 promoter contained cis-acting elements such as ABRE, Box 4 and CGTCA-motif et.al. GUS activity analysis showed that the gene acted at the cotyledon attachment site. Taken together, these studies identified a significant expansion of the RcWOX gene family, inferred roles of certain branch members in adventitious root formation, elucidated the function of RhWOX331 in adventitious root initiation, and laid the foundation for further research on the function of WOX gene family in roses.

Genome-Wide Identification and Analysis of the Aux/IAA Gene Family in Rosa hybrida—“The Fairy”: Evidence for the Role of RhIAA25 in Adventitious Root Development

Propagation of cuttings is the primary method of rose multiplication. Aux/IAA, early response genes to auxin, play an important role in regulating the process of adventitious root formation in plants. However, systematic research on the identification of RhAux/IAA genes and their role in adventitious root formation in roses is lacking. In this study, 34 RhAux/IAA genes were identified by screening the rose genome, distributed on seven chromosomes, and classified into three clades based on the evolutionary tree. An analysis of the cis-acting elements in the promoters of RhAux/IAA genes revealed the presence of numerous elements related to plant hormones, the light signal response, the growth and development of plants, and abiotic stress. RNA-seq analysis identified a key RhIAA25 gene that may play an important role in the generation of adventitious roots in roses. Subcellular localization, yeast self-activation, and tissue-specific expression experiments indicated that RhIAA25 encoded a nuclear protein, had no yeast self-activated activity, and was highly expressed in the stem. The overexpression of RhIAA25 promoted the elongation of the primary root in Arabidopsis but inhibited adventitious root formation. This study systematically identified and analyzed the RhAux/IAA gene family and identified a key gene, RhIAA25, that regulates adventitious root generation in roses. This study offers a valuable genetic resource for investigating the regulatory mechanism of adventitious root formation in roses.

Proteomic insights into adventitious root formation in Larix kaempferi

The adventitious root formaton (ARF) in excised plant parts is essential for the survival of isolated plant fragments. In this study, we explored the complex mechanisms of ARF in Larix kaempferi by conducting a comprehensive proteomic analysis across three distinct stages: the induction of adventitious root primordia (C1, 0–25 d), the formation of adventitious root primordia (C2, 25–35 d), and the elongation of adventitious roots (C3, 35–45 d). We identified 1976 proteins, with 263 and 156 proteins exhibiting increased abundance in the C2/C1 and C3/C2 transitions, respectively. In contrast, a decrease in the abundance of 106 and 132 proteins suggests a significant demand for metabolic processes during the C2/C1 phase. The abundance of IAA-amino acid hydrolase and S-adenosylmethionine synthase were increased in the C2/C1 phase, underscoring the role of auxin in adventitious root induction. The decrease in abundance of photosynthesis-related proteins during the C2/C1 phase highlights the significance of initial light conditions in adventitious root induction. Moreover, variation in cell wall synthesis and metabolic proteins in the C2/C1 and C3/C2 stages suggests that cell wall metabolism is integral to adventitious root regeneration. Gene Ontology enrichment analysis revealed pathways related to protein modification enzymes, including deubiquitinases and kinases, which are crucial for modulating protein modifications to promote ARF. Furthermore, the increased abundance of antioxidant enzymes, such as peroxidases and glutathione peroxidases, indicates a potential approach for enhancing ARF by supplementing the culture medium with antioxidants. Our study provides insights into metabolic changes during ARF in L. kaempferi, offering strategies to enhance adventitious root regeneration. These findings have the potential to refine plant propagation techniques and expedite breeding processes. SignficanceThe main challenge in the asexual reproduction technology of Larix kaempferi lies in adventitious root formation (ARF). While numerous studies have concentrated on the efficiency of ARF, proteomic data are currently scarce. In this study, we collected samples from three stages of ARF in L. kaempferi and subsequently performed proteomic analysis. The data generated not only reveal changes in protein abundance but also elucidate key metabolic processes involved in ARF. These insights offer a novel perspective on addressing the challenge of adventurous root regeneration.

