Highly Cited Articles
The following is a list of the most cited articles published since 2020, according to Web of Science.
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Abscisic acid dynamics, signaling, and functions in plants
Kong Chen, Guo-Jun Li, Ray A. Bressan, Chun-Peng Song, Jian-Kang Zhu and Yang Zhao
J Integr Plant Biol 2020, 62 (1): 25-54.  
doi: 10.1111/jipb.12899
Abstract (Browse 1660)  |   Save

Abscisic acid (ABA) is an important phytohormone regulating plant growth, development, and stress responses. It has an essential role in multiple physiological processes of plants, such as stomatal closure, cuticular wax accumulation, leaf senescence, bud dormancy, seed germination, osmotic regulation, and growth inhibition among many others. Abscisic acid controls downstream responses to abiotic and biotic environmental changes through both transcriptional and posttranscriptional mechanisms. During the past 20 years, ABA biosynthesis and many of its signaling pathways have been well characterized. Here we review the dynamics of ABA metabolic pools and signaling that affects many of its physiological functions.

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Cited: Web of Science(376)
Contribution of phenylpropanoid metabolism to plant development and plant–environment interactions
Nai-Qian Dong and Hong-Xuan Lin
J Integr Plant Biol 2021, 63 (1): 180-209.  
doi: 10.1111/jipb.13054
Abstract (Browse 599)  |   Save
Phenylpropanoid metabolism is one of the most important metabolisms in plants, yielding more than 8,000 metabolites contributing to plant development and plant–environment interplay. Phenylpropanoid metabolism materialized during the evolution of early freshwater algae that were initiating terrestrialization and land plants have evolved multiple branches of this pathway, which give rise to metabolites including lignin, flavonoids, lignans, phenylpropanoid esters, hydroxycinnamic acid amides, and sporopollenin. Recent studies have revealed that many factors participate in the regulation of phenylpropanoid metabolism, and modulate phenylpropanoid homeostasis when plants undergo successive developmental processes and are subjected to stressful environments. In this review, we summarize recent progress on elucidating the contribution of phenylpropanoid metabolism to the coordination of plant development and plant–environment interaction, and metabolic flux redirection among diverse metabolic routes. In addition, our review focuses on the regulation of phenylpropanoid metabolism at the transcriptional, post‐transcriptional, post‐translational, and epigenetic levels, and in response to phytohormones and biotic and abiotic stresses.
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Cited: Web of Science(186)
Epigenetic regulation in plant abiotic stress responses
Ya-Nan Chang, Chen Zhu, Jing Jiang, Huiming Zhang, Jian-Kang Zhu and Cheng-Guo Duan
J Integr Plant Biol 2020, 62 (5): 563-580.  
doi: 10.1111/jipb.12901
Abstract (Browse 769)  |   Save

In eukaryotic cells, gene expression is greatly influenced by the dynamic chromatin environment. Epigenetic mechanisms, including covalent modifications to DNA and histone tails and the accessibility of chromatin, create various chromatin states for stress‐responsive gene expression that is important for adaptation to harsh environmental conditions. Recent studies have revealed that many epigenetic factors participate in abiotic stress responses, and various chromatin modifications are changed when plants are exposed to stressful environments. In this review, we summarize recent progress on the cross‐talk between abiotic stress response pathways and epigenetic regulatory pathways in plants. Our review focuses on epigenetic regulation of plant responses to extreme temperatures, drought, salinity, the stress hormone abscisic acid, nutrient limitations and ultraviolet stress, and on epigenetic mechanisms of stress memory.

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Cited: Web of Science(151)
Protein kinases in plant responses to drought, salt, and cold stress
Xuexue Chen, Yanglin Ding, Yongqing Yang, Chunpeng Song, Baoshan Wang, Shuhua Yang, Yan Guo and Zhizhong Gong
J Integr Plant Biol 2021, 63 (1): 53-78.  
doi: 10.1111/jipb.13061
Abstract (Browse 992)  |   Save
Protein kinases are major players in various signal transduction pathways. Understanding the molecular mechanisms behind plant responses to biotic and abiotic stresses has become critical for developing and breeding climate‐resilient crops. In this review, we summarize recent progress on understanding plant drought, salt, and cold stress responses, with a focus on signal perception and transduction by different protein kinases, especially sucrose nonfermenting1 (SNF1)‐related protein kinases (SnRKs), mitogen‐activated protein kinase (MAPK) cascades, calcium‐dependent protein kinases (CDPKs/CPKs), and receptor‐like kinases (RLKs). We also discuss future challenges in these research fields.
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Cited: Web of Science(123)
Melatonin: A master regulator of plant development and stress responses
Chengliang Sun, Lijuan Liu, Luxuan Wang, Baohai Li, Chongwei Jin and Xianyong Lin
J Integr Plant Biol 2021, 63 (1): 126-145.  
doi: 10.1111/jipb.12993
Abstract (Browse 448)  |   Save
Melatonin is a pleiotropic molecule with multiple functions in plants. Since the discovery of melatonin in plants, numerous studies have provided insight into the biosynthesis, catabolism, and physiological and biochemical functions of this important molecule. Here, we describe the biosynthesis of melatonin from tryptophan, as well as its various degradation pathways in plants. The identification of a putative melatonin receptor in plants has led to the hypothesis that melatonin is a hormone involved in regulating plant growth, aerial organ development, root morphology, and the floral transition. The universal antioxidant activity of melatonin and its role in preserving chlorophyll might explain its anti‐senescence capacity in aging leaves. An impressive amount of research has focused on the role of melatonin in modulating postharvest fruit ripening by regulating the expression of ethylene‐related genes. Recent evidence also indicated that melatonin functions in the plant's response to biotic stress, cooperating with other phytohormones and well‐known molecules such as reactive oxygen species and nitric oxide. Finally, great progress has been made towards understanding how melatonin alleviates the effects of various abiotic stresses, including salt, drought, extreme temperature, and heavy metal stress. Given its diverse roles, we propose that melatonin is a master regulator in plants.
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Cited: Web of Science(116)
Plant immune signaling: Advancing on two frontiers
Wei Wang, Baomin Feng, Jian-Min Zhou and Dingzhong Tang
J Integr Plant Biol 2020, 62 (1): 2-24.  
doi: 10.1111/jipb.12898
Abstract (Browse 730)  |   Save

Plants have evolved multiple defense strategies to cope with pathogens, among which plant immune signaling that relies on cell‐surface localized and intracellular receptors takes fundamental roles. Exciting breakthroughs were made recently on the signaling mechanisms of pattern recognition receptors (PRRs) and intracellular nucleotide‐binding site (NBS) and leucine‐rich repeat (LRR) domain receptors (NLRs). This review summarizes the current view of PRRs activation, emphasizing the most recent discoveries about PRRs’ dynamic regulation and signaling mechanisms directly leading to downstream molecular events including mitogen‐activated protein kinase (MAPK) activation and calcium (Ca2+) burst. Plants also have evolved intracellular NLRs to perceive the presence of specific pathogen effectors and trigger more robust immune responses. We also discuss the current understanding of the mechanisms of NLR activation, which has been greatly advanced by recent breakthroughs including structures of the first full‐length plant NLR complex, findings of NLR sensor‐helper pairs and novel biochemical activity of Toll/interleukin‐1 receptor (TIR) domain.

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Cited: Web of Science(101)
New insights into gibberellin signaling in regulating flowering in Arabidopsis
Shengjie Bao, Changmei Hua, Lisha Shen and Hao Yu
J Integr Plant Biol 2020, 62 (1): 118-131.  
doi: 10.1111/jipb.12892
Abstract (Browse 407)  |   Save

In angiosperms, floral transition is a key developmental transition from the vegetative to reproductive growth, and requires precise regulation to maximize the reproductive success. A complex regulatory network governs this transition through integrating flowering pathways in response to multiple exogenous and endogenous cues. Phytohormones are essential for proper plant developmental regulation and have been extensively studied for their involvement in the floral transition. Among various phytohormones, gibberellin (GA) plays a major role in affecting flowering in the model plant Arabidopsis thaliana. The GA pathway interact with other flowering genetic pathways and phytohormone signaling pathways through either DELLA proteins or mediating GA homeostasis. In this review, we summarize the recent advances in understanding the mechanisms of DELLA‐mediated GA pathway in flowering time control in Arabidopsis, and discuss its possible link with other phytohormone pathways during the floral transition.

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Cited: Web of Science(80)
Potassium and phosphorus transport and signaling in plants
Yi Wang, Yi-Fang Chen and Wei-Hua Wu
J Integr Plant Biol 2021, 63 (1): 34-52.  
doi: 10.1111/jipb.13053
Abstract (Browse 450)  |   Save
Nitrogen (N), potassium (K), and phosphorus (P) are essential macronutrients for plant growth and development, and their availability affects crop yield. Compared with N, the relatively low availability of K and P in soils limits crop production and thus threatens food security and agricultural sustainability. Improvement of plant nutrient utilization efficiency provides a potential route to overcome the effects of K and P deficiencies. Investigation of the molecular mechanisms underlying how plants sense, absorb, transport, and use K and P is an important prerequisite to improve crop nutrient utilization efficiency. In this review, we summarize current understanding of K and P transport and signaling in plants, mainly taking Arabidopsis thaliana and rice (Oryza sativa) as examples. We also discuss the mechanisms coordinating transport of N and K, as well as P and N.
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Cited: Web of Science(72)
The plant cell wall: Biosynthesis, construction, and functions
Baocai Zhang, Yihong Gao, Lanjun Zhang and Yihua Zhou
J Integr Plant Biol 2021, 63 (1): 251-272.  
doi: 10.1111/jipb.13055
Abstract (Browse 401)  |   Save
The plant cell wall is composed of multiple biopolymers, representing one of the most complex structural networks in nature. Hundreds of genes are involved in building such a natural masterpiece. However, the plant cell wall is the least understood cellular structure in plants. Due to great progress in plant functional genomics, many achievements have been made in uncovering cell wall biosynthesis, assembly, and architecture, as well as cell wall regulation and signaling. Such information has significantly advanced our understanding of the roles of the cell wall in many biological and physiological processes and has enhanced our utilization of cell wall materials. The use of cutting‐edge technologies such as single‐molecule imaging, nuclear magnetic resonance spectroscopy, and atomic force microscopy has provided much insight into the plant cell wall as an intricate nanoscale network, opening up unprecedented possibilities for cell wall research. In this review, we summarize the major advances made in understanding the cell wall in this era of functional genomics, including the latest findings on the biosynthesis, construction, and functions of the cell wall.
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Cited: Web of Science(63)
Hydrogen sulfide, a signaling molecule in plant stress responses
Jing Zhang, Mingjian Zhou, Heng Zhou, Didi Zhao, Cecilia Gotor, Luis C. Romero, Jie Shen, Zhenglin Ge, Zhirong Zhang, Wenbiao Shen, Xingxing Yuan and Yanjie Xie
J Integr Plant Biol 2021, 63 (1): 146-160.  
doi: 10.1111/jipb.13022
Abstract (Browse 409)  |   Save
Gaseous molecules, such as hydrogen sulfide (H2S) and nitric oxide (NO), are crucial players in cellular and (patho)physiological processes in biological systems. The biological functions of these gaseous molecules, which were first discovered and identified as gasotransmitters in animals, have received unprecedented attention from plant scientists in recent decades. Researchers have arrived at the consensus that H2S is synthesized endogenously and serves as a signaling molecule throughout the plant life cycle. However, the mechanisms of H2S action in redox biology is still largely unexplored. This review highlights what we currently know about the characteristics and biosynthesis of H2S in plants. Additionally, we summarize the role of H2S in plant resistance to abiotic stress. Moreover, we propose and discuss possible redox‐dependent mechanisms by which H2S regulates plant physiology.
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Cited: Web of Science(60)
Jasmonic acid alleviates cadmium toxicity in Arabidopsis via suppression of cadmium uptake and translocation
Gui Jie Lei, Li Sun, Ying Sun, Xiao Fang Zhu, Gui Xin Li and Shao Jian Zheng
J Integr Plant Biol 2020, 62 (2): 218-227.  
DOI: 10.1111/jipb.12801
Abstract (Browse 283)  |   Save
Jasmonic acid (JA) is thought to be involved in plant responses to cadmium (Cd) stress, but the underlying molecular mechanisms are poorly understood. Here, we show that Cd treatment rapidly induces the expression of genes promoting endogenous JA synthesis, and subsequently increases the JA concentration in Arabidopsis roots. Furthermore, exogenous methyl jasmonate (MeJA) alleviates Cd‐generated chlorosis of new leaves by decreasing the Cd concentration in root cell sap and shoot, and decreasing the expression of the AtIRT1, AtHMA2 and AtHMA4 genes promoting Cd uptake and long‐distance translocation, respectively. In contrast, mutation of a key JA synthesis gene, AtAOS, greatly enhances the expression of AtIRT1, AtHMA2 and AtHMA4, increases Cd concentration in both roots and shoots, and confers increased sensitivity to Cd. Exogenous MeJA recovers the enhanced Cd‐sensitivity of the ataos mutant, but not of atcoi1, a JA receptor mutant. In addition, exogenous MeJA reduces NO levels in Cd‐stressed Arabidopsis root tips. Taken together, our results suggest that Cd‐induced JA acts via the JA signaling pathway and its effects on NO levels to positively restrict Cd accumulation and alleviates Cd toxicity in Arabidopsis via suppression of the expression of genes promoting Cd uptake and long‐distance translocation.
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Cited: Web of Science(56)
Light signaling and UV-B-mediated plant growth regulation
Arpita Yadav, Deeksha Singh, Maneesh Lingwan, Premachandran Yadukrishnan, Shyam Kumar Masakapalli and Sourav Datta
J Integr Plant Biol 2020, 62 (9): 1270-1292.  
doi: 10.1111/jipb.12932
Abstract (Browse 320)  |   Save

