Ethylene Biosynthesis Is Promoted by Very-Long-Chain Fatty Acids during Lysigenous Aerenchyma Formation in Rice Roots

Cotton GhMAX2 promotes single-celled fiber elongation by releasing the GhS1FA-mediated inhibition of fatty acid biosynthesis

KEY MESSAGE

Cotton GhMAX2 positively regulates fiber elongation by mediating the degradation of GhS1FA, which transcriptionally represses GhKCS9 expression. Strigolactones (SLs) are known to promote cotton fiber development. However, the precise molecular relationship between SL signaling and fiber cell elongation remains unclear. In this study, we investigate the role of F-box E3 ligase MORE AXILLARY GROWTH2 (MAX2) in upland cotton in relation to the regulation of fiber development. GhMAX2b and GhMAX2f act as key components for SL signal transduction, with their loss-of-function leading to a notable reduction in fiber length. Biochemical analysis showed that GhMAX2b/f trigger the ubiquitination and subsequent degradation of the transcription repressor strigolactone-1-factor-At (GhS1FA), which function as a substrate for these E3 ligases. Furthermore, GhS1FA inhibits fatty acids biosynthesis by directly binding to the W-box element within the promoter of 3-ketoacyl-CoA synthases 9 (GhKCS9) and repressing its expression. In summary, we propose that GhMAX2b/f promote fiber elongation, potentially operating partially independently of GhD53 degradation.

Formation of Apoplastic Barriers to Radial O₂ Loss in Rice Roots: Effects of Low-O₂ and High-Fe Conditions, and the Roles of Suberin, Glycerol Esters, and Iron Plaques

Lack of O2 and high concentrations of iron (Fe) are common in flooded soils where Rice (Oryza sativa L.) is cultivated. We tested the hypothesis that growing in stagnant or high Fe conditions might induce the formation of apoplastic barriers in roots with different properties and chemical compositions. We measured radial O2 loss (ROL) from intact roots, the chemical composition of roots and the formation of root iron plaques in Fe-sensitive and Fe-tolerant rice genotypes grown in aerated, deoxygenated stagnant solutions or in aerated solutions containing high concentrations of Fe. Roots of plants grown in stagnant conditions developed tight barriers to ROL, while those grown in high Fe conditions developed only partial barriers. Chemical analysis of enzymatically isolated sclerenchyma/exodermal root cells indicated that roots grown in stagnant conditions showed increased amounts of suberin and glycerol esters. In contrast, roots in high Fe conditions showed an increase in suberization along with formation of iron plaques covering the roots. In high Fe conditions, exodermal suberization and the formation of partial ROL barriers were not influenced by the genotype's tolerance to Fe. The amount of O2 diffused from roots is influenced by the various layers that impede O2 diffusion. Specifically, increased amounts of glycerol esters in the suberized exodermis provide the greater resistance to ROL.

Brassinosteroids in cotton: orchestrating fiber development

Cotton cultivation spans over 30 million hectares across 85 countries and regions, with more than half participating in the global cotton textile trade. The elongated cotton fiber cell is an ideal model for studying cell elongation and understanding plant growth and development. Brassinosteroids (BRs), recognized for their role in cell elongation, offer the potential for improving cotton fiber quality and yield. Despite extensive research highlighting BR's positive impact on fiber development, a comprehensive review on this topic has been lacking. This review addresses this gap, providing a detailed analysis of the latest advancements in BR signaling and its effects on cotton fiber development. We explore the complex network of BR biosynthesis components, signaling molecules, and regulators, including crosstalk with other pathways and transcriptional control mechanisms. Additionally, we propose molecular strategies and highlight key genetic elements for optimizing BR-related genes to enhance fiber quality and yield. The review emphasizes the importance of BR homeostasis and the hormonal landscape during cotton fiber development, offering insights into targeted manipulation opportunities and challenges. This consolidation offers a comprehensive understanding of BR's multifaceted roles in fiber development, outlining a strategic approach for BR optimization in cotton fiber quality and yield.

Transcriptome Analysis of Rice Root Tips Reveals Auxin, Gibberellin and Ethylene Signaling Underlying Nutritropism

Nutritropism is a positive tropism toward nutrients in plant roots. An NH4+ gradient is a nutritropic stimulus in rice (Oryza sativa L.). When rice roots are exposed to an NH4+ gradient generated around nutrient sources, root tips bend toward and coil around the sources. The molecular mechanisms are largely unknown. Here, we analyzed the transcriptomes of the inside and outside of bending root tips exhibiting nutritropism to reveal nutritropic signal transduction. Tissues facing the nutrient sources (inside) and away (outside) were separately collected by laser microdissection. Principal component analysis revealed distinct transcriptome patterns between the two tissues. Annotations of 153 differentially expressed genes implied that auxin, gibberellin and ethylene signaling were activated differentially between the sides of the root tips under nutritropism. Exogenous application of transport and/or biosynthesis inhibitors of these phytohormones largely inhibited the nutritropism. Thus, signaling and de novo biosynthesis of the three phytohormones are necessary for nutritropism. Expression patterns of IAA genes implied that auxins accumulated more in the inside tissues, meaning that ammonium stimulus is transduced to auxin signaling in nutritropism similar to gravity stimulus in gravitropism. SAUR and expansin genes, which are known to control cell wall modification and to promote cell elongation in shoot gravitropism, were highly expressed in the inside tissues rather than the outside tissues, and our transcriptome data are unexplainable for differential elongation in root nutritropism.