Transcriptome analysis of Sesuvium portulacastrum L. uncovers key genes and pathways involved in root formation in response to low-temperature stress.

Sesuvium portulacastrum L., a perennial facultative halophyte, is extensively distributed across tropical and subtropical coastal regions. Its limited cold tolerance significantly impacts both the productivity and the geographical distribution of this species in higher-latitude areas. In this study, we employed RNA-Seq technology to delineate the transcriptomic alterations in Sesuvium plants exposed to low temperatures, thus advancing our comprehension of the molecular underpinnings of this physiological adaptation and root formation. Our findings demonstrated differential expression of 10,805, 16,389, and 10,503 genes in the low versus moderate temperature (LT vs. MT), moderate versus high temperature (MT vs. HT), and low versus high temperature (LT vs. HT) comparative analyses, respectively. Notably, the gene categories "structural molecule activity", "ribosome biogenesis", and "ribosome" were particularly enriched among the LT vs. HT-specific differentially expressed genes (DEGs). When synthesizing the insights from these three comparative studies, the principal pathways associated with the cold response mechanism were identified as "carbon fixation in photosynthetic organisms", "starch and sucrose metabolism", "plant hormone signal transduction", "glycolysis/gluconeogenesis", and "photosynthesis". In addition, we elucidated the involvement of auxin signaling pathways, adventitious root formation (ARF), lateral root formation (LRF), and novel genes associated with shoot system development in root formation. Subsequently, we constructed a network diagram to investigate the interplay between hormone levels and pivotal genes, thereby clarifying the regulatory pathways of plant root formation under low-temperature stress and isolating key genes instrumental in root development. This study has provided critical insights into the molecular mechanisms that facilitate the adaptation to cold stress and root formation in S. portulacastrum.

Molecular Manipulation of the miR160/AUXIN RESPONSE FACTOR Expression Module Impacts Root Development in Arabidopsis thaliana.

In Arabidopsis thaliana (Arabidopsis), microRNA160 (miR160) regulates the expression of AUXIN RESPONSE FACTOR10 (ARF10), ARF16 and ARF17 throughout development, including the development of the root system. We have previously shown that in addition to DOUBLE-STRANDED RNA BINDING1 (DRB1), DRB2 is also involved in controlling the rate of production of specific miRNA cohorts in the tissues where DRB2 is expressed in wild-type Arabidopsis plants. In this study, a miR160 overexpression transgene (MIR160B) and miR160-resistant transgene versions of ARF10 and ARF16 (mARF10 and mARF16) were introduced into wild-type Arabidopsis plants and the drb1 and drb2 single mutants to determine the degree of requirement of DRB2 to regulate the miR160 expression module as part of root development. Via this molecular modification approach, we show that in addition to DRB1, DRB2 is required to regulate the level of miR160 production from its precursor transcripts in Arabidopsis roots. Furthermore, we go on to correlate the altered abundance of miR160 or its ARF10, ARF16 and ARF17 target genes in the generated series of transformant lines with the enhanced development of the root system displayed by these plant lines. More specifically, promotion of primary root elongation likely stemmed from enhancement of miR160-directed ARF17 expression repression, while the promotion of lateral and adventitious root formation was the result of an elevated degree of miR160-directed regulation of ARF17 expression, and to a lesser degree, ARF10 and ARF16 expression. Taken together, the results presented in this study identify the requirement of the functional interplay between DRB1 and DRB2 to tightly control the rate of miR160 production, to in turn ensure the appropriate degree of miR160-directed ARF10, ARF16 and ARF17 gene expression regulation as part of normal root system development in Arabidopsis.

Advances in studies on adventitious root formation determined by juvenility and auxin in plants

Advances in studies on adventitious root formation determined by juvenility and auxin in plants

Transcriptome Reveals the Regulation of Exogenous Auxin Inducing Rooting of Non-Rooting Callus of Tea Cuttings.