Light plays an important role in plants’ growth and development throughout their life cycle. Plants alter their morphological features in response to light cues of varying intensity and quality. Dedicated photoreceptors help plants to perceive light signals of different wavelengths. Activated photoreceptors stimulate the downstream signaling cascades that lead to extensive gene expression changes responsible for physiological and developmental responses. Proteins such as ELONGATED HYPOCOTYL5 (HY5) and CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) act as important factors which modulate light‐regulated gene expression, especially during seedling development. These factors function as central regulatory intermediates not only in red, far‐red, and blue light pathways but also in the UV‐B signaling pathway. UV‐B radiation makes up only a minor fraction of sunlight, yet it imparts many positive and negative effects on plant growth. Studies on UV‐B perception, signaling, and response in plants has considerably surged in recent times. Plants have developed different strategies to use UV‐B as a developmental cue as well as to withstand high doses of UV‐B radiation. Plants’ responses to UV‐B are an integration of its cross‐talks with both environmental factors and phytohormones. This review outlines the current developments in light signaling with a major focus on UV‐B‐mediated plant growth regulation.

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Cited: Web of Science(54)
Exploring the molecular basis of heterosis for plant breeding
Jie Liu, Mengjie Li, Qi Zhang, Xin Wei and Xuehui Huang
J Integr Plant Biol 2020, 62 (3): 287-298.  
doi: 10.1111/jipb.12804
Abstract (Browse 455)  |   Save

Since approximate a century ago, many hybrid crops have been continually developed by crossing two inbred varieties. Owing to heterosis (hybrid vigor) in plants, these hybrids often have superior agricultural performances in yield or disease resistance succeeding their inbred parental lines. Several classical hypotheses have been proposed to explain the genetic causes of heterosis. During recent years, many new genetics and genomics strategies have been developed and used for the identifications of heterotic genes in plants. Heterotic effects of the heterotic loci and molecular functions of the heterotic genes are being investigated in many plants such as rice, maize, sorghum, Arabidopsis and tomato. More and more data and knowledge coming from the molecular studies of heterotic loci and genes will serve as a valuable resource for hybrid breeding by molecular design in future. This review aims to address recent advances in our understanding of the genetic and molecular mechanisms of heterosis in plants. The remaining scientific questions on the molecular basis of heterosis and the potential applications in breeding are also proposed and discussed.

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Cited: Web of Science(53)
Molecular mechanisms for the photoperiodic regulation of flowering in soybean
Xiaoya Lin, Baohui Liu, James L. Weller, Jun Abe and Fanjiang Kong
J Integr Plant Biol 2021, 63 (6): 981-994.  
doi: 10.1111/jipb.13021
Abstract (Browse 392)  |   Save
Photoperiodic flowering is one of the most important factors affecting regional adaptation and yield in soybean (Glycine max). Plant adaptation to long-day conditions at higher latitudes requires early flowering and a reduction or loss of photoperiod sensitivity; adaptation to short-day conditions at lower latitudes involves delayed flowering, which prolongs vegetative growth for maximum yield potential. Due to the influence of numerous major loci and quantitative trait loci (QTLs), soybean has broad adaptability across latitudes. Forward genetic approaches have uncovered the molecular basis for several of these major maturity genes and QTLs. Moreover, the molecular characterization of orthologs of Arabidopsis thaliana flowering genes has enriched our understanding of the photoperiodic flowering pathway in soybean. Building on early insights into the importance of the photoreceptor phytochrome A, several circadian clock components have been integrated into the genetic network controlling flowering in soybean: E1, a repressor of FLOWERING LOCUS T orthologs, plays a central role in this network. Here, we provide an overview of recent progress in elucidating photoperiodic flowering in soybean, how it contributes to our fundamental understanding of flowering time control, and how this information could be used for molecular design and breeding of high-yielding soybean cultivars.
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Cited: Web of Science(53)
SmMYB2 promotes salvianolic acid biosynthesis in the medicinal herb Salvia miltiorrhiza
Changping Deng, Yao Wang, Fenfen Huang, Sunjie Lu, Limei Zhao, Xingyuan Ma and Guoyin Kai
J Integr Plant Biol 2020, 62 (11): 1688-1702.  
DOI: 10.1111/jipb.12943
Abstract (Browse 323)  |   Save

MYB transcription factors play vital roles in plant growth and metabolism. The phytohormone methyl jasmonate (MeJA) promotes phenolic acid accumulation in the medicinal herb Salvia miltiorrhiza, but the regulatory mechanism is poorly understood. Here, we identified the MeJA‐responsive R2R3‐MYB transcription factor gene SmMYB2 from a transcriptome library produced from MeJA‐treated S. miltiorrhiza hairy roots. SmMYB2 expression was tightly correlated with the expression of key salvianolic acid biosynthetic genes including CYP98A14. SmMYB2 was highly expressed in the periderm of S. miltiorrhiza and SmMYB2 localized to the nucleus. Overexpressing SmMYB2 in S. miltiorrhiza hairy roots significantly increased the levels of salvianolic acids (including rosmarinic acid and salvianolic acid B) by upregulating salvianolic acid biosynthetic genes such as CYP98A14. SmMYB2 binds to the MYB‐binding motifs in the promoter of CYP98A14, as confirmed by a dual‐luciferase assay and electrophoretic mobility shift assays. Anthocyanin contents were significantly higher in SmMYB2‐overexpressing hairy root lines than the control, primarily due to the increased expression of CHI, DFR, and ANS. These findings reveal the novel regulatory role of SmMYB2 in MeJA‐mediated phenolic acid biosynthesis, providing a useful target gene for metabolic engineering and shedding light on the salvianolic acid regulatory network.

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Cited: Web of Science(49)
The transcription factor ICE1 functions in cold stress response by binding to the promoters of CBF and COR genes
Kai Tang, Lun Zhao, Yuying Ren, Shuhua Yang, Jian-Kang Zhu and Chunzhao Zhao
J Integr Plant Biol 2020, 62 (3): 258-263.  
doi: 10.1111/jipb.12918
Abstract (Browse 338)  |   Save

A recent paper by Kidokoro et al. (2020) in The Plant Cell reported a transgene‐dependent transcriptional silencing phenomenon in the dominant ice1‐1 Arabidopsis mutant containing the CBF3‐LUC reporter, and questioned whether ICE1 may regulate CBF genes and may be involved in plant cold response. Here, we evaluate available evidence supporting the involvement of ICE1 in plant cold response, and provide ChIP‐seq data showing ICE1 binding to the promoters of CBF genes and other regulatory genes known to be critical for cold response as well as to the promoters of some COR genes.

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Cited: Web of Science(48)
B-box proteins: Pivotal players in light-mediated development in plants
Zhaoqing Song, Yeting Bian, Jiujie Liu, Yuting Sun and Dongqing Xu
J Integr Plant Biol 2020, 62 (9): 1293-1309.  
doi: 10.1111/jipb.12935
Abstract (Browse 296)  |   Save

Light signals mediate a number of physiological and developmental processes in plants, such as flowering, photomorphogenesis, and pigment accumulation. Emerging evidence has revealed that a group of B‐box proteins (BBXs) function as central players in these light‐mediated developmental processes. B‐box proteins are a class of zinc‐coordinated transcription factors or regulators that not only directly mediate the transcription of target genes but also interact with various other factors to create a complex regulatory network involved in the precise control of plant growth and development. This review summarizes and highlights the recent findings concerning the critical regulatory functions of BBXs in photoperiodic flowering, light signal transduction and light‐induced pigment accumulation and their molecular modes of action at the transcriptional and post‐translational levels in plants

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Cited: Web of Science(46)
Natural variation in the promoter of OsHMA3 contributes to differential grain cadmium accumulation between Indica and Japonica rice
Chao-Lei Liu, Zhen-Yu Gao, Lian-Guang Shang, Chang-Hong Yang, Ban-Pu Ruan, Da-Li Zeng, Long-Biao Guo, Fang-Jie Zhao, Chao-Feng Huang and Qian Qian
J Integr Plant Biol 2020, 62 (3): 314-329.  
doi: 10.1111/jipb.12794
Abstract (Browse 448)  |   Save

Rice is a major source of cadmium (Cd) intake for Asian people. Indica rice usually accumulates more Cd in shoots and grains than Japonica rice. However, underlying genetic bases for differential Cd accumulation between Indica and Japonica rice are still unknown. In this study, we cloned a quantitative trait locus (QTL) grain Cd concentration on chromosome 7 (GCC7) responsible for differential grain Cd accumulation between two rice varieties by performing QTL analysis and map‐based cloning. We found that the two GCC7 alleles, GCC7PA64s and GCC793‐11, had different promoter activity of OsHMA3, leading to different OsHMA3 expression and different shoot and grain Cd concentrations. By analyzing the distribution of different haplotypes of GCC7 among diverse rice accessions, we discovered that the high and low Cd accumulation alleles, namely GCC793‐11 and GCC7PA64s, were preferentially distributed in Indica and Japonica rice, respectively. We further showed that the GCC7PA64s allele can be used to replace the GCC793‐11 allele in the super cultivar 93‐11 to reduce grain Cd concentration without adverse effect on agronomic traits. Our results thus reveal that the QTL GCC7 with sequence variation in the OsHMA3 promoter is an important determinant controlling differential grain Cd accumulation between Indica and Japonica rice.