Plant Adaptation to Flooding Stress under Changing Climate Conditions: Ongoing Breakthroughs and Future Challenges

Climate-change-induced variations in temperature and rainfall patterns are a serious threat across the globe. Flooding is the foremost challenge to agricultural productivity, and it is believed to become more intense under a changing climate. Flooding is a serious form of stress that significantly reduces crop yields, and future climatic anomalies are predicted to make the problem even worse in many areas of the world. To cope with the prevailing flooding stress, plants have developed different morphological and anatomical adaptations in their roots, aerenchyma cells, and leaves. Therefore, researchers are paying more attention to identifying developed and adopted molecular-based plant mechanisms with the objective of obtaining flooding-resistant cultivars. In this review, we discuss the various physiological, anatomical, and morphological adaptations (aerenchyma cells, ROL barriers (redial O2 loss), and adventitious roots) and the phytohormonal regulation in plants under flooding stress. This review comprises ongoing innovations and strategies to mitigate flooding stress, and it also provides new insights into how this knowledge can be used to improve productivity in the scenario of a rapidly changing climate and increasing flood intensity.

Elucidating the molecular responses to waterlogging stress in onion (Allium cepa L.) leaf by comparative transcriptome profiling

Introduction

Waterlogging is a major stress that severely affects onion cultivation worldwide, and developing stress-tolerant varieties could be a valuable measure for overcoming its adverse effects. Gathering information regarding the molecular mechanisms and gene expression patterns of waterlogging-tolerant and sensitive genotypes is an effective method for improving stress tolerance in onions. To date, the waterlogging tolerance-governing molecular mechanism in onions is unknown.

Methods

This study identified the differentially expressed genes (DEGs) through transcriptome analysis in leaf tissue of two onion genotypes (Acc. 1666; tolerant and W-344; sensitive) presenting contrasting responses to waterlogging stress.

Results

Differential gene expression analysis revealed that in Acc. 1666, 1629 and 3271 genes were upregulated and downregulated, respectively. In W-344, 2134 and 1909 genes were upregulated and downregulated, respectively, under waterlogging stress. The proteins coded by these DEGs regulate several key biological processes to overcome waterlogging stress such as phytohormone production, antioxidant enzymes, programmed cell death, and energy production. The clusters of orthologous group pathway analysis revealed that DEGs contributed to the post-translational modification, energy production, and carbohydrate metabolism-related pathways under waterlogging stress. The enzyme assay demonstrated higher activity of antioxidant enzymes in Acc. 1666 than in W-344. The differential expression of waterlogging tolerance related genes, such as those related to antioxidant enzymes, phytohormone biosynthesis, carbohydrate metabolism, and transcriptional factors, suggested that significant fine reprogramming of gene expression occurs in response to waterlogging stress in onion. A few genes such as ADH, PDC, PEP carboxylase, WRKY22, and Respiratory burst oxidase D were exclusively upregulated in Acc. 1666.

Discussion

The molecular information about DEGs identified in the present study would be valuable for improving stress tolerance and for developing waterlogging tolerant onion varieties.

Brassinosteroids regulate cotton fiber elongation by modulating very-long-chain fatty acid biosynthesis

Brassinosteroid (BR), a growth-promoting phytohormone, regulates many plant growth processes including cell development. However, the mechanism by which BR regulates fiber growth is poorly understood. Cotton (Gossypium hirsutum) fibers are an ideal single-cell model in which to study cell elongation due to their length. Here we report that BR controls cotton fiber elongation by modulating very-long-chain fatty acid (VLCFA) biosynthesis. BR deficiency reduces the expression of 3-ketoacyl-CoA synthases (GhKCSs), the rate-limiting enzymes involved in VLCFA biosynthesis, leading to lower saturated VLCFA contents in pagoda1 (pag1) mutant fibers. In vitro ovule culture experiments show that BR acts upstream of VLCFAs. Silencing of BRI1-EMS-SUPPRESOR 1.4 (GhBES1.4), encoding a master transcription factor of the BR signaling pathway, significantly reduces fiber length, whereas GhBES1.4 overexpression produces longer fibers. GhBES1.4 regulates endogenous VLCFA contents and directly binds to BR RESPONSE ELEMENTS (BRREs) in the GhKCS10_At promoter region, which in turn regulates GhKCS10_At expression to increase endogenous VLCFA contents. GhKCS10_At overexpression promotes cotton fiber elongation, whereas GhKCS10_At silencing inhibits cotton fiber growth, supporting a positive regulatory role for GhKCS10_At in fiber elongation. Overall, these results uncover a mechanism of fiber elongation through crosstalk between BR and VLCFAs at the single-cell level.

Physiological, biochemical, and metabolic changes in diploid and triploid watermelon leaves during flooding

Background

Flooding is a major stress factor impacting watermelon growth and production globally. Metabolites play a crucial role in coping with both biotic and abiotic stresses.

Methods

In this study, diploid (2X) and triploid (3X) watermelons were investigated to determine their flooding tolerance mechanisms by examining physiological, biochemical, and metabolic changes at different stages. Metabolite quantification was done using UPLC-ESI-MS/MS and a total of 682 metabolites were detected.

Results

The results showed that 2X watermelon leaves had lower chlorophyll content and fresh weights compared to 3X. The activities of antioxidants, such as superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), were higher in 3X than in 2X. 3X watermelon leaves showed lower O2 production rates, MDA, and hydrogen peroxide (H2O2) levels in response to flooding, while higher ethylene production was observed. 3X had higher levels of dehydrogenase activity (DHA) and ascorbic acid + dehydrogenase (AsA + DHA), but both 2X and 3X showed a significant decline in the AsA/DHA ratio at later stages of flooding. Among them, 4-guanidinobutyric acid (mws0567), an organic acid, may be a candidate metabolite responsible for flooding tolerance in watermelon and had higher expression levels in 3X watermelon, suggesting that triploid watermelon is more tolerant to flooding.