Cuttage is the main propagation method of tea plant cultivars in China. However, some tea softwood cuttings just form an expanded and loose callus at the base, without adventitious root (AR) formation during the propagation period. Meanwhile, exogenous auxin could promote the AR formation of tea plant cuttings, but the regulation mechanism has not yet explained clearly. We conducted this study to elucidate the regulatory mechanism of exogenous auxin-induced adventitious root (AR) formation of such cuttings. The transcriptional expression profile of non-rooting tea calluses in response to exogenous IBA and NAA was analyzed using ONT RNA Seq technology. In total, 56,178 differentially expressed genes (DEGs) were detected, and most of genes were significantly differentially expressed after 12 h of exogenous auxin treatment. Among these DEGs, we further identified 80 DEGs involved in the auxin induction pathway and AR formation. Specifically, 14 auxin respective genes (ARFs, GH3s, and AUX/IAAs), 3 auxin transporters (AUX22), 19 auxin synthesis- and homeostasis-related genes (cytochrome P450 (CYP450) and calmodulin-like protein (CML) genes), and 44 transcription factors (LOB domain-containing protein (LBDs), SCARECROW-LIKE (SCL), zinc finger protein, WRKY, MYB, and NAC) were identified from these DEGs. Moreover, we found most of these DEGs were highly up-regulated at some stage before AR formation, suggesting that they may play a potential role in the AR formation of tea plant cuttings. In summary, this study will provide a theoretical foundation to deepen our understanding of the molecular mechanism of AR formation in tea cuttings induced by auxin during propagation time.

PoARRO-1 regulates adventitious rooting through interaction with PoIAA27b in Paeonia ostii

Adventitious root (AR) formation is a limiting factor in the vegetative propagation of tree peony (Paeonia suffruticosa Andr.). PoARRO-1, which encodes an auxin oxidase involved in AR formation, plays a role in the root development of P. ostii, but its associated molecular regulatory mechanisms are not yet understood. In this study, we examined the role of PoARRO-1 in AR formation in P. ostii. The overexpression of PoARRO-1 in P. ostii test-tube plantlets led to a notable enhancement in both the rooting rate and the average number of ARs in vitro, as well as increased activities of peroxidase (POD), superoxide dismutase (SOD), and indoleacetic acid oxidase (IAAO). PoARRO-1 was involved in the conversion of IAA-Asp and IAA-Glu to OxIAA and promoted IAA oxidation. RNA sequencing analysis revealed that PoARRO-1 overexpression led to upregulation of enzyme activity, auxin metabolism related genes. Further analyses showed that PoARRO-1 interacted with the 1–175 aa position of PoIAA27b to regulate the formation of ARs. We therefore propose that PoARRO-1 interacts with PoIAA27b to promote AR formation, and it may be useful targets for enhancing the in vitro propagation of P. ostii.

Factors governing cellular reprogramming competence in Arabidopsis adventitious root formation

Developmental reprogramming allows for flexibility in growth and adaptation to changing environmental conditions. In plants, wounding events can result in new stem cell niches and lateral organs. Adventitious roots develop from aerial parts of the plant and are regulated by multiple stimuli, including wounding. Here, we find that Arabidopsis thaliana seedlings wounded at the hypocotyl-root junction reprogram certain pericycle cells to produce adventitious roots proximal to the wound site. We have determined that competence for this reprogramming is controlled; basal cells close to the wound site can produce adventitious roots, whereas cells distal from the wound site mostly cannot. We found that altering cytokinin response or indole-3-butyric acid (IBA)-to-(indole-3-acetic acid) IAA conversion resulted in an expanded adventitious root competence zone and delineated the connection between these pathways. Our work highlights the importance of endogenous IBA-derived auxin and its interaction with cytokinin in adventitious root formation and the regenerative properties of plants.

The auxin-responsive CsSPL9-CsGH3.4 module finely regulates auxin levels to suppress the development of adventitious roots in tea (Camellia sinensis).