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Cited: Web of Science(45)
Experiencing winter for spring flowering: A molecular epigenetic perspective on vernalization
Xiao Luo and Yuehui He
J Integr Plant Biol 2020, 62 (1): 104-117.  
doi: 10.1111/jipb.12896
Abstract (Browse 315)  |   Save

Many over‐wintering plants, through vernalization, overcome a block to flowering and thus acquire competence to flower in the following spring after experiencing prolonged cold exposure or winter cold. The vernalization pathways in different angiosperm lineages appear to have convergently evolved to adapt to temperate climates. Molecular and epigenetic mechanisms for vernalization regulation have been well studied in the crucifer model plant Arabidopsis thaliana. Here, we review recent progresses on the vernalization pathway in Arabidopsis. In addition, we summarize current molecular and genetic understandings of vernalization regulation in temperate grasses including wheat and Brachypodium, two monocots from Pooideae, followed by a brief discussion on divergence of the vernalization pathways between Brassicaceae and Pooideae.

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Cited: Web of Science(44)
Ethylene signaling in rice and Arabidopsis: New regulators and mechanisms
He Zhao, Cui-Cui Yin, Biao Ma, Shou-Yi Chen and Jin-Song Zhang
J Integr Plant Biol 2021, 63 (1): 102-125.  
doi: 10.1111/jipb.13028
Abstract (Browse 374)  |   Save
Ethylene is a gaseous hormone which plays important roles in both plant growth and development and stress responses. Based on studies in the dicot model plant species Arabidopsis, a linear ethylene signaling pathway has been established, according to which ethylene is perceived by ethylene receptors and transduced through CONSTITUTIVE TRIPLE RESPONSE 1 (CTR1) and ETHYLENE‐INSENSITIVE 2 (EIN2) to activate transcriptional reprogramming. In addition to this canonical signaling pathway, an alternative ethylene receptor‐mediated phosphor‐relay pathway has also been proposed to participate in ethylene signaling. In contrast to Arabidopsis, rice, a monocot, grows in semiaquatic environments and has a distinct plant structure. Several novel regulators and/or mechanisms of the rice ethylene signaling pathway have recently been identified, indicating that the ethylene signaling pathway in rice has its own unique features. In this review, we summarize the latest progress and compare the conserved and divergent aspects of the ethylene signaling pathway between Arabidopsis and rice. The crosstalk between ethylene and other plant hormones is also reviewed. Finally, we discuss how ethylene regulates plant growth, stress responses and agronomic traits. These analyses should help expand our knowledge of the ethylene signaling mechanism and could further be applied for agricultural purposes.
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Cited: Web of Science(43)
Autophagy in plants: Physiological roles and post‐translational regulation
Hua Qi, Fan-Nv Xia and Shi Xiao
J Integr Plant Biol 2021, 63 (1): 161-179.  
doi: 10.1111/jipb.12941
Abstract (Browse 300)  |   Save
In eukaryotes, autophagy helps maintain cellular homeostasis by degrading and recycling cytoplasmic materials via a tightly regulated pathway. Over the past few decades, significant progress has been made towards understanding the physiological functions and molecular regulation of autophagy in plant cells. Increasing evidence indicates that autophagy is essential for plant responses to several developmental and environmental cues, functioning in diverse processes such as senescence, male fertility, root meristem maintenance, responses to nutrient starvation, and biotic and abiotic stress. Recent studies have demonstrated that, similar to nonplant systems, the modulation of core proteins in the plant autophagy machinery by posttranslational modifications such as phosphorylation, ubiquitination, lipidation, S‐sulfhydration, S‐nitrosylation, and acetylation is widely involved in the initiation and progression of autophagy. Here, we provide an overview of the physiological roles and posttranslational regulation of autophagy in plants.
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Cited: Web of Science(42)
Osa‐miR167d facilitates infection of Magnaporthe oryzae in rice
Zhi-Xue Zhao, Qin Feng, Xiao-Long Cao, Yong Zhu, He Wang, Viswanathan Chandran, Jing Fan, Ji-Qun Zhao, Mei Pu, Yan Li and Wen-Ming Wang
J Integr Plant Biol 2020, 62 (5): 702-715.  
doi: 10.1111/jipb.12816
Abstract (Browse 365)  |   Save

MicroRNAs (miRNAs) play important roles in rice response to Magnaporthe oryzae, the causative agent of rice blast disease. Studying the roles of rice miRNAs is of great significance for the disease control. Osa‐miR167d belongs to a conserved miRNA family targeting auxin responsive factor (ARF) genes that act in developmental and stress‐induced responses. Here, we show that Osa‐miR167d plays a negative role in rice immunity against M. oryzae by suppressing its target gene. The expression of Osa‐miR167d was significantly suppressed in a resistant accession at and after 24 h post inoculation (hpi), however, its expression was significantly increased at 24 hpi in the susceptible accession upon M. oryzae infection. Transgenic rice lines over‐expressing Osa‐miR167d were highly susceptible to multiple blast fungal strains. By contrast, transgenic lines expressing a target mimicry to block Osa‐miR167d enhanced resistance to rice blast disease. In addition, knocking out the target gene ARF12 led to hyper‐susceptibility to multiple blast fungal strains. Taken together, our results indicate that Osa‐miR167d negatively regulate rice immunity to facilitate the infection of M. oryzae by downregulating ARF12. Thus, Osa‐miR167d‐ARF12 regulatory module could be valuable in improvement of blast‐disease resistance.

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Cited: Web of Science(41)
A WRKY transcription factor confers aluminum tolerance via regulation of cell wall modifying genes
Chun Xiao Li, Jing Ying Yan, Jiang Yuan Ren, Li Sun, Chen Xu, Gui Xin Li, Zhong Jie Ding and Shao Jian Zheng
J Integr Plant Biol 2020, 62 (8): 1176-1192.  
doi: 10.1111/jipb.12888
Abstract (Browse 331)  |   Save

Modification of cell wall properties has been considered as one of the determinants that confer aluminum (Al) tolerance in plants, while how cell wall modifying processes are regulated remains elusive. Here, we present a WRKY transcription factor WRKY47 involved in Al tolerance and root growth. Lack of WRKY47 significantly reduces, while overexpression of it increases Al tolerance. We show that lack of WRKY47 substantially affects subcellular Al distribution in the root, with Al content decreased in apoplast and increased in symplast, which is attributed to the reduced cell wall Al‐binding capacity conferred by the decreased content of hemicellulose I in the wrky47‐1 mutant. Based on microarray, real time‐quantitative polymerase chain reaction and chromatin immunoprecipitation assays, we further show that WRKY47 directly regulates the expression of EXTENSIN‐LIKE PROTEIN (ELP ) and XYLOGLUCAN ENDOTRANSGLUCOSYLASE‐HYDROLASES17 (XTH17 ) responsible for cell wall modification. Increasing the expression of ELP and XTH17 rescued Al tolerance as well as root growth in wrky47‐1 mutant. In summary, our results demonstrate that WRKY47 is required for root growth under both normal and Al stress conditions via direct regulation of cell wall modification genes, and that the balance of Al distribution between root apoplast and symplast conferred by WRKY47 is important for Al tolerance.

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Cited: Web of Science(41)
The roles of endomembrane trafficking in plant abiotic stress responses
Xiangfeng Wang, Min Xu, Caiji Gao, Yonglun Zeng, Yong Cui, Wenjin Shen and Liwen Jiang
J Integr Plant Biol 2020, 62 (1): 55-69.  
doi: 10.1111/jipb.12895
Abstract (Browse 289)  |   Save

Endomembrane trafficking is a fundamental cellular process in all eukaryotic cells and its regulatory mechanisms have been extensively studied. In plants, the endomembrane trafficking system needs to be constantly adjusted to adapt to the ever‐changing environment. Evidence has accumulated supporting the idea that endomembrane trafficking is tightly linked to stress signaling pathways to meet the demands of rapid changes in cellular processes and to ensure the correct delivery of stress‐related cargo molecules. However, the underlying mechanisms remain unknown. In this review, we summarize the recent findings on the functional roles of both secretory trafficking and endocytic trafficking in different types of abiotic stresses. We also highlight and discuss the unique properties of specific regulatory molecules beyond their conventional functions in endosomal trafficking during plant growth under stress conditions.

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The role of light in regulating seed dormancy and germination
Liwen Yang, Shuangrong Liu and Rongcheng Lin
J Integr Plant Biol 2020, 62 (9): 1310-1326.  
doi: 10.1111/jipb.13001
Abstract (Browse 302)  |   Save

Seed dormancy is an adaptive trait in plants. Breaking seed dormancy determines the timing of germination and is, thereby essential for ensuring plant survival and agricultural production. Seed dormancy and the subsequent germination are controlled by both internal cues (mainly hormones) and environmental signals. In the past few years, the roles of plant hormones in regulating seed dormancy and germination have been uncovered. However, we are only beginning to understand how light signaling pathways modulate seed dormancy and interaction with endogenous hormones. In this review, we summarize current views of the molecular mechanisms by which light controls the induction, maintenance and release of seed dormancy, as well as seed germination, by regulating hormone metabolism and signaling pathways.

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Soybean AP1 homologs control flowering time and plant height
Liyu Chen, Haiyang Nan, Lingping Kong, Lin Yue, Hui Yang, Qingsong Zhao, Chao Fang, Haiyang Li, Qun Cheng, Sijia Lu, Fanjiang Kong, Baohui Liu and Lidong Dong
J Integr Plant Biol 2020, 62 (12): 1868-1879.  
DOI: 10.1111/jipb.12988
Abstract (Browse 284)  |   Save

Flowering time and plant height are key agronomic traits that directly affect soybean (Glycine max) yield. APETALA1 (AP1) functions as a class A gene in the ABCE model for floral organ development, helping to specify carpel, stamen, petal, and sepal identities. There are four AP1 homologs in soybean, all of which are mainly expressed in the shoot apex. Here, we used clustered regularly interspaced short palindromic repeats (CRISPR) – CRISPR‐associated protein 9 technology to generate a homozygous quadruple mutant, gmap1, with loss‐of‐function mutations in all four GmAP1 genes. Under short‐day (SD) conditions, the gmap1 quadruple mutant exhibited delayed flowering, changes in flower morphology, and increased node number and internode length, resulting in plants that were taller than the wild type. Conversely, overexpression of GmAP1a resulted in early flowering and reduced plant height compared to the wild type under SD conditions. The gmap1 mutant and the overexpression lines also exhibited altered expression of several genes related to flowering and gibberellic acid metabolism, thereby providing insight into the role of GmAP1 in the regulatory networks controlling flowering time and plant height in soybean. Increased node number is the trait with the most promise for enhancing soybean pod number and grain yield. Therefore, the mutant alleles of the four AP1 homologs described here will be invaluable for molecular breeding of improved soybean yield.

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MYC2, MYC3, and MYC4 function additively in wounding-induced jasmonic acid biosynthesis and catabolism
Cuiping Zhang, Yunting Lei, Chengkai Lu, Lei Wang and Jianqiang Wu
J Integr Plant Biol 2020, 62 (8): 1159-1175.  
DOI: 10.1111/jipb.12902
Abstract (Browse 403)  |   Save

Jasmonic acid (JA) plays a critical role in plant defenses against insects and necrotrophic fungi. Wounding or lepidopteran insect feeding rapidly induces a burst of JA in plants, which usually reaches peak values within 1 to 2 h. The induced JA is converted to JA‐Ile and perceived by the COI1‐JAZ co‐receptor, leading to activation of the transcription factors MYC2 and its homologs, which further induce JA‐responsive genes. Although much is known about JA biosynthesis and catabolism enzymes and JA signaling, how JA biosynthesis and catabolism are regulated remain unclear. Here, we show that in Arabidopsis thaliana MYC2 functions additively with MYC3 and MYC4 to regulate wounding‐induced JA accumulation by directly binding to the promoters of genes function in JA biosynthesis and catabolism to promote their transcription. MYC2 also controls the transcription of JAV1 and JAM1 , which are key factors controlling JA biosynthesis and catabolism, respectively. In addition, we also found that MYC2 could bind to the MYC2 promoter and self‐inhibit its own expression. This work illustrates the central role of MYC2/3/4 in controlling wounding‐induced JA accumulation by regulating the transcription of genes involved in JA biosynthesis and catabolism.