Conclusion

This study provides insights into the response of 2X and 3X watermelon to flooding and the physiological, biochemical, and metabolic changes involved. It will serve as a foundation for future in-depth molecular and genetic studies on flooding response in watermelon.

Flooding tolerance in Rice: adaptive mechanism and marker-assisted selection breeding approaches

Natural and man-made ecosystems worldwide are subjected to flooding, which is a form of environmental stress. Genetic variability in the plant response to flooding involves variations in metabolism, architecture, and elongation development that are related with a low oxygen escape strategy and an opposing quiescence scheme that enables prolonged submergence endurance. Flooding is typically associated with a decrease in O₂ in the cells, which is especially severe when photosynthesis is absent or limited, leading to significant annual yield losses globally. Over the past two decades, considerable advancements have been made in understanding of mechanisms of rice adaptation and tolerance to flooding/submergence. The mapping and identification of Sub1 QTL have led to the development of marker-assisted selection (MAS) breeding approach to improve flooding-tolerant rice varieties in submergence-prone ecosystems. The Sub1 incorporated in rice varieties showed tolerance during flash flood, but not during stagnant conditions. Hence, gene pyramiding techniques can be applied to combine/stack multiple resistant genes for developing flood-resilient rice varieties for different types of flooding stresses. This review contains an update on the latest advances in understanding the molecular mechanisms, metabolic adaptions, and genetic factors governing rice flooding tolerance. A better understanding of molecular genetics and adaptation mechanisms that enhance flood-tolerant varieties under different flooding regimes was also discussed.

Foliar Application of Spermidine Alleviates Waterlogging-Induced Damages to Maize Seedlings by Enhancing Antioxidative Capacity, Modulating Polyamines and Ethylene Biosynthesis

Waterlogging is a major threat to maize production worldwide. The exogenous application of spermidine is well known to enhance plant tolerance to abiotic stresses. The role of exogenous spermidine application in waterlogging tolerance in maize was investigated in this study. Two maize varieties (a waterlogging-tolerant variety: Xundan 20 (XD20) and a waterlogging-sensitive variety: Denghai 662 (DH662)) were subjected to waterlogging stress at the seedling stage, and then foliar spraying of 0.75 mM spermidine or purified water. Findings demonstrated lower chlorophyll content, reduced growth indices, considerable increase in superoxide anion (O2-) generation rate, and H2O2/malondialdehyde accumulation in the two maize varieties under waterlogging stress compared to the control treatment. However, the tolerance variety performed better than the sensitive one. Foliar application of spermidine significantly increased antioxidant enzyme activities under waterlogging stress. In addition, the application of spermidine increased polyamine levels and led to the reduction of ethylene levels under waterlogging. Consequences of spermidine application were most apparent for the waterlogging-sensitive cultivar DH662 under waterlogging than the waterlogging-tolerant variety XD20.

A very-long-chain fatty acid synthesis gene, SD38, influences plant height by activating ethylene biosynthesis in rice

As an important trait in crop breeding, plant height is associated with lodging resistance and yield. With the identification and cloning of several semi-dwarfing genes, increasing numbers of semi-dwarf cultivars have emerged, which has led to a 'green revolution' in rice (Oryza sativa) production. In this study, we identified a rice semi-dwarf mutant, semi-dwarf 38 (sd38), which showed significantly reduced cell length. SD38 encodes a fatty acid elongase, β-ketoacyl-CoA synthase, which is involved in the synthesis of very-long-chain fatty acids (VLCFAs). Expression analysis showed that SD38 was localized on the membrane of the endoplasmic reticulum, and was expressed in all analyzed tissues with differential abundance. The mutation of SD38 affected lipid metabolism in the sd38 mutant. A functional complementarity test in Saccharomyces cerevisiae indicated that SD38 was capable of complementing the deficiency of ELO3p activity in BY4741-elo3 knockout yeast cells by participating in the synthesis of C24:0 VLCFA. Significant changes were observed in the expression of genes involved in ethylene synthesis, which resulted in reduced content of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) in the sd38 mutant. Exogenously supplied VLCFA (C24:0) increased the expression levels of OsACS3, OsACS4, and OsACO7 and the plant height of sd38 mutant seedlings, similar to the effect of exogenous application of ACC and ethephon. These results reveal a relationship among VLCFAs, ethylene biosynthesis, and plant height and improve our understanding of plant height development in crops.

Biocontrol potential of Pseudomonas rhodesiae GC-7 against the root-knot nematode Meloidogyne graminicola through both antagonistic effects and induced plant resistance