The cutting technique is extensively used in tea breeding, with key emphasis on promoting the growth of adventitious roots (ARs). Despite its importance in tea cultivation, the mechanisms underlying AR development in tea remain unclear. In this study, we demonstrated the essential role of auxins in the initiation and progression of AR and established that the application of exogenous 1-naphthaleneacetic acid-enhanced AR formation in tissue-cultured seedlings and cuttings. Then, we found that the auxin-responsive transcription factor CsSPL9 acted as a negative regulator of AR development by reducing the levels of free indole-3-acetic acid (IAA) in tea plants. Furthermore, we identified CsGH3.4 as a downstream target of CsSPL9, which was activated by direct binding to its promoter. CsGH3.4 also inhibited AR development and maintained low levels of free IAA. Thus, these results revealed the inhibitory effect of the auxin-responsive CsSPL9-CsGH3.4 module on AR development by reducing free IAA levels in tea. These findings have significant theoretical and practical value for enhancing tea breeding practices.

Transcriptomic profiling and discovery of key transcription factors involved in adventitious roots formation from root cuttings of mulberry

ARs plays a crucial role in plant morphogenesis and development. The limited and inefficient rooting of scions poses a significant challenge to the efficiency and quality of clonal propagation of forest trees in silvicultural practices. Building on previous research conducted by our team, we found that applying IBA at a concentration of 1000 mg/L significantly enhanced mulberry rooting. This study aims to uncover the molecular mechanisms underlying this effect by analyzing RNA sequencing data from mulberry phloem before and after treatment with IBA over time intervals of 10, 20, 30, and 40 days. We identified 5226 DEGs, which were then classified into GO terms and KEGG pathways, showing significant enrichment in hormone signaling processes. Using WGCNA, we identified eight co-expression modules, two of which were significantly correlated with the IBA treatment. Additionally, 18 transcription factors that potentially facilitate ARs formation in mulberry were identified, and an exploratory analysis on the cis-regulatory elements associated with these transcription factors was conducted. The findings of this study provide a comprehensive understanding of the mechanisms of ARs in mulberry and offer theoretical support for the discovery and utilization of exceptional genetic resources within the species.

Physio-biochemical Changes during Adventitious Root Formation in Gmelina arborea Roxb. Bud Sprout Cuttings

Changes in the endogenous moisture content and biochemical viz., soluble sugar), phenols, o-phenol and peroxidase activity at different stages of adventitious rooting in auxin-treated (5 mM IBA) and non-treated miniature bud sprout cuttings of Gmelina arborea Roxb. were investigated at 0 h, 24 h, 3 days, 7 days, 2 weeks and 3 weeks of planting to elucidate the process of adventitious root formation at physio-biochemical level. Simultaneously adventitious rhizogenesis parameters viz., proportion of live green sprouts (%), callusing (%) and rooting (%) were recorded. Two weeks after planting, the marked difference for adventitious rhizogenesis was noticeable between treated and non-treated sprout cuttings. More than 20% rooting and 75% callusing were recorded in treated sprout cuttings. In contrast, only 7.4% non-treated sprout cuttings exhibited callusing. At the end of Week 3, more than 90% rooting was observed in treated sprout cuttings while it was absent in non-treated ones. All biochemicals exhibited changes in the first 24 h, indicating early incidence of consequential process(s), which influenced the differential response of cuttings to adventitious rhizogenesis in auxin-treated and non-treated state. Overall, the results indicate two possible phases of adventitious rhizogenesis – Phase I of Induction -the initial phase exhibiting low endogenous moisture and o-phenol but elevated phenol and peroxidase activity and Phase II of Initiation – the later phase coinciding with higher endogenous moisture and low phenol content and peroxidase activity. Both phases appear to be separated by an intervening unstable duration (Gap Phase of Stabilization) which may vary among different types of cuttings/species.