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Trehalose‐6‐phosphate phosphatase E modulates ABA‐controlled root growth and stomatal movement in Arabidopsis
Wenjing Wang, Qingbin Chen, Shouming Xu, Wen-Cheng Liu, Xiaohong Zhu, and Chun-Peng Song
J Integr Plant Biol 2020, 62 (10): 1518-1534.  
doi: 10.1111/jipb.12925
Abstract (Browse 442)  |   Save

Trehalose plays important roles in plant growth and stress responses and is synthesized from trehalose‐6‐phosphate by trehalose‐6‐phosphate phosphatase (TPP). Here, we show that trehalose and abscisic acid (ABA) have synergistic effects on root growth and stomatal closure. The Arabidopsis thaliana genome contains ten genes encoding TPPs and the expression level of one, TPPE, and trehalose contents increased in response to ABA. In the presence of ABA, the ABA‐responsive transcription factor ABA RESPONSE ELEMENT BINDING FACTOR2 (ABF2) directly binds to the TPPE promoter to activate its expression. Genetic analysis revealed that TPPE acts downstream of ABF2, which is supported by the findings that TPPE expression and trehalose content are reduced in the abf2 mutant and that a mutation in TPPE abolished the ABA‐sensitive root elongation phenotype of 35S:ABF2 plants. Reactive oxygen species (ROS) accumulation in response to ABA failed to occur in tppe mutant plants, suggesting that TPPE is involved in ABA‐controlled root elongation and stomatal movement by inducing ROS accumulation. This study uncovers a new branch of the ABA signaling pathway and provides a molecular basis for the role of trehalose in plant responses to abiotic stress.

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COP9 signalosome: Discovery, conservation, activity, and function
Nanxun Qin, Dongqing Xu, Jigang Li and Xingwang Deng
J Integr Plant Biol 2020, 62 (1): 90-103.  
doi: 10.1111/jipb.12903
Abstract (Browse 337)  |   Save

The COP9 signalosome (CSN) is a conserved protein complex, typically composed of eight subunits (designated as CSN1 to CSN8) in higher eukaryotes such as plants and animals, but of fewer subunits in some lower eukaryotes such as yeasts. The CSN complex is originally identified in plants from a genetic screen for mutants that mimic light‐induced photomorphogenic development when grown in the dark. The CSN complex regulates the activity of cullin‐RING ligase (CRL) families of E3 ubiquitin ligase complexes, and play critical roles in regulating gene expression, cell proliferation, and cell cycle. This review aims to summarize the discovery, composition, structure, and function of CSN in the regulation of plant development in response to external (light and temperature) and internal cues (phytohormones).

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Plant plasma membrane‐resident receptors: Surveillance for infections and coordination for growth and development
Ana Marcia Escocard de Azevedo Manhães, Fausto Andres Ortiz‐Morea, Ping He and Libo Shan
J Integr Plant Biol 2021, 63 (1): 79-101.  
doi: 10.1111/jipb.13051
Abstract (Browse 268)  |   Save
As sessile organisms, plants are exposed to pathogen invasions and environmental fluctuations. To overcome the challenges of their surroundings, plants acquire the potential to sense endogenous and exogenous cues, resulting in their adaptability. Hence, plants have evolved a large collection of plasma membrane‐resident receptors, including RECEPTOR‐LIKE KINASEs (RLKs) and RECEPTOR‐LIKE PROTEINs (RLPs) to perceive those signals and regulate plant growth, development, and immunity. The ability of RLKs and RLPs to recognize distinct ligands relies on diverse categories of extracellular domains evolved. Co‐regulatory receptors are often required to associate with RLKs and RLPs to facilitate cellular signal transduction. RECEPTOR‐LIKE CYTOPLASMIC KINASEs (RLCKs) also associate with the complex, bifurcating the signal to key signaling hubs, such as MITOGEN‐ACTIVATED PROTEIN KINASE (MAPK) cascades, to regulate diverse biological processes. Here, we discuss recent knowledge advances in understanding the roles of RLKs and RLPs in plant growth, development, and immunity, and their connection with co‐regulatory receptors, leading to activation of diverse intracellular signaling pathways.
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Tissue‐specific Hi‐C analyses of rice, foxtail millet and maize suggest non‐canonical function of plant chromatin domains
Pengfei Dong, Xiaoyu Tu, Haoxuan Li, Jianhua Zhang, Donald Grierson, Pinghua Li and Silin Zhong
J Integr Plant Biol 2020, 62 (2): 201-217.  
DOI: 10.1111/jipb.12809
Abstract (Browse 491)  |   Save
Chromatins are not randomly packaged in the nucleus and their organization plays important roles in transcription regulation, which is best studied in the mammalian models. Using in situ Hi-C, we have compared the 3D chromatin architectures of rice mesophyll and endosperm, foxtail millet bundle sheath and mesophyll, and maize bundle sheath, mesophyll and endosperm tissues. We found that their global A/B compartment partitions are stable across tissues, while local A/B compartment has tissue-specific dynamic associated with differential gene expression. Plant domains are largely stable across tissues, while new domain border formations are often associated with transcriptional activation in the region. Genes inside plant domains are not conserved across species, and lack significant co-expression behavior unlike those in mammalian TADs. Although we only observed chromatin loops between gene islands in the large genomes, the maize loop gene pairs’ syntenic orthologs have shorter physical distances in small genome monocots, suggesting that loops instead of domains might have conserved biological function. Our study showed that plants’ chromatin features might not have conserved biological functions as the mammalian ones.
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Application and future perspective of CRISPR/Cas9 genome editing in fruit crops
Junhui Zhou, Dongdong Li, Guoming Wang, Fuxi Wang, Merixia Kunjal, Dirk Joldersma and Zhongchi Liu
J Integr Plant Biol 2020, 62 (3): 269-286.  
doi: 10.1111/jipb.12793
Abstract (Browse 349)  |   Save

Fruit crops, including apple, orange, grape, banana, strawberry, watermelon, kiwifruit and tomato, not only provide essential nutrients for human life but also contribute to the major agricultural output and economic growth of many countries and regions in the world. Recent advancements in genome editing provides an unprecedented opportunity for the genetic improvement of these agronomically important fruit crops. Here, we summarize recent reports of applying CRISPR/Cas9 to fruit crops, including efforts to reduce disease susceptibility, change plant architecture or flower morphology, improve fruit quality traits, and increase fruit yield. We discuss challenges facing fruit crops as well as new improvements and platforms that could be used to facilitate genome editing in fruit crops, including dCas9‐base‐editing to introduce desirable alleles and heat treatment to increase editing efficiency. In addition, we highlight what we see as potentially revolutionary development ranging from transgene‐free genome editing to de novo domestication of wild relatives. Without doubt, we now see only the beginning of what will eventually be possible with the use of the CRISPR/Cas9 toolkit. Efforts to communicate with the public and an emphasis on the manipulation of consumer‐friendly traits will be critical to facilitate public acceptance of genetically engineered fruits with this new technology.

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The involvement of wheat U‐box E3 ubiquitin ligase TaPUB1 in salt stress tolerance
Wenlong Wang, Wenqiang Wang, Yunzhen Wu, Qinxue Li, Guangqiang Zhang, Ruirui Shi, Junjiao Yang, Yong Wang and Wei Wang
J Integr Plant Biol 2020, 62 (5): 631-651.  
DOI: 10.1111/jipb.12842
Abstract (Browse 311)  |   Save

U‐box E3 ubiquitin ligases play important roles in the ubiquitin/26S proteasome machinery and in abiotic stress responses. TaPUB1‐overexpressing wheat (Triticum aestivum L.) were generated to evaluate its function in salt tolerance. These plants had more salt stress tolerance during seedling and flowering stages, whereas the TaPUB1‐RNA interference (RNAi)‐mediated knock‐down transgenic wheat showed more salt stress sensitivity than the wild type (WT). TaPUB1 overexpression upregulated the expression of genes related to ion channels and increased the net root Na+ efflux, but decreased the net K+ efflux and H+ influx, thereby maintaining a low cytosolic Na+/K+ ratio, compared with the WT. However, RNAi‐mediated knock‐down plants showed the opposite response to salt stress. TaPUB1 could induce the expression of some genes that improved the antioxidant capacity of plants under salt stress. TaPUB1 also interacted with TaMP (Triticum aestivum α‐mannosidase protein), a regulator playing an important role in salt response in yeast and in plants. Thus, low cytosolic Na+/K+ ratios and better antioxidant enzyme activities could be maintained in wheat with overexpression of TaPUB1 under salt stress. Therefore, we conclude that the U‐box E3 ubiquitin ligase TaPUB1 positively regulates salt stress tolerance in wheat.