Plant-parasitic nematodes (PPNs) cause serious damage to agricultural production worldwide. Currently, because of a lack of effective and environmental-friendly chemical nematicides, the use of microbial nematicides has been proposed as an eco-friendly management strategy to control PPNs. A nematicidal bacterium GC-7 was originally isolated from the rice rhizosphere, and was identified as Pseudomonas rhodesiae. Treatment with the fermentation supernatant of GC-7 in vitro showed a highly lethal effect on second-stage juveniles of Meloidogyne graminicola, with the mortality rate increasing to 95.82% at 24 h and egg hatching significantly inhibited, with a hatch inhibition rate of 60.65% at 96 h. The bacterium significantly reduced the level of damage caused by M. graminicola infestations to rice (Oryza sativa) in greenhouse and field experiments. Under greenhouse conditions, the GC-7 culture efficiently reduced the gall index and nematode population in rice roots and soils, as well as inhibited nematode development compared to the control. Under field conditions, application of the GC-7 consistently showed a high biocontrol efficacy against M. graminicola (with a control efficiency of 58.85%) and promoted plant growth. In addition, the inoculation of GC-7 in M. graminicola-infested rice plant fields significantly suppressed final nematode populations in soil under natural conditions. Furthermore, activities of plant defense-related enzymes, peroxidase, polyphenol oxidase, and phenylalanine ammonia-lyase were remarkably increased in plant roots treated with GC-7 compared with roots that were challenge to M. graminicola. Moreover, quantitative real-time PCR analysis showed that GC-7 significantly enhanced the expression of defense genes (PR1a, WRKY45, JaMYB, AOS2, ERF1, and ACS1) related to salicylic acid, jasmonic acid, and ethylene signaling pathways in rice roots after inoculation with GC-7 at different levels. The results indicated that GC-7 could be an effective biological component in the integrated management of M. graminicola infecting rice.

The involvement of nitric oxide and ethylene on the formation of endodermal barriers in response to Cd in hyperaccumulator Sedum alfredii

Nitric oxide (NO) and ethylene are both important signaling molecules which participate in numerous plant development processes and environmental stress resistance. Here, we investigate whether and how NO interacts with ethylene during the development of endodermal barriers that have major consequences for the apoplastic uptake of cadmium (Cd) in the hyperaccumulator Sedum alfredii. In response to Cd, an increased NO accumulation, while a decrease in ethylene production was observed in the roots of S. alfredii. Exogenous supplementation of NO donor SNP (sodium nitroprusside) decreased the ethylene production in roots, while NO scavenger cPTIO (2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide) had the opposite effect. The exogenous addition of NO affected the ethylene production through regulating the expression of genes related to ethylene synthesis. However, upon exogenous ethylene addition, roots retained their NO accumulation. The abovementioned results suggest that ethylene is downstream of the NO signaling pathway in S. alfredii. Regardless of Cd, addition of SNP promoted the deposition of endodermal barriers via regulating the genes related to Casparian strips deposition and suberization. Correlation analyses indicate that NO positively modifies the formation of endodermal barriers via the NO-ethylene signaling pathway, Cd-induced NO accumulation interferes with the synthesis of ethylene, leading to a deposition of endodermal barriers in S. alfredii.

The Pyramiding of Three Key Root Traits Aid Breeding of Flood-Tolerant Rice

Flooding is constantly threatening the growth and yield of crops worldwide. When flooding kicks in, the soil becomes water-saturated and, therefore, the roots are the first organs to be exposed to excess water. Soon after flooding, the soil turns anoxic and the roots can no longer obtain molecular oxygen for respiration from the rhizosphere, rendering the roots dysfunctional. Rice, however, is a semi-aquatic plant and therefore relatively tolerant to flooding due to adaptive traits developed during evolution. In the present review, we have identified three key root traits, viz. cortical aerenchyma formation, a barrier to radial oxygen loss and adventitious root growth. The understanding of the physiological function, the molecular mechanisms, and the genetic regulation of these three traits has grown substantially and therefore forms the backbone of this review. Our synthesis of the recent literature shows each of the three key root traits contributes to flood tolerance in rice. One trait, however, is generally insufficient to enhance plant tolerance to flooding. Consequently, we suggest comprehensive use of all three adaptive traits in a pyramiding approach in order to improve tolerance to flooding in our major crops, in general, and in rice, in particular.

Modeling-based age-dependent analysis reveals the net patterns of ethylene-dependent and -independent aerenchyma formation in rice and maize roots

Plants require oxygen for the functioning of roots, and thus the establishment of a long-distance diffusion path from above-water tissues to the submerged roots is essential to survive flooding. Rice (Oryza sativa) constitutively forms aerenchyma (gas spaces) under aerobic conditions, and induces its formation in response to low-oxygen conditions. Constitutive aerenchyma formation in rice roots is regulated by the phytohormone auxin, whereas ethylene stimulates inducible aerenchyma formation. However, the net patterns of the ethylene-dependent and -independent (auxin-dependent) aerenchyma formation remain unclear. In the present study, we used a modeling approach to determine age-dependent aerenchyma formation in the wild-type rice and reduced culm number 1 mutant, in which ethylene production is reduced, to reveal the net patterns of ethylene-dependent and -independent aerenchyma formation. Subsequent comparison of age-dependent aerenchyma formation between rice and maize roots suggested that more rapid induction of ethylene-dependent aerenchyma formation and more aerenchyma in rice roots are essential to achieve efficient oxygen diffusion under low-oxygen conditions. Moreover, rice roots showed rapid increase in the expression levels of ethylene biosynthesis and responsive genes, suggesting that the local ethylene production at an early time point after root-cell emergence contributes to the rapid induction of the ethylene-dependent aerenchyma formation in rice. DATA AVAILABILITY: All data included in this study are available upon request by contact with the corresponding author.