Physiological, Cellular, and Transcriptomic Analyses Provide Insights into the Tolerance Response of Arundo donax to Waterlogging Stress

Arundo donax is widely used as an ornamental plant in landscape gardening because of its adaptability to varying degrees of waterlogged conditions. However, to date, little information is available about the adaptive mechanism of A. donax under waterlogging stress. The results showed that long-term mild waterlogging efficiently induced the formation of adventitious roots (ARs) and further promoted root aerenchyma development, and that the activity of antioxidant enzymes (SOD, POD, and CAT) in Ars also was greatly enhanced after waterlogging. At the transcriptomic level, the expression of genes related to apoptosis, the regulation of cell division, ethylene biosynthesis, alginate synthesis, auxin signaling pathways, and anaerobic respiration was mostly up-regulated after the occurrence of waterlogging stress but genes involved in the abscisic acid signaling pathways were partly down-regulated, which indicated a preferential and favorable transcriptional response in regulating adventitious root development. Taken together, this study definitely advances our knowledge of the morphological, physiological, and transcriptomic responses of A. donax under waterlogging stress and sheds new lights on its adaptive mechanisms.

Using RNA sequencing to unravel molecular changes underlying the defense response in chickpea induced by Phytophthora medicaginis.

Phytophthora root rot (PRR), caused by Phytophthora medicaginis, is a major soil-borne disease of chickpea in Australia. Breeding for PRR resistance is an effective approach to avoid significant yield loss. Genetic resistance has been identified in cultivated chickpea (Cicer arietinum) and in the wild relative C. echinospermum, with previous studies identifying independent genetic loci associated with each of these sources. However, the molecular mechanisms associated with PRR resistance are not known. RNA sequencing analysis employed in this study identified changes in gene expression in roots of three chickpea genotypes grown hydroponically, early post-infection with P. medicaginis zoospores. Analyses of differentially expressed genes (DEG) identified the activation of a higher number of non-specific R-genes in a PRR-susceptible variety than in the resistant genotypes, suggesting a whole plant resistance response occurring in chickpea against the pathogen. Contrasting molecular changes in signaling profiles, proteolysis and transcription factor pathways were observed in the cultivated and wild Cicer-derived resistant genotypes. DEG patterns supported a hypothesis that increased root elongation and reduced adventitious root formation limit the pathogen entry points in the genotype containing the wild Cicer source of PRR resistance. Candidate resistance genes, including an aquaporin and a maltose transporter in the wild Cicer source and GDSL esterases/lipases in the cultivated source of resistance, were oppositely regulated. Increased knowledge of these genes and pathways will improve our understanding of molecular mechanisms controlling PRR resistance in chickpea, and support the development of elite chickpea varieties through molecular breeding approaches.

Raffinose catabolism enhances maize waterlogging tolerance by stimulating adventitious root growth and development.

Raffinose mitigates plant heat, drought, and cold stresses; however, whether raffinose contributes to plant waterlogging tolerance is unknown. The maize raffinose synthase mutant zmrafs-1 had seedlings that lack raffinose, generated fewer and shorter adventitious roots, and were more sensitive to waterlogging stress, while overexpression of the raffinose synthase gene, ZmRAFS, increased raffinose content, stimulated adventitious root formation, and enhanced waterlogging tolerance of maize seedlings. Transcriptome analysis of null segregant seedlings compared with zmrafs-1, particularly when waterlogged, revealed that the expression of genes related to galactose metabolism and the auxin biosynthetic pathway were up-regulated by raffinose. Additionally, indole-3-acetic acid content was significantly decreased in zmrafs-1 seedlings and increased in ZmRAFS-overexpressing seedlings. Inhibition of the hydrolysis of raffinose by 1-deoxygalactonojirimycin decreased the waterlogging tolerance of maize seedlings, the expression of genes encoding proteins related to auxin transport-related genes, and the indole-3-acetic acid level in the seedlings, indicating that the hydrolysis of raffinose is necessary for maize waterlogging tolerance. These data demonstrate that raffinose catabolism stimulates adventitious root formation via the auxin signaling pathway to enhance maize waterlogging tolerance.