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Genome editing for plant research and crop improvement
Xiangqiang Zhan, Yuming Lu, Jian-Kang Zhu and Jose Ramon Botella
J Integr Plant Biol 2021, 63 (1): 3-33.  
doi: 10.1111/jipb.13063
Abstract (Browse 635)  |   Save
The advent of clustered regularly interspaced short palindromic repeat (CRISPR) has had a profound impact on plant biology, and crop improvement. In this review, we summarize the state‐of‐the‐art development of CRISPR technologies and their applications in plants, from the initial introduction of random small indel (insertion or deletion) mutations at target genomic loci to precision editing such as base editing, prime editing and gene targeting. We describe advances in the use of class 2, types II, V, and VI systems for gene disruption as well as for precise sequence alterations, gene transcription, and epigenome control.
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Plant cell totipotency: Insights into cellular reprogramming
Ying Hua Su, Li Ping Tang, Xiang Yu Zhao and Xian Sheng Zhang
J Integr Plant Biol 2021, 63 (1): 228-243.  
doi: 10.1111/jipb.12972
Abstract (Browse 282)  |   Save
Plant cells have a powerful capacity in their propagation to adapt to environmental change, given that a single plant cell can give rise to a whole plant via somatic embryogenesis without the need for fertilization. The reprogramming of somatic cells into totipotent cells is a critical step in somatic embryogenesis. This process can be induced by stimuli such as plant hormones, transcriptional regulators and stress. Here, we review current knowledge on how the identity of totipotent cells is determined and the stimuli required for reprogramming of somatic cells into totipotent cells. We highlight key molecular regulators and associated networks that control cell fate transition from somatic to totipotent cells. Finally, we pose several outstanding questions that should be addressed to enhance our understanding of the mechanisms underlying plant cell totipotency.
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A rare Waxy allele coordinately improves rice eating and cooking quality and grain transparency
Changquan Zhang, Yong Yang, Shengjie Chen, Xueju Liu, Jihui Zhu, Lihui Zhou, Yan Lu, Qianfeng Li, Xiaolei Fan, Shuzhu Tang, Minghong Gu and Qiaoquan Liu
J Integr Plant Biol 2021, 63 (5): 889-901.  
doi: 10.1111/jipb.13010
Abstract (Browse 392)  |   Save
In rice (Oryza sativa), amylose content (AC) is the major factor that determines eating and cooking quality (ECQ). The diversity in AC is largely attributed to natural allelic variation at the Waxy (Wx) locus. Here we identified a rare Wx allele, Wxmw, which combines a favorable AC, improved ECQ and grain transparency. Based on a phylogenetic analysis of Wx genomic sequences from 370 rice accessions, we speculated that Wxmw may have derived from recombination between two important natural Wx alleles, Wxin and Wxb. We validated the effects of Wxmw on rice grain quality using both transgenic lines and near‐isogenic lines (NILs). When introgressed into the japonica Nipponbare (NIP) background, Wxmw resulted in a moderate AC that was intermediate between that of NILs carrying the Wxb allele and NILs with the Wxmp allele. Notably, mature grains of NILs fixed for Wxmw had an improved transparent endosperm relative to soft rice. Further, we introduced Wxmw into a high‐yielding japonica cultivar via molecular marker‐assisted selection: the introgressed lines exhibited clear improvements in ECQ and endosperm transparency. Our results suggest that Wxmw is a promising allele to improve grain quality, especially ECQ and grain transparency of high‐yielding japonica cultivars, in rice breeding programs.
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The calcium‐dependent protein kinase ZmCDPK7 functions in heat‐stress tolerance in maize
Yulong Zhao, Hanwei Du, Yankai Wang, Huali Wang, Shaoyu Yang, Chaohai Li, Ning Chen, Hao Yang, Yihao Zhang, Yulin Zhu, Luyao Yang and Xiuli Hu
J Integr Plant Biol 2021, 63 (3): 510-527.  
doi: 10.1111/jipb.13056
Abstract (Browse 440)  |   Save
Global warming poses a serious threat to crops. Calcium‐dependent protein kinases (CDPKs)/CPKs play vital roles in plant stress responses, but their exact roles in plant thermotolerance remains elusive. Here, we explored the roles of heat‐induced ZmCDPK7 in thermotolerance in maize. ZmCDPK7‐overexpressing maize plants displayed higher thermotolerance, photosynthetic rates, and antioxidant enzyme activity but lower H2O2 and malondialdehyde (MDA) contents than wild‐type plants under heat stress. ZmCDPK7‐knockdown plants displayed the opposite patterns. ZmCDPK7 is attached to the plasma membrane but can translocate to the cytosol under heat stress. ZmCDPK7 interacts with the small heat shock protein sHSP17.4, phosphorylates sHSP17.4 at Ser‐44 and the respiratory burst oxidase homolog RBOHB at Ser‐99, and upregulates their expression. Site‐directed mutagenesis of sHSP17.4 to generate a Ser‐44‐Ala substitution reduced ZmCDPK7's enhancement of catalase activity but enhanced ZmCDPK7's suppression of MDA accumulation in heat‐stressed maize protoplasts. sHSP17.4, ZmCDPK7, and RBOHB were less strongly upregulated in response to heat stress in the abscisic acid‐deficient mutant vp5 versus the wild type. Pretreatment with an RBOH inhibitor suppressed sHSP17.4 and ZmCDPK7 expression. Therefore, abscisic acid‐induced ZmCDPK7 functions both upstream and downstream of RBOH and participates in thermotolerance in maize by mediating the phosphorylation of sHSP17.4, which might be essential for its chaperone function.
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Arabidopsis E3 ligase KEG associates with and ubiquitinates MKK4 and MKK5 to regulate plant immunity
Chenyang Gao, Pengwei Sun, Wei Wang and Dingzhong Tang
J Integr Plant Biol 2021, 63 (2): 327-339.  
doi: 10.1111/jipb.13007
Abstract (Browse 573)  |   Save
Mitogen‐activated protein kinase (MAPK) cascades are highly conserved signaling modules that regulate plant immune responses. The Arabidopsis thaliana Raf‐like MAPK kinase kinase ENHANCED DISEASE RESISTANCE1 (EDR1) is a key negative regulator of plant immunity that affects the protein levels of MKK4 and MKK5, two important MAPK cascade members, but the underlying mechanism is poorly understood. Here, genome‐wide phosphorylation analysis demonstrated that the E3 ligase KEEP ON GOING (KEG) is phosphorylated in the edr1 mutant but not the wild type, suggesting that EDR1 negatively affects KEG phosphorylation. The identified phosphorylation sites in KEG appear to be important for its accumulation. The keg‐4 mutant, a previously identified edr1 suppressor, enhances susceptibility to the powdery mildew pathogen Golovinomyces cichoracearum. In addition, MKK4 and MKK5 protein levels are reduced in the keg‐4 mutant. Furthermore, we demonstrate that MKK4 and MKK5 associate with full‐length KEG, but not with truncated KEG‐RK or KEG‐RKA, and that KEG ubiquitinates and mediates the degradation of MKK4 and MKK5. Taken together, these results indicate that MKK4 and MKK5 protein levels are regulated by KEG via ubiquitination, uncovering a mechanism by which plants fine‐tune immune responses by regulating the homeostasis of key MAPK cascade members via ubiquitination and degradation.
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The origin of Wxla provides new insights into the improvement of grain quality in rice
Hao Zhou, Duo Xia, Da Zhao, Yanhua Li, Pingbo Li, Bian Wu, Guanjun Gao, Qinglu Zhang, Gongwei Wang, Jinghua Xiao, Xianghua Li, Sibin Yu, Xingming Lian and Yuqing He
J Integr Plant Biol 2021, 63 (5): 878-888.  
doi: 10.1111/jipb.13011
Abstract (Browse 345)  |   Save
Appearance and taste are important factors in rice (Oryza sativa) grain quality. Here, we investigated the taste scores and related eating‐quality traits of 533 diverse cultivars to assess the relationships between—and genetic basis of—rice taste and eating‐quality. A genome‐wide association study highlighted the Wx gene as the major factor underlying variation in taste and eating quality. Notably, a novel waxy (Wx) allele, Wxla, which combined two mutations from Wxb and Wxin, exhibited a unique phenotype. Reduced GBSSI activity conferred Wxla rice with both a transparent appearance and good eating quality. Haplotype analysis revealed that Wxla was derived from intragenic recombination. In fact, the recombination rate at the Wx locus was estimated to be 3.34 kb/cM, which was about 75‐fold higher than the genome‐wide mean, indicating that intragenic recombination is a major force driving diversity at the Wx locus. Based on our results, we propose a new network for Wx evolution, noting that new Wx alleles could easily be generated by crossing genotypes with different Wx alleles. This study thus provides insights into the evolution of the Wx locus and facilitates molecular breeding for quality in rice.
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Integrated metabolo‐transcriptomics and functional characterization reveals that the wheat auxin receptor TIR1 negatively regulates defense against Fusarium graminearum
Peisen Su, Lanfei Zhao, Wen Li, Jinxiao Zhao, Jun Yan, Xin Ma, Anfei Li, Hongwei Wang and Lingrang Kong
J Integr Plant Biol 2021, 63 (2): 340-352.  
doi: 10.1111/jipb.12992
Abstract (Browse 373)  |   Save
Fusarium head blight (FHB) caused by Fusarium graminearum Schwabe (teleomorph Gibberella zeae (Schw.) Perch) results in large yield losses in annual global wheat production. Although studies have identified a number of wheat FHB resistance genes, a deeper understanding of the mechanisms underlying host plant resistance to F. graminearum is required for the control of FHB. Here, an integrated metabolomics and transcriptomics analysis of infected wheat plants (Triticum aestivum L.) enabled identification of 789 differentially accumulated metabolites, including flavonoids, phenolamides, tryptamine derivatives, and phytohormones, and revealed altered expression of more than 100 genes that function in the biosynthesis or regulation of these pathways. Our data regarding the effects of F. graminearum infection on flavonoids and auxin signaling led to follow‐up experiments that showed that exogenous kaempferide and apigenin application on spikes increased wheat resistance to FHB, while exogenous auxin treatment increased FHB susceptibility. RNAi‐mediated knockdown of the gene encoding the auxin receptor, TaTIR1, increased FHB resistance. Our data supported the use of TaTIR1 knockdown in controlling FHB. Our study provides insights on the wheat response to F. graminearum infection and its FHB resistance mechanisms while illustrating the potential of TaTIR1 knockdown in increasing FHB resistance during crop improvement programs.
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Hydrogen sulfide: A novel component in Arabidopsis peroxisomes which triggers catalase inhibition
Francisco J. Corpas, Juan B. Barroso, Salvador González-Gordo, María A. Muñoz-Vargas and José M. Palma
J Integr Plant Biol 2019, 61 (7): 871-883.  
doi: 10.1111/jipb.12779
Abstract (Browse 302)  |   Save