Abscisic acid is required for exodermal suberization to form a barrier to radial oxygen loss in the adventitious roots of rice (Oryza sativa)

To acclimate to waterlogged conditions, wetland plants form a barrier to radial oxygen loss (ROL) that can enhance oxygen transport to the root apex. We hypothesized that one or more hormones are involved in the induction of the barrier and searched for such hormones in rice. We previously identified 98 genes that were tissue-specifically upregulated during ROL barrier formation in rice. The RiceXPro database showed that most of these genes were highly enhanced by exogenous abscisic acid (ABA). We then examined the effect of ABA on ROL barrier formation by using an ABA biosynthesis inhibitor (fluridone, FLU), by applying exogenous ABA and by examining a mutant with a defective ABA biosynthesis gene (osaba1). FLU suppressed barrier formation in a stagnant solution that mimics waterlogged soil. Under aerobic conditions, rice does not naturally form a barrier, but 24 h of ABA treatment induced barrier formation. osaba1 did not form a barrier under stagnant conditions, but the application of ABA rescued the barrier. In parallel with ROL barrier formation, suberin lamellae formed in the exodermis. These findings strongly suggest that ABA is an inducer of suberin lamellae formation in the exodermis, resulting in an ROL barrier formation in rice.

Salt-induced inhibition of rice seminal root growth is mediated by ethylene-jasmonate interaction

The phytohormones ethylene and jasmonate play important roles in the adaptation of rice plants to salt stress. However, the molecular interactions between ethylene and jasmonate on rice seminal root growth under salt stress are unknown. In this study, the effects of NaCl on the homeostasis of ethylene and jasmonate, and on rice seminal root growth were investigated. Our results indicate that NaCl treatment promotes ethylene biosynthesis by up-regulating the expression of ethylene biosynthesis genes, whereas NaCl-induced ethylene does not inhibit rice seminal root growth directly, but rather indirectly, by promoting jasmonate biosynthesis. NaCl treatment also promotes jasmonate biosynthesis through an ethylene-independent pathway. Moreover, NaCl-induced jasmonate reduces meristem cell number and cell division activity via down-regulated expression of Oryza sativa PLETHORA (OsPLT) and cell division-related genes, respectively. Additionally, NaCl-induced jasmonate inhibits seminal root cell elongation by down-regulating the expression of cell elongation-related genes. Overall, salt stress promotes jasmonate biosynthesis through ethylene-dependent and -independent pathways in rice seminal roots, and jasmonate inhibits rice seminal root growth by inhibiting root meristem cell proliferation and root cell elongation.

Transcriptomic Analysis of the Photosynthetic, Respiration, and Aerenchyma Adaptation Strategies in Bermudagrass (Cynodon dactylon) under Different Submergence Stress

Submergence impedes photosynthesis and respiration but facilitates aerenchyma formation in bermudagrass. Still, the regulatory genes underlying these physiological responses are unclear in the literature. To identify differentially expressed genes (DEGs) related to these physiological mechanisms, we studied the expression of DEGs in aboveground and underground tissues of bermudagrass after a 7 d treatment under control (CK), shallow submergence (SS), and deep submergence (DS). Results show that compared with CK, 12276 and 12559 DEGs were identified under SS and DS, respectively. Among them, the DEGs closely related to the metabolism of chlorophyll biosynthesis, light-harvesting, protein complex, and carbon fixation were down-regulated in SS and DS. Meanwhile, a large number of DEGs involved in starch and sucrose hydrolase activities, glycolysis/gluconeogenesis, tricarboxylic acid (TCA) cycle, and oxidative phosphorylation were down-regulated in aboveground tissues of bermudagrass in SS and DS. Whereas in underground tissues of bermudagrass these DEGs were all up-regulated under SS, only beta-fructofuranosidase and α-amylase related genes were up-regulated under DS. In addition, we found that DEGs associated with ethylene signaling, Ca²⁺-ROS signaling, and cell wall modification were also up-regulated during aerenchyma formation in underground tissues of bermudagrass under SS and DS. These results provide the basis for further exploration of the regulatory and functional genes related to the adaptability of bermudagrass to submergence.

Development of EST-SSR markers for Pongamia pinnata by transcriptome database mining: cross-species amplification and genetic diversity

EST-SSR markers were developed from Pongamia pinnata transcriptome libraries. We have successfully utilised EST-SSRs to study the genetic diversity of Indian P. pinnata germplasms and transferability study on legume plants. P. pinnata is a non-edible oil, seed-bearing leguminous tree well known for its multipurpose benefits and acts as a potential source for medicine and biodiesel preparation. Moreover, the plant is not grazable by animal and wildly grown in different agro climatic condition of India. Recently, it is much used in reforestation and rehabilitation of marginal and coal mined land in different part of India. Due to increasing demand for cultivation, understanding of the genetic diversity is important parameter for further breeding and cultivation program. In this investigation, an attempt has been undertaken to develop novel EST-SSR markers by analyzing the assembled transcriptome from previously published Illumina libraries of P. pinnata, which is cross transferrable to legume plants. Twenty EST-SSR markers were developed from oil yielding and secondary metabolite biosynthesis genes. To our knowledge, this is the first EST-SSR marker based genetic diversity study on Indian P. pinnata germplasms. The genetic diversity parameter analysis of P. pinnata showed that the Gangetic plain and Eastern India are highly diverse compared to the Central Deccan and Western germplasms. The lowest genetic diversity in the Western region may be due to the pressure of lower precipitation, high-temperature stress and reduced groundwater availability. Nevertheless, the highest genetic diversity of Gangetic plain and Eastern India may be due to the higher groundwater availability, high precipitation, higher temperature fluctuations and growing by the side of glacier-fed river water. Thus, our study shows the evidence of natural selection on the genetic diversity of P. pinnata germplasms of the Indian subcontinent.

Radial oxygen loss is correlated with nitrogen nutrition in mangroves

The present study aimed to explore the possible functions of radial oxygen loss (ROL) on mangrove nutrition. A field survey was conducted to explore the relations among ROL, root anatomy and leaf N in different mangrove species along a continuous tidal gradient. Three mangroves with different ROL (Avicennia marina [A. marina], Kandelia obovata and Rhizophora stylosa) were then selected to further explore the dynamics of N at the root-soil interface. The results showed that seaward pioneer mangrove species such as A. marina appeared to exhibit higher leaf N despite growing under poorer nutrient conditions. Greater leaf N in pioneer mangroves coincided with their special root structure (e.g., high porosity together with a thin lignified/suberized exodermis) and powerful ROL. An interesting positive relation was observed between ROL and leaf N in mangroves. Moreover, rhizo-box data further showed that soil nitrification was also strongly correlated with ROL. A. marina, which had the highest ROL among the three mangrove species studied, consistently possessed the highest levels of NO3-, nitrification and ammonia-oxidizing bacteria and archaea gene copies in the rhizosphere. Besides, both NO3- and NH4+ influxes were found to be higher in the roots of A. marina when compared to those of K. obovata and R. stylosa. In summary, greater N acquisition by pioneer mangroves such as A. marina was strongly correlated with ROL which would regulate N transformation and translocation at the root-soil interface. The implications of this study may be significant in mangrove nutrition and the mechanisms involved in mangrove zonation.

A Role for Auxin in Ethylene-Dependent Inducible Aerenchyma Formation in Rice Roots

Internal oxygen diffusion from shoot to root tips is enhanced by the formation of aerenchyma (gas space) in waterlogged soils. Lysigenous aerenchyma is created by programmed cell death and subsequent lysis of the root cortical cells. Rice (Oryza sativa) forms aerenchyma constitutively under aerobic conditions and increases its formation under oxygen-deficient conditions. Recently, we have demonstrated that constitutive aerenchyma formation is regulated by auxin signaling mediated by Auxin/indole-3-acetic acid protein (AUX/IAA; IAA). While ethylene is involved in inducible aerenchyma formation, the relationship of auxin and ethylene during aerenchyma formation remains unclear. Here, we examined the effects of oxygen deficiency and ethylene on aerenchyma formation in the roots of a rice mutant (iaa13) in which auxin signaling is suppressed by a mutation in the degradation domain of IAA13 protein. The results showed that AUX/IAA-mediated auxin signaling contributes to ethylene-dependent inducible aerenchyma formation in rice roots. An auxin transport inhibitor abolished aerenchyma formation under oxygen-deficient conditions and reduced the expression of genes encoding ethylene biosynthesis enzymes, further supporting the idea that auxin is involved in ethylene-dependent inducible aerenchyma formation. Based on these studies, we propose a mechanism that underlies the relationship between auxin and ethylene during inducible aerenchyma formation in rice roots.

RNA-Seq reveals novel genes and pathways associated with hypoxia duration and tolerance in tomato root

Due to climate change, economically important crop plants will encounter flooding periods causing hypoxic stress more frequently. This may lead to reduced yields and endanger food security. As roots are the first organ to be affected by hypoxia, the ability to sense and respond to hypoxic stress is crucial. At the molecular level, therefore, fine-tuning the regulation of gene expression in the root is essential for hypoxia tolerance. Using an RNA-Seq approach, we investigated transcriptome modulation in tomato roots of the cultivar 'Moneymaker', in response to short- (6 h) and long-term (48 h) hypoxia. Hypoxia duration appeared to have a significant impact on gene expression such that the roots of five weeks old tomato plants showed a distinct time-dependent transcriptome response. We observed expression changes in 267 and 1421 genes under short- and long-term hypoxia, respectively. Among these, 243 genes experienced changed expression at both time points. We identified tomato genes with a potential role in aerenchyma formation which facilitates oxygen transport and may act as an escape mechanism enabling hypoxia tolerance. Moreover, we identified differentially regulated genes related to carbon and amino acid metabolism and redox homeostasis. Of particular interest were the differentially regulated transcription factors, which act as master regulators of downstream target genes involved in responses to short and/or long-term hypoxia. Our data suggest a temporal metabolic and anatomic adjustment to hypoxia in tomato root which requires further investigation. We propose that the regulated genes identified in this study are good candidates for further studies regarding hypoxia tolerance in tomato or other crops.

PUCHI regulates very long chain fatty acid biosynthesis during lateral root and callus formation

Lateral root organogenesis plays an essential role in elaborating plant root system architecture. In Arabidopsis, the AP2 family transcription factor PUCHI controls cell proliferation in lateral root primordia. To identify potential targets of PUCHI, we analyzed a time course transcriptomic dataset of lateral root formation. We report that multiple genes coding for very long chain fatty acid (VLCFA) biosynthesis enzymes are induced during lateral root development in a PUCHI-dependent manner. Significantly, several mutants perturbed in VLCFA biosynthesis show similar lateral root developmental defects as puchi-1 Moreover, puchi-1 roots display the same disorganized callus formation phenotype as VLCFA biosynthesis-deficient mutants when grown on auxin-rich callus-inducing medium. Lipidomic profiling of puchi-1 roots revealed reduced VLCFA content compared with WT. We conclude that PUCHI-regulated VLCFA biosynthesis is part of a pathway controlling cell proliferation during lateral root and callus formation.