Plant peroxisomes have the capacity to generate different reactive oxygen and nitrogen species (ROS and RNS), such as H2O2, superoxide radical (O2· ), nitric oxide and peroxynitrite (ONOO). These organelles have an active nitro-oxidative metabolism which can be exacerbated by adverse stress conditions. Hydrogen sulfide (H2S) is a new signaling gasotransmitter which can mediate the posttranslational modification (PTM) persulfidation. We used Arabidopsis thaliana transgenic seedlings expressing cyan fluorescent protein (CFP) fused to a canonical peroxisome targeting signal 1 (PTS1) to visualize peroxisomes in living cells, as well as a specific fluorescent probe which showed that peroxisomes contain H2S. H2S was also detected in chloroplasts under glyphosate-induced oxidative stress conditions. Peroxisomal enzyme activities, including catalase, photorespiratory H2O2-generating glycolate oxidase (GOX) and hydroxypyruvate reductase (HPR), were assayed in vitro with a H2S donor. In line with the persulfidation of this enzyme, catalase activity declined significantly in the presence of the H2S donor. To corroborate the inhibitory effect of H2S on catalase activity, we also assayed pure catalase from bovine liver and pepper fruit-enriched samples, in which catalase activity was inhibited. Taken together, these data provide evidence of the presence of H2S in plant peroxisomes which appears to regulate catalase activity and, consequently, the peroxisomal H2O2 metabolism.
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Plant peroxisomes at the crossroad of NO and H2O2 metabolism
Francisco J Corpas, Luis A. del Río and José M Palma
J Integr Plant Biol 2019, 61 (7): 803-816.  
doi: 10.1111/jipb.12772
Abstract (Browse 249)  |   Save
Plant peroxisomes are subcellular compartments involved in many biochemical pathways during the life cycle of a plant but also in the mechanism of response against adverse environmental conditions. These organelles have an active nitro-oxidative metabolism under physiological conditions but this could be exacerbated under stress situations. Furthermore, peroxisomes have the capacity to proliferate and also undergo biochemical adaptations depending on the surrounding cellular status. An important characteristic of peroxisomes is that they have a dynamic metabolism of reactive nitrogen and oxygen species (RNS and ROS) which generates two key molecules, nitric oxide (NO) and hydrogen peroxide (H2O2). These molecules can exert signaling functions by means of post-translational modifications that affect the functionality of target molecules like proteins, peptides or fatty acids. This review provides an overview of the endogenous metabolism of ROS and RNS in peroxisomes with special emphasis on polyamine and uric acid metabolism as well as the possibility that these organelles could be a source of signal molecules involved in the functional interconnection with other subcellular compartments.
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Seed germination and dormancy: The classic story, new puzzles, and evolution
Hiroyuki Nonogaki
J Integr Plant Biol 2019, 61 (5): 541-563.  
doi: 10.1111/jipb.12762
Abstract (Browse 342)  |   Save
This review highlights recent progresses in seed germination and dormancy research. Research on the weakening of the endosperm during germination, which is almost a classic theme in seed biology, was resumed by α-xylosidase studies. Strong genetic evidence was presented to suggest that the quality control of xyloglucan biosynthesis in the endosperm (and the embryo) plays a critical role in germination. Further analyses on the endosperm and the adjacent layers have suggested that the cutin coat in the endosperm-testa interphase negatively affects germination while the endosperm-embryo interphase produces a sheath that facilitates germination. These progresses significantly advanced our understanding of seed germination mechanisms. A breakthrough in dormancy research, on the other hand, revealed the unique abscisic acid signaling pathway that is regulated by DELAY OF GERMINATION1 (DOG1). The detailed analysis of DOG1 expression uncovered the intriguing story of reciprocal regulation of the sense-antisense pair, which generated new questions. Recent studies also suggested that the DOG1 function is not limited to dormancy but extended through general seed maturation, which provokes questions about the evolution of DOG1 family proteins. Seed biology is becoming more exciting with the classic stories being revitalized and new puzzles emerging from the frontier.
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A methylated-DNA-binding complex required for plant development mediates transcriptional activation of promoter methylated genes
Qiang-Qiang Zhao, Rong-Nan Lin, Lin Li, She Chen and Xin-Jian He
J Integr Plant Biol 2019, 61 (2): 120-139.  
doi: 10.1111/jipb.12767
Abstract (Browse 686)  |   Save
Although the mechanism of DNA methylation-mediated gene silencing is extensively studied, relatively little is known about how promoter methylated genes are protected from transcriptional silencing. SUVH1, an Arabidopsis Su(var)3‐9 homolog, was previously shown to be required for the expression of a few promoter methylated genes. By chromatin immunoprecipitation combined with sequencing, we demonstrate that SUVH1 binds to methylated genomic loci targeted by RNA-directed DNA methylation. SUVH1 and its homolog SUVH3 function partially redundantly and interact with three DNAJ domain-containing homologs, SDJ1, SDJ2, and SDJ3, thus forming a complex which we named SUVH-SDJ. The SUVH-SDJ complex components are co-localized in a large number of methylated promoters and are required for the expression of a subset of promoter methylated genes. We demonstrate that the SUVH-SDJ complex components have transcriptional activation activity. SUVH1 and SUVH3 function synergistically with SDJ1, SDJ2, and SDJ3 and are required for plant viability. This study reveals how the SUVH-SDJ complex protects promoter methylated genes from transcriptional silencing and suggests that the transcriptional activation of promoter methylated genes mediated by the SUVH-SDJ complex may play a critical role in plant growth and development.
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A reductionist approach to dissecting grain weight and yield in wheat
Jemima Brinton and Cristobal Uauy
J Integr Plant Biol 2019, 61 (3): 337-358.  
doi: 10.1111/jipb.12741
Abstract (Browse 347)  |   Save
Grain yield is a highly polygenic trait that is influenced by the environment and integrates events throughout the life cycle of a plant. In wheat, the major grain yield components often present compensatory effects among them, which alongside the polyploid nature of wheat, makes their genetic and physiological study challenging. We propose a reductionist and systematic approach as an initial step to understand the gene networks regulating each individual yield component. Here, we focus on grain weight and discuss the importance of examining individual sub-components, not only to help in their genetic dissection, but also to inform our mechanistic understanding of how they interrelate. This knowledge should allow the development of novel combinations, across homoeologs and between complementary modes of action, thereby advancing towards a more integrated strategy for yield improvement. We argue that this will break barriers in terms of phenotypic variation, enhance our understanding of the physiology of yield, and potentially deliver improved on-farm yield.
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Developmental pathways for shaping spike inflorescence architecture in barley and wheat
Ravi Koppolu and Thorsten Schnurbusch
J Integr Plant Biol 2019, 61 (3): 278-295.  
doi: 10.1111/jipb.12771
Abstract (Browse 288)  |   Save
Grass species display a wide array of inflorescences ranging from highly branched compound/panicle inflorescences to unbranched spike inflorescences. The unbranched spike is a characteristic feature of the species of tribe Triticeae, including economically important crops, such as wheat and barley. In this review, we describe two important developmental genetic mechanisms regulating spike inflorescence architecture in barley and wheat. These include genetic regulation of (i) row-type pathway specific to Hordeum species and (ii) unbranched spike development in barley and wheat. For a comparative understanding, we describe the branched inflorescence phenotypes of rice and maize along with unbranched Triticeae inflorescences. In the end, we propose a simplified model describing a probable mechanism leading to unbranched spike formation in Triticeae species.
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A group of SUVH methyl-DNA binding proteins regulate expression of the DNA demethylase ROS1 in Arabidopsis
Xinlong Xiao, Jieqiong Zhang, Tao Li, Xing Fu, Viswanathan Satheesh, Qingfeng Niu, Zhaobo Lang, Jian-Kang Zhu and Mingguang Lei
J Integr Plant Biol 2019, 61 (2): 110-119.  
doi: 10.1111/jipb.12768
Abstract (Browse 431)  |   Save
DNA methylation is typically regarded as a repressive epigenetic marker for gene expression. Genome-wide DNA methylation patterns in plants are dynamically regulated by the opposing activities of DNA methylation and demethylation reactions. In Arabidopsis, a DNA methylation monitoring sequence (MEMS) in the promoter of the DNA demethylase gene ROS1 functions as a methylstat that senses these opposing activities and regulates genome DNA methylation levels by adjusting ROS1 expression. How DNA methylation in the MEMS region promotes ROS1 expression is not known. Here, we show that several Su(var)3‐9 homologs (SUVHs) can sense DNA methylation levels at the MEMS region and function redundantly to promote ROS1 expression. The SUVHs bind to the MEMS region, and the extent of binding is correlated with the methylation level of the MEMS. Mutations in the SUVHs lead to decreased ROS1 expression, causing DNA hypermethylation at more than 1,000 genomic regions. Thus, the SUVHs function to mediate the activation of gene transcription by DNA methylation.
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Translating auxin responses into ovules, seeds and yield: Insight from Arabidopsis and the cereals
Neil J Shirley, Matthew K. Aubert, Laura G. Wilkinson, Dayton C. Bird, Jorge Lora, Xiujuan Yang and Matthew R. Tucker
J Integr Plant Biol 2019, 61 (3): 310-336.  
doi: 10.1111/jipb.12747
Abstract (Browse 156)  |   Save
Grain production in cereal crops depends on the stable formation of male and female gametes in the flower. In most angiosperms, the female gamete is produced from a germline located deep within the ovary, protected by several layers of maternal tissue, including the ovary wall, ovule integuments and nucellus. In the field, germline formation and floret fertility are major determinants of yield potential, contributing to traits such as seed number, weight and size. As such, stimuli affecting the timing and duration of reproductive phases, as well as the viability, size and number of cells within reproductive organs can significantly impact yield. One key stimulant is the phytohormone auxin, which influences growth and morphogenesis of female tissues during gynoecium development, gametophyte formation, and endosperm cellularization. In this review we consider the role of the auxin signaling pathway during ovule and seed development, first in the context of Arabidopsis and then in the cereals. We summarize the gene families involved and highlight distinct expression patterns that suggest a range of roles in reproductive cell specification and fate. This is discussed in terms of seed production and how targeted modification of different tissues might facilitate improvements.
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ZmOST1 mediates abscisic acid regulation of guard cell ion channels and drought stress responses
Qiqi Wu, Mei Wang, Jianlin Shen, Donghua Chen, Yu Zheng and Wei Zhang
J Integr Plant Biol 2019, 61 (4): 478-491.  
DOI: 10.1111/jipb.12714
Abstract (Browse 243)  |   Save

The phytohormone abscisic acid (ABA) is an important mediator in the drought response, participating in, among other processes, stomatal movements. In Arabidopsis thaliana, the serine/threonine protein kinase, OST1, regulates this response, but the function of its maize homolog has yet to be established. Here, we isolated ZmOST1 and show that its encoded protein indeed acts to regulate guard cell movement. ZmOST1 was ubiquitously expressed throughout the plant, being highly expressed in guard cells, and inducible both by exogenous ABA and water stress. Transient expression of a ZmOST1-GFP fusion protein, in maize mesophyll protoplasts, indicated its subcellular localization in the cytoplasm and nucleus. A Zmost1 loss-of-function mutant exhibited reduced sensitivity to ABA-activated slow anion channels in maize guard cells, and reduced drought tolerance. Constitutive expression of ZmOST1, in an A. thaliana ost1-1 mutant rescued the phenotype with respect both to the sensitivity of guard cell slow anion currents to ABA treatment and stomatal closure. Our findings indicate a positive regulatory role for ZmOST1 in guard cell ABA signaling and drought response in maize plants.

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Protein S-Nitrosylation in plants: Current progresses and challenges
Jian Feng, Lichao Chen and Jianru Zuo
J Integr Plant Biol 2019, 61 (12): 1206-1223.  
doi: 10.1111/jipb.12780
Abstract (Browse 225)  |   Save
Nitric oxide (NO) is an important signaling molecule regulating diverse biological processes in all living organisms. A major physiological function of NO is executed via protein S‐nitrosylation, a redox‐based posttranslational modification by covalently adding a NO molecule to a reactive cysteine thiol of a target protein. S‐nitrosylation is an evolutionarily conserved mechanism modulating multiple aspects of cellular signaling. During the past decade, significant progress has been made in functional characterization of S‐nitrosylated proteins in plants. Emerging evidence indicates that protein S‐nitrosylation is ubiquitously involved in the regulation of plant development and stress responses. Here we review current understanding on the regulatory mechanisms of protein S‐nitrosylation in various biological processes in plants and highlight key challenges in this field.
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CLE25 peptide regulates phloem initiation in Arabidopsis through a CLERK-CLV2 receptor complex
Shi-Chao Ren, Xiu-Fen Song, Wen-Qiang Chen, Ran Lu, William J. Lucas and Chun-Ming Liu
J Integr Plant Biol 2019, 61 (10): 1043-1061.  
doi: 10.1111/jipb.12846
Abstract (Browse 674)  |   Save
The phloem, located within the vascular system, is critical for delivery of nutrients and signaling molecules throughout the plant body. Although the morphological process and several factors regulating phloem differentiation have been reported, the molecular mechanism underlying its initiation remains largely unknown. Here, we report that the small peptide‐coding gene, CLAVATA 3 (CLV3)/EMBEYO SURROUNDING REGION 25 (CLE25), the expression of which begins in provascular initial cells of 64‐cell‐staged embryos, and continues in sieve element‐procambium stem cells and phloem lineage cells, during post‐embryonic root development, facilitates phloem initiation in Arabidopsis. Knockout of CLE25 led to delayed protophloem formation, and in situ expression of an antagonistic CLE25G6T peptide compromised the fate‐determining periclinal division of the sieve element precursor cell and the continuity of the phloem in roots. In stems of CLE25G6T plants the phloem formation was also compromised, and procambial cells were over‐accumulated. Genetic and biochemical analyses indicated that a complex, consisting of the CLE‐RESISTANT RECEPTOR KINASE (CLERK) leucine‐rich repeat (LRR) receptor kinase and the CLV2 LRR receptor‐like protein, is involved in perceiving the CLE25 peptide. Similar to CLE25, CLERK was also expressed during early embryogenesis. Taken together, our findings suggest that CLE25 regulates phloem initiation in Arabidopsis through a CLERK‐CLV2 receptor complex.
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Central role of the LEAFY COTYLEDON1 transcription factor in seed development
Leonardo Jo, Julie M. Pelletier and John J. Harada
J Integr Plant Biol 2019, 61 (5): 564-580.  
doi: 10.1111/jipb.12806
Abstract (Browse 287)  |   Save
Seed development is a complex period of the flowering plant life cycle. After fertilization, the three main regions of the seed, embryo, endosperm and seed coat, undergo a series of developmental processes that result in the production of a mature seed that is developmentally arrested, desiccated, and metabolically quiescent. These processes are highly coordinated, both temporally and spatially, to ensure the proper growth and development of the seed. The transcription factor, LEAFY COTYLEDON1 (LEC1), is a central regulator that controls several aspects of embryo and endosperm development, including embryo morphogenesis, photosynthesis, and storage reserve accumulation. Thus, LEC1 regulates distinct sets of genes at different stages of seed development. Despite its critical importance for seed development, an understanding of the mechanisms underlying LEC1's multifunctionality is only beginning to be obtained. Recent studies describe the roles of specific transcription factors and the hormones, gibberellic acid and abscisic acid, in controlling the activity and transcriptional specificity of LEC1 across seed development. Moreover, studies indicate that LEC1 acts as a pioneer transcription factor to promote epigenetic reprogramming during embryogenesis. In this review, we discuss the mechanisms that enable LEC1 to serve as a central regulator of seed development.
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Alleviation by abscisic acid of Al toxicity in rice bean is not associated with citrate efflux but depends on ABI5-mediated signal transduction pathways
Wei Fan, Jia Meng Xu, Pei Wu, Zhi Xin Yang, He Qiang Lou, Wei Wei Chen, Jian Fen Jin, Shao Jian Zheng and Jian Li Yang
J Integr Plant Biol 2019, 61 (2): 140-154.  
DOI: 10.1111/jipb.12695
Abstract (Browse 244)  |   Save
Under conditions of aluminum (Al) toxicity, which severely inhibits root growth in acidic soils, plants rapidly alter their gene expression to optimize physiological fitness for survival. Abscisic acid (ABA) has been suggested as a mediator between Al stress and gene expression, but the underlying mechanisms remain largely unknown. Here, we investigated ABA-mediated Al-stress responses, using integrated physiological and molecular biology approaches. We demonstrate that Al stress caused ABA accumulation in the root apex of rice bean (Vigna umbellata [Thunb.] Ohwi & Ohashi), which positively regulated Al tolerance. However, this was not associated with known Al-tolerance mechanisms. Transcriptomic analysis revealed that nearly one-third of the responsive genes were shared between the Al-stress and ABA treatments. We further identified a transcription factor, ABI5, as being positively involved in Al tolerance. Arabidopsis abi5 mutants displayed increased sensitivity to Al, which was not related to the regulation of AtALMT1 and AtMATE expression. Functional categorization of ABI5-mediated genes revealed the importance of cell wall modification and osmoregulation in Al tolerance, a finding supported by osmotic stress treatment on Al tolerance. Our results suggest that ABA signal transduction pathways provide an additional layer of regulatory control over Al tolerance in plants.
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Big Grain3, encoding a purine permease, regulates grain size via modulating cytokinin transport in rice
Yunhua Xiao, Dapu Liu, Guoxia Zhang, Shaopei Gao, Linchuan Liu, Fan Xu, Ronghui Che, Yiqin Wang, Hongning Tong and Chengcai Chu
J Integr Plant Biol 2019, 61 (5): 581-597.  
doi: 10.1111/jipb.12727
Abstract (Browse 312)  |   Save
Grain size is an important agronomic trait affecting grain yield, but the underlying molecular mechanisms remain to be elucidated. Here, we isolated a dominant mutant, big grain3 (bg3-D), which exhibits a remarkable increase of grain size caused by activation of the PURINE PERMEASE gene, OsPUP4. BG3/OsPUP4 is predominantly expressed in vascular tissues and is specifically suppressed by exogenous cytokinin application. Hormone profiling revealed that the distribution of different cytokinin forms, in roots and shoots of the bg3-D mutant, is altered. Quantitative reverse transcription-PCR (qRT-PCR) analysis indicated that expression of rice cytokinin type-A RESPONSE REGULATOR (OsRR) genes is enhanced in the roots of the bg3-D mutant. These results suggest that OsPUP4 might contribute to the long-distance transport of cytokinin, by reinforcing cytokinin loading into vascular bundle cells. Furthermore, plants overexpressing OsPUP7, the closest homolog of OsPUP4, also exhibited a similar phenotype to the bg3-D mutant. Interestingly, subcellular localization demonstrated that OsPUP4 was localized on the plasma membrane, whereas OsPUP7 was localized to the endoplasmic reticulum. Based on these findings, we propose that OsPUP4 and OsPUP7 function in a linear pathway to direct cytokinin cell-to-cell transport, affecting both its long-distance movement and local allocation.
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Genetic pathways controlling inflorescence architecture and development in wheat and barley
Adam Gauley and Scott A. Boden
J Integr Plant Biol 2019, 61 (3): 296-309.  
doi: 10.1111/jipb.12732
Abstract (Browse 234)  |   Save
Modifications of inflorescence architecture have been crucial for the successful domestication of wheat and barley, which are central members of the Triticeae tribe that provide essential grains for the human diet. Investigation of the genes and alleles that underpin domestication-related traits has provided valuable insights into the molecular regulation of inflorescence development of the Triticeae, and further investigation of modified forms of architecture are proving to be equally fruitful. The identified genes are involved in diverse biological processes, including transcriptional regulation, hormone biosynthesis and metabolism, post-transcriptional and post-translational regulation, which alter inflorescence architecture by modifying the development and fertility of lateral organs, called spikelets and florets. Recent advances in sequencing capabilities and the generation of mutant populations are accelerating the identification of genes that influence inflorescence development, which is important given that genetic variation for this trait promises to be a valuable resource for optimizing grain production. This review assesses recent advances in our understanding of the genes controlling inflorescence development in wheat and barley, with the aim of highlighting the importance of improvements in developmental biology for optimizing the agronomic performance of staple crop plants.
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Plant lncRNAs are enriched in and move systemically through the phloem in response to phosphate deficiency
Zhaoliang Zhang, Yi Zheng, Byung-Kook Ham, Shupei Zhang, Zhangjun Fei and William J. Lucas
J Integr Plant Biol 2019, 61 (4): 492-508.  
DOI: 10.1111/jipb.12715
Abstract (Browse 213)  |   Save

In response to phosphate (Pi) deficiency, it has been shown that micro-RNAs (miRNAs) and mRNAs are transported through the phloem for delivery to sink tissues. Growing evidence also indicates that long non-coding RNAs (lncRNAs) are critical regulators of Pi homeostasis in plants. However, whether lncRNAs are present in and move through the phloem, in response to Pi deficiency, remains to be established. Here, using cucumber as a model plant, we show that lncRNAs are enriched in the phloem translocation stream and respond, systemically, to an imposed Pi-stress. A well-known lncRNA, IPS1, the target mimic (TM) of miRNA399, accumulates to a high level in the phloem, but is not responsive to early Pi deficiency. An additional 24 miRNA TMs were also detected in the phloem translocation stream; among them miRNA171 TMs and miR166 TMs were induced in response to an imposed Pi stress. Grafting studies identified 22 lncRNAs which move systemically into developing leaves and root tips. A CU-rich PTB motif was further identified in these mobile lncRNAs. Our findings revealed that lncRNAs respond to Pi deficiency, non-cell-autonomously, and may act as systemic signaling agents to coordinate early Pi deficiency signaling, at the whole-plant level.

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Rhizosheath formation and involvement in foxtail millet (Setaria italica) root growth under drought stress
Tie-Yuan Liu, Nenghui Ye, Tao Song, Yunying Cao, Bei Gao, Di Zhang, Fuyuan Zhu, Moxian Chen, Yingjiao Zhang, Weifeng Xu and Jianhua Zhang
J Integr Plant Biol 2019, 61 (4): 449-462.  
DOI: 10.1111/jipb.12716
Abstract (Browse 233)  |   Save
The rhizosheath, a layer of soil particles that adheres firmly to the root surface by a combination of root hairs and mucilage, may improve tolerance to drought stress. Setaria italica (L.) P. Beauv. (foxtail millet), a member of the Poaceae family, is an important food and fodder crop in arid regions and forms a larger rhizosheath under drought conditions. Rhizosheath formation under drought conditions has been studied, but the regulation of root hair growth and rhizosheath size in response to soil moisture remains unclear. To address this question, in this study we monitored root hair growth and rhizosheath development in response to a gradual decline in soil moisture. Here, we determined that a soil moisture level of 10%–14% (w/w) stimulated greater rhizosheath production compared to other soil moisture levels. Root hair density and length also increased at this soil moisture level, which was validated by measurement of the expression of root hair-related genes. These findings contribute to our understanding of rhizosheath formation in response to soil water stress.
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A strategy for generating rice apomixis by gene editing
En Xie, Yafei Li, Ding Tang, Yanli Lv, Yi Shen and Zhukuan Cheng
J Integr Plant Biol 2019, 61 (8): 911-916.  
doi: 10.1111/jipb.12785
Abstract (Browse 422)  |   Save

Apomixis is an asexual reproduction way of plants that can produce clonal offspring through seeds. In this study, we introduced apomixis into rice (Oryza sativa) by mutating OsSPO11‐1, OsREC8, OsOSD1, and OsMATL through a CRISPR/Cas9 system. The quadruple mutant showed a transformation from meiosis to mitosis and produced clonal diploid gametes. With mutated Osmatl, which gives rise to haploid induction in plants, the quadruple mutant is expected to be able to be produced apomictic diploid offspring. We named this quadruple mutant as AOP (Apomictic Offspring Producer) for its ability to produce apomictic offspring.

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Critical function of DNA methyltransferase 1 in tomato development and regulation of the DNA methylome and transcriptome
Yu Yang, Kai Tang, Tatsiana U Datsenka, Wenshan Liu, Suhui Lv, Zhaobo Lang, Xingang Wang, Jinghui Gao, Wei Wang, Wenfeng Nie, Zhaoqing Chu, Heng Zhang, Avtar K Handa, Jian-Kang Zhu and Huiming Zhang
J Integr Plant Biol 2019, 61 (12): 1224-1242.  
DOI: 10.1111/jipb.12778
Abstract (Browse 222)  |   Save
DNA methylation confers epigenetic regulation on gene expression and thereby on various biological processes. Tomato has emerged as an excellent system to study the function of DNA methylation in plant development. To date, regulation and function of DNA methylation maintenance remains unclear in tomato plants. Here, we report the critical function of tomato (Solanum lycopersicum) Methyltransferase 1 (SlMET1) in plant development and DNA methylome and transcriptome regulation. Using CRISPR‐Cas9 gene editing, we generated slmet1 mutants and observed severe developmental defects with a frame‐shift mutation, including small and curly leaves, defective inflorescence, and parthenocarpy. In leaf tissues, mutations in SlMET1 caused CG hypomethylation and CHH hypermethylation on a whole‐genome scale, leading to a disturbed transcriptome including ectopic expression of many RIN target genes such as ACC2 in leaf tissues, which are normally expressed in fruits. Neither the CG hypomethylation nor CHH hypermethylation in the slmet1 mutants is related to tissue culture. Meanwhile, tissue culture induces non‐CG hypomethylation, which occurs more frequently at gene regions than at TE regions. Our results depict SlMET1‐ and tissue culture‐dependent tomato DNA methylomes, and that SlMET1 is required for maintaining a normal transcriptome and normal development of tomato.
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A common metabolomic signature is observed upon inoculation of rice roots with various rhizobacteria
Marine Valette, Marjolaine Rey, Florence Gerin, Gilles Comte and Florence WisniewskiDyé
J Integr Plant Biol 2020, 62 (2): 228-246.  
DOI: 10.1111/jipb.12810
Abstract (Browse 153)  |   Save
Plant growth‐promoting rhizobacteria (PGPR), whose growth is stimulated by root exudates, are able to improve plant growth and health. Among those, bacteria of the genus Azospirillum were shown to affect root secondary metabolite content in rice and maize, sometimes without visible effects on root architecture. Transcriptomic studies also revealed that expression of several genes involved in stress and plant defense was affected, albeit with fewer genes when a strain was inoculated onto its original host cultivar. Here, we investigated, via a metabolic profiling approach, whether rice roots responded differently and with gradual intensity to various PGPR, isolated from rice or not. A common metabolomic signature of nine compounds was highlighted, with the reduced accumulation of three alkylresorcinols and increased accumulation of two hydroxycinnamic acid amides (HCAA), identified as Np‐coumaroylputrescine and N‐feruloylputrescine. This was accompanied by the increased transcription of two genes involved in the N‐feruloylputrescine biosynthetic pathway. Interestingly, exposure to a rice bacterial pathogen triggered a reduced accumulation of these HCAA in roots, a result contrasting with previous reports of increased HCAA content in leaves upon pathogen infection. Accumulation of HCAA, that are potential antimicrobial compounds, might be considered as a primary reaction of plant to bacterial perception.
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The interaction of CaM7 and CNGC14 regulates root hair growth in Arabidopsis
Qudsia Zeb, Xiaohan Wang, Congcong Hou, Xiwen Zhang, Mengqi Dong, Sisi Zhang, Qian Zhang, Zhijie Ren, Wang Tian, Huifen Zhu, Legong Li and Liangyu Liu
J Integr Plant Biol 2020, 62 (7): 887-896.  
DOI: 10.1111/jipb.12890
Abstract (Browse 417)  |   Save