Programmed Cell Death and Aerenchyma Formation in Water-Logged Sunflower Stems and Its Promotion by Ethylene and ROS

Previous studies have shown that waterlogging/ hypoxic conditions induce aerenchyma formation to facilitate gas exchange. Ethylene (ET) and reactive oxygen species (ROS), as regulatory signals, might also be involved in these adaptive responses. However, the interrelationships between these signals have seldom been reported. Herein, we showed that programmed cell death (PCD) was involved in aerenchyma formation in the stem of Helianthus annuus. Lysigenous aerenchyma formation in the stem was induced through waterlogging (WA), ethylene and ROS. Pre-treatment with the NADPH oxidase inhibitor diphenyleneiodonium (DPI) partially suppressed aerenchyma formation in the seedlings after treatment with WA, ET and 3-amino-1, 2, 4-triazole (AT, catalase inhibitor). In addition, pre-treatment with the ethylene perception inhibitor 1-methylcyclopropene (1-MCP) partially suppressed aerenchyma formation induced through WA and ET in the seedlings, but barely inhibited aerenchyma formation induced through ROS. These results revealed that ethylene-mediated ROS signaling plays a role in aerenchyma formation, and there is a causal and interdependent relationship during WA, ET and ROS in PCD, which regulates signal networks in the stem of H. annuus.

Supraoptimal Cytokinin Content Inhibits Rice Seminal Root Growth by Reducing Root Meristem Size and Cell Length via Increased Ethylene Content

Cytokinins (CKs), a class of phytohormone, regulate root growth in a dose-dependent manner. A certain threshold content of CK is required for rapid root growth, but supraoptimal CK content inhibits root growth, and the mechanism of this inhibition remains unclear in rice. In this study, treatments of lovastatin (an inhibitor of CK biosynthesis) and kinetin (KT; a synthetic CK) were found to inhibit rice seminal root growth in a dose-dependent manner, suggesting that endogenous CK content is optimal for rapid growth of the seminal root in rice. KT treatment strongly increased ethylene level by upregulating the transcription of ethylene biosynthesis genes. Ethylene produced in response to exogenous KT inhibited rice seminal root growth by reducing meristem size via upregulation of OsIAA3 transcription and reduced cell length by downregulating transcription of cell elongation-related genes. Moreover, the effects of KT treatment on rice seminal root growth, root meristem size and cell length were rescued by treatment with aminoethoxyvinylglycine (an inhibitor of ethylene biosynthesis), which restored ethylene level and transcription levels of OsIAA3 and cell elongation-related genes. Supraoptimal CK content increases ethylene level by promoting ethylene biosynthesis, which in turn inhibits rice seminal root growth by reducing root meristem size and cell length.

Towards Identification of the Substrates of ATP-Binding Cassette Transporters

Most ATP-binding cassette (ABC) proteins function in transmembrane transport, and plant genomes encode a large number of ABC transporters compared with animal or fungal genomes. These transporters have been classified into eight subfamilies according to their topology and phylogenetic relationships. Transgenic plants and mutants with altered ABC transporter expression or function have contributed to deciphering the physiological roles of these proteins, such as in plant development, responses to biotic and abiotic stress, or detoxification activities within the cell. In agreement with the diversity of these functions, a large range of substrates (e.g. hormones and primary and secondary metabolites) have been identified. We review in detail transporters for which substrates have been unambiguously identified. However, some cases are far from clear, because some ABC transporters have the ability to transport several structurally unrelated substrates or because the identification of their substrates was performed indirectly without any flux measurement. Various heterologous or homologous expression systems have been used to better characterize the transport activity and other biochemical properties of ABC transporters, opening the way to addressing new issues such as the particular structural features of plant ABC transporters, the bidirectionality of transport, or the role of posttranslational modifications.

Hormonal regulation in adventitious roots and during their emergence under waterlogged conditions in wheat

To gain insights into the molecular mechanisms underlying hormonal regulation in adventitious roots and during their emergence under waterlogged conditions in wheat, the present study investigated transcriptional regulation of genes related to hormone metabolism and transport in the root and stem node tissues. Waterlogging-induced inhibition of axile root elongation and lateral root formation, and promotion of surface adventitious and axile root emergence and aerenchyma formation are associated with enhanced expression levels of ethylene biosynthesis genes, ACS7 and ACO2, in both tissues. Inhibition of axile root elongation is also related to increased root indole acetic acid (IAA) and jasmonate (JA) levels that are associated with up-regulation of specific IAA biosynthesis/transport (TDC, YUC1, and PIN9) and JA metabolism (LOX8, AOS1, AOC1, and JAR1) genes, and transcriptional alteration of gibberellin (GA) metabolism genes (GA3ox2 and GA2ox8). Adventitious root emergence from waterlogged stem nodes is associated with increased levels of IAA and GA but decreased levels of cytokinin and abscisic acid (ABA), which are regulated through the expression of specific IAA biosynthesis/transport (TDC, YUC1, and PIN9), cytokinin metabolism (IPT5-2, LOG1, CKX5, and ZOG2), ABA biosynthesis (NCED1 and NCED2), and GA metabolism (GA3ox2 and GA2ox8) genes. These results enhance our understanding of the molecular mechanisms underlying the adaptive response of wheat to waterlogging.

METALLOTHIONEIN genes encoding ROS scavenging enzymes are down-regulated in the root cortex during inducible aerenchyma formation in rice

Under waterlogged conditions, roots of gramineous plants form lysigenous aerenchyma (internal gas spaces) by inducing the death of cortical cells. Rice (Oryza sativa) roots induce aerenchyma formation through ethylene- and reactive oxygen species (ROS)-mediated signaling. Metallothionein (MT) is a small, cysteine-rich protein that acts as a ROS scavenger. In rice roots, the expression of MT1a, MT1b, MT1c and MT1Ld were higher than those of the other MT genes. In the root cortex, where aerenchyma forms exclusively, the expression of MT1a, MT1b and MT1Ld was reduced prior to aerenchyma formation. These findings suggest that ROS accumulation in the cortex, which is aided by downregulation of MT1 genes, is needed for aerenchyma formation in rice roots.