Oscillations in cytosolic free calcium determine the polarity of tip‐growing root hairs. The Ca2+ channel cyclic nucleotide gated channel 14 (CNGC14) contributes to the dynamic changes in Ca2+ concentration gradient at the root hair tip. However, the mechanisms that regulate CNGC14 are unknown. In this study, we detected a direct interaction between calmodulin 7 (CaM7) and CNGC14 through yeast two‐hybrid and bimolecular fluorescence complementation assays. We demonstrated that the third EF‐hand domain of CaM7 specifically interacts with the cytosolic C‐terminal domain of CNGC14. A two‐electrode voltage clamp assay showed that CaM7 completely inhibits CNGC14‐mediated Ca2+ influx, suggesting that CaM7 negatively regulates CNGC14‐mediated calcium signaling. Furthermore, CaM7 overexpressing lines phenocopy the short root hair phenotype of a cngc14 mutant and this phenotype is insensitive to changes in external Ca2+ concentrations. We, thus, identified CaM7‐CNGC14 as a novel interacting module that regulates polar growth in root hairs by controlling the tip‐focused Ca2+ signal.

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Lectin receptor kinase OsLecRK-S.7 is required for pollen development and male fertility
Xiaoqun Peng, Menglong Wang, Yiqi Li, Wei Yan, Zhenyi Chang, Zhufeng Chen, Chunjue Xu, Chengwei Yang, Xing Wang Deng, Jianxin Wu, and Xiaoyan Tang
J Integr Plant Biol 2020, 62 (8): 1227-1245.  
doi: 10.1111/jipb.12897
Abstract (Browse 406)  |   Save

Pollen grains are covered by exine that protects the pollen from stress and facilitates pollination. Here we isolated a male sterile mutant s13283 in rice exhibiting aborted pollen with abnormal exine and defective aperture. The mutant gene encodes a novel plasma membrane‐localized legume‐lectin receptor kinase that we named OsLecRK‐S.7. OsLecRK‐S.7 was expressed at different levels in all tested tissues and throughout anther development. In vitro kinase assay showed OsLecRK‐S.7 capable of autophosporylation. Mutation in s13283 (E560K) and mutation of the conserved ATP binding site (K418E) both knocked out the kinase activity. Mass spectrometry showed Thr376, Ser378, Thr386, Thr403, and Thr657 to be the autophosphorylation sites. Mutation of individual autophosphorylation site affected the in vitro kinase activity to different degrees, but did not abolish the gene function in fertility complementation. oslecrk‐s.7 mutant plant overexpressing OsLecRK‐S.7 recovered male fertility but showed severe growth retardation with reduced number of tillers, and these phenotypes were abolished by E560K or K418E mutation. The results indicated that OsLecRK‐S.7 was a key regulator of pollen development.

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Cell polarity: Regulators and mechanisms in plants
Kezhen Yang, Lu Wang, Jie Le and Juan Dong
J Integr Plant Biol 2020, 62 (1): 132-147.  
doi: 10.1111/jipb.12904
Abstract (Browse 228)  |   Save

Cell polarity plays an important role in a wide range of biological processes in plant growth and development. Cell polarity is manifested as the asymmetric distribution of molecules, for example, proteins and lipids, at the plasma membrane and/or inside of a cell. Here, we summarize a few polarized proteins that have been characterized in plants and we review recent advances towards understanding the molecular mechanism for them to polarize at the plasma membrane. Multiple mechanisms, including membrane trafficking, cytoskeletal activities, and protein phosphorylation, and so forth define the polarized plasma membrane domains. Recent discoveries suggest that the polar positioning of the proteo‐lipid membrane domain may instruct the formation of polarity complexes in plants. In this review, we highlight the factors and regulators for their functions in establishing the membrane asymmetries in plant development. Furthermore, we discuss a few outstanding questions to be addressed to better understand the mechanisms by which cell polarity is regulated in plants.

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Expanding the scope of CRISPR/Cas9-mediated genome editing in plants using an xCas9 and Cas9-NG hybrid
Qingfeng Niu, Siqun Wu, Yansha Li, Xiaoxuan Yang, Ping Liu, Yaping Xu and Zhaobo Lang
J Integr Plant Biol 2020, 62 (4): 398-402.  
doi: 10.1111/jipb.12886
Abstract (Browse 239)  |   Save

The widely used Streptococcus pyogenes Cas9 (SpCas9) requires NGG as a protospacer adjacent motif (PAM) for genome editing. Although SpCas9 is a powerful genome‐editing tool, its use has been limited on the targetable genomic locus lacking NGG PAM. The SpCas9 variants xCas9 and Cas9‐NG have been developed to recognize NG, GAA, and GAT PAMs in human cells. Here, we show that xCas9 cannot recognize NG PAMs in tomato, and Cas9‐NG can recognize some of our tested NG PAMs in the tomato and Arabidopsis genomes. In addition, we engineered SpCas9 (XNG‐Cas9) based on mutations from both xCas9 and Cas9‐NG, and found that XNG‐Cas9 can efficiently mutagenize endogenous target sites with NG, GAG, GAA, and GAT PAMs in the tomato or Arabidopsis genomes. The PAM compatibility of XNG‐Cas9 is the broadest reported to date among Cas9s (SpCas9 and Cas9‐NG) active in plant.

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Gibberellin repression of axillary bud formation in Arabidopsis by modulation of DELLA-SPL9 complex activity
Qi-Qi Zhang, Jia-Gang Wang, Ling-Yan Wang, Jun-Fang Wang, Qun Wang, Ping Yu, Ming-Yi Bai and Min Fan
J Integr Plant Biol 2020, 62 (4): 421-432.  
DOI: 10.1111/jipb.12818
Abstract (Browse 425)  |   Save

The formation of lateral branches has an important and fundamental contribution to the remarkable developmental plasticity of plants, which allows plants to alter their architecture to adapt to the challenging environment conditions. The Gibberellin (GA) phytohormones have been known to regulate the outgrowth of axillary meristems (AMs), but the specific molecular mechanisms remain unclear. Here we show that DELLA proteins regulate axillary bud formation by interacting and regulating the DNA‐binding ability of SQUAMOSA‐PROMOTER BINDING PROTEIN LIKE 9 (SPL9), a microRNA156‐targeted squamosa promoter binding protein‐like transcription factor. SPL9 participates in the initial regulation of axillary buds by repressing the expression of LATERAL SUPPRESSOR (LAS), a key regulator in the initiation of AMs, and LAS contributes to the specific expression pattern of the GA deactivation enzyme GA2ox4, which is specifically expressed in the axils of leaves to form a low‐GA cell niche in this anatomical region. Nevertheless, increasing GA levels in leaf axils by ectopically expressing the GA‐biosynthesis enzyme GA20ox2 significantly impaired axillary meristem initiation. Our study demonstrates that DELLA‐SPL9‐LAS‐GA2ox4 defines a core feedback regulatory module that spatially pattern GA content in the leaf axil and precisely control the axillary bud formation in different spatial and temporal.

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miR164c and miR168a regulate seed vigor in rice
Yan Zhou, Shiqi Zhou, Liping Wang, Duo Wu, Hailan Cheng, Xu Du, Dandan Mao, Chunlai Zhang and Xiaocheng Jiang
J Integr Plant Biol 2020, 62 (4): 470-486.  
doi: 10.1111/jipb.12792
Abstract (Browse 678)  |   Save

MicroRNAs (miRNAs) are key regulators of gene expression in many important biological processes of plants. However, few miRNAs have been shown to regulate seed vigor. Here, we conducted microarray assays to analyze miRNA expression levels in seeds of the rice (Oryza sativa L.) cultivar ZR02. Results showed significant differences in the expression of 11 miRNAs between artificially aged and untreated control seeds. Among these, osa‐miR164c was transcriptionally upregulated, while osa‐miR168a was downregulated in artificially aged seeds; this was verified by quantitative real‐time PCR analysis. Under the same aging condition, osa‐miR164c overexpression in OE164c transgenic seeds and osa‐miR168a silencing in MIM168a transgenic seeds of the rice cultivar Kasalath led to lower germination rates, whereas osa‐miR164c silencing in MIM164c and osa‐miR168a overexpression in OE168a resulted in higher seed germination rates compared with wild‐type seeds. Meanwhile, changes in cytomembrane permeability of seeds and in the expression level of osa‐miR164c target genes (OsPM27 and OsPSK5) and osa‐miR168a target genes (OsAGO1 and OsPTR2) under aging conditions coincided with changes in seed vigor induced by osa‐miR164c and osa‐miR168a. Thus, genetic manipulation of miRNAs has important implications in the development of crop cultivars with high vigor and extended life span of seeds.

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SHY2 as a node in the regulation of root meristem development by auxin, brassinosteroids, and cytokinin
Taotao Li, Xinke Kang, Wei Lei, Xiuhong Yao, Lijuan Zou, Dawei Zhang and Honghui Lin
J Integr Plant Biol 2020, 62 (10): 1500-1517.  
DOI: 10.1111/jipb.12931
Abstract (Browse 274)  |   Save
In multicellular organisms, the balance between cell division and differentiation determines organ size, and represents a central unknown in developmental biology. In Arabidopsis roots, this balance is mediated between cytokinin and auxin through a regulatory circuit converging on the IAA3/SHORT HYPOCOTYL 2 (SHY2) gene. Here, we show that crosstalk between brassinosteroids (BRs) and auxin occurs in the vascular transition zone to promote root meristem development. We found that BR increases root meristem size by up‐regulating expression of the PINFORMED 7 (PIN7) gene and down‐regulating expression of the SHY2 gene. In addition, BES1 could directly bind to the promoter regions of both PIN7 and SHY2, indicating that PIN7 and SHY2 mediate the BR‐induced growth of the root meristem by serving as direct targets of BES1. Moreover, the PIN7 overexpression and loss‐of‐function SHY2 mutant were sensitive to the effects of BR and could partially suppress the short‐root phenotypes associated with deficient BR signaling. Interestingly, BRs could inhibit the accumulation of SHY2 protein in response to cytokinin. Taken together, these findings suggest that a complex equilibrium model exists in which regulatory interactions among BRs, auxin, and cytokinin regulate optimal root growth.
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