Transcriptomic Analysis of Gibberellin- and Paclobutrazol-Treated Rice Seedlings under Submergence

Submergence stress is a limiting factor for rice growing in rainfed lowland areas of the world. It is known that the phytohormone gibberellin (GA) has negative effects on submergence tolerance in rice, while its inhibitor paclobutrazol (PB) does the opposite. However, the physiological and molecular basis underlying the GA- and PB-regulated submergence response remains largely unknown. In this study, we reveal that PB could significantly enhance rice seedling survival by retaining a higher level of chlorophyll content and alcohol dehydrogenase activity, and decelerating the consumption of non-structure carbohydrate when compared with the control and GA-treated samples. Further transcriptomic analysis identified 3936 differentially expressed genes (DEGs) among the GA- and PB-treated samples and control, which are extensively involved in the submergence and other abiotic stress responses, phytohormone biosynthesis and signaling, photosynthesis, and nutrient metabolism. The results suggested that PB enhances rice survival under submergence through maintaining the photosynthesis capacity and reducing nutrient metabolism. Taken together, the current study provided new insight into the mechanism of phytohormone-regulated submergence response in rice.

An NADPH Oxidase RBOH Functions in Rice Roots during Lysigenous Aerenchyma Formation under Oxygen-Deficient Conditions

Reactive oxygen species (ROS) produced by the NADPH oxidase, respiratory burst oxidase homolog (RBOH), trigger signal transduction in diverse biological processes in plants. However, the functions of RBOH homologs in rice (Oryza sativa) and other gramineous plants are poorly understood. Ethylene induces the formation of lysigenous aerenchyma, which consists of internal gas spaces created by programmed cell death of cortical cells, in roots of gramineous plants under oxygen-deficient conditions. Here, we report that, in rice, one RBOH isoform (RBOHH) has a role in ethylene-induced aerenchyma formation in roots. Induction of RBOHH expression under oxygen-deficient conditions was greater in cortical cells than in cells of other root tissues. In addition, genes encoding group I calcium-dependent protein kinases (CDPK5 and CDPK13) were strongly expressed in root cortical cells. Coexpression of RBOHH with CDPK5 or CDPK13 induced ROS production in Nicotiana benthamiana leaves. Inhibitors of RBOH activity or cytosolic calcium influx suppressed ethylene-induced aerenchyma formation. Moreover, knockout of RBOHH by CRISPR/Cas9 reduced ROS accumulation and inducible aerenchyma formation in rice roots. These results suggest that RBOHH-mediated ROS production, which is stimulated by CDPK5 and/or CDPK13, is essential for ethylene-induced aerenchyma formation in rice roots under oxygen-deficient conditions.

Lipidomic profiling analysis reveals the dynamics of phospholipid molecules in Arabidopsis thaliana seedling growth

High-throughput lipidomic profiling provides a sensitive approach for discovering minor lipid species. By using an advance in electrospray ionization tandem mass spectrometry, a large set of phospholipid molecular species (126 species) with high resolution were identified from Arabidopsis seedling; of them 31 species are newly identified (16 are unique in plants), including 13 species of phosphatidic acid (PA), nine phosphatidylcholine, six phosphatidylinositol and three phosphatidylserine. Further analysis of the lipidomic profile reveals dynamics of phospholipids and distinct species alterations during seedling development. PA molecules are found at the lowest levels in imbibition and follow an increasing trend during seedling growth, while phosphatidylethanolamine (PE) molecules show the opposite pattern with highest levels at imbibition and a general decreasing trend at later stages. Of PA molecular species, 34:2-, 34:3-, 36:4-, 36:5-, 38:3- and 38:4-PA increase during radicle emergence, and 34:2- and 34:3-PA reach highest levels during hypocotyl and cotyledon emergence from the seed coat. Conversely, molecular species of PE show higher levels in imbibition and decrease in later stages. These results suggest the crucial roles of specific molecular species and homeostasis of phospholipid molecules in seedling growth and provide insights into the mechanisms of how phospholipid molecules are involved in regulating plant development.

Ethylene-dependent aerenchyma formation in adventitious roots is regulated differently in rice and maize

In roots of gramineous plants, lysigenous aerenchyma is created by the death and lysis of cortical cells. Rice (Oryza sativa) constitutively forms aerenchyma under aerobic conditions, and its formation is further induced under oxygen-deficient conditions. However, maize (Zea mays) develops aerenchyma only under oxygen-deficient conditions. Ethylene is involved in lysigenous aerenchyma formation. Here, we investigated how ethylene-dependent aerenchyma formation is differently regulated between rice and maize. For this purpose, in rice, we used the reduced culm number1 (rcn1) mutant, in which ethylene biosynthesis is suppressed. Ethylene is converted from 1-aminocyclopropane-1-carboxylic acid (ACC) by the action of ACC oxidase (ACO). We found that OsACO5 was highly expressed in the wild type, but not in rcn1, under aerobic conditions, suggesting that OsACO5 contributes to aerenchyma formation in aerated rice roots. By contrast, the ACO genes in maize roots were weakly expressed under aerobic conditions, and thus ACC treatment did not effectively induce ethylene production or aerenchyma formation, unlike in rice. Aerenchyma formation in rice roots after the initiation of oxygen-deficient conditions was faster and greater than that in maize. These results suggest that the difference in aerenchyma formation in rice and maize is due to their different mechanisms for regulating ethylene biosynthesis.