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OsEDM2L mediates m6A of EAT1 transcript for proper alternative splicing and polyadenylation regulating rice tapetal degradation
Kun Ma, Jingluan Han, Zixu Zhang, Heying Li, Yanchang Zhao, Qinlong Zhu, Yongyao Xie, Yao‐Guang Liu and Letian Chen
J Integr Plant Biol 2021, 63 (11): 1982-1994.  
DOI: 10.1111/jipb.13167
Abstract (Browse 1426)  |   Save
N6-methyladenosine (m6A) modification affects the post-transcriptional regulation of eukaryotic gene expression, but the underlying mechanisms and their effects in plants remain largely unknown. Here, we report that the N6-adenine methyltransferase-like domain-containing protein ENHANCED DOWNY MILDEW 2-LIKE (OsEDM2L) is essential for rice (Oryza sativa L.) anther development. The osedm2l knockout mutant showed delayed tapetal programmed cell death (PCD) and defective pollen development. OsEDM2L interacts with the transcription factors basic helix-loop-helix 142 and TAPETUM DEGENERATION RETARDATION to regulate the expression of ETERNAL TAPETUM 1 (EAT1), a positive regulator of tapetal PCD. Mutation of OsEDM2L altered the transcriptomic m6A landscape, and caused a distinct m6A modification of the EAT1 transcript leading to dysregulation of its alternative splicing and polyadenylation, followed by suppression of the EAT1 target genes OsAP25 and OsAP37 for tapetal PCD. Therefore, OsEDM2L is indispensable for proper messenger RNA m6A modification in rice anther development.
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Single-cell RNA sequencing reveals a high-resolution cell atlas of xylem in Populus
Hui Li, Xinren Dai, Xiong Huang, Mengxuan Xu, Qiao Wang, Xiaojing Yan, Ronald R. Sederoff and Quanzi Li
J Integr Plant Biol 2021, 63 (11): 1906-1921.  
DOI: 10.1111/jipb.13159
Abstract (Browse 1001)  |   Save
High-throughput single-cell RNA sequencing (scRNA-seq) has advantages over traditional RNA-seq to explore spatiotemporal information on gene dynamic expressions in heterogenous tissues. We performed Drop-seq, a method for the dropwise sequestration of single cells for sequencing, on protoplasts from the differentiating xylem of Populus alba×Populus glandulosa. The scRNA-seq profiled 9,798 cells, which were grouped into 12 clusters. Through characterization of differentially expressed genes in each cluster and RNA in situ hybridizations, we identified vessel cells, fiber cells, ray parenchyma cells and xylem precursor cells. Diffusion pseudotime analyses revealed the differentiating trajectory of vessels, fiber cells and ray parenchyma cells and indicated a different differentiation process between vessels and fiber cells, and a similar differentiation process between fiber cells and ray parenchyma cells. We identified marker genes for each cell type (cluster) and key candidate regulators during developmental stages of xylem cell differentiation. Our study generates a high-resolution expression atlas of wood formation at the single cell level and provides valuable information on wood formation.
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A global alfalfa diversity panel reveals genomic selection signatures in Chinese varieties and genomic associations with root development
Lin Chen, Fei He, Ruicai Long, Fan Zhang, Mingna Li, Zhen Wang, Junmei Kang and Qingchuan Yang
J Integr Plant Biol 2021, 63 (11): 1937-1951.  
DOI: 10.1111/jipb.13172
Abstract (Browse 538)  |   Save
Alfalfa (Medicago sativa L.) is an important forage crop worldwide. However, little is known about the effects of breeding status and different geographical populations on alfalfa improvement. Here, we sequenced 220 alfalfa core germplasms and determined that Chinese alfalfa cultivars form an independent group, as evidenced by comparisons of FST values between different subgroups, suggesting that geographical origin plays an important role in group differentiation. By tracing the influence of geographical regions on the genetic diversity of alfalfa varieties in China, we identified 350 common candidate genetic regions and 548 genes under selection. We also defined 165 loci associated with 24 important traits from genome-wide association studies. Of those, 17 genomic regions closely associated with a given phenotype were under selection, with the underlying haplotypes showing significant differences between subgroups of distinct geographical origins. Based on results from expression analysis and association mapping, we propose that 6-phosphogluconolactonase (MsPGL) and a gene encoding a protein with NHL domains (MsNHL) are critical candidate genes for root growth. In conclusion, our results provide valuable information for alfalfa improvement via molecular breeding.
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PP2A interacts with KATANIN to promote microtubule organization and conical cell morphogenesis
Huibo Ren, Jinqiu Rao, Min Tang, Yaxing Li, Xie Dang and Deshu Lin
J Integr Plant Biol 2022, 64 (8): 1514-1530.  
DOI: 10.1111/jipb.13281
Abstract (Browse 488)  |   Save

The organization of the microtubule cytoskeleton is critical for cell and organ morphogenesis. The evolutionarily conserved microtubule-severing enzyme KATANIN plays critical roles in microtubule organization in the plant and animal kingdoms. We previously used conical cell of Arabidopsis thaliana petals as a model system to investigate cortical microtubule organization and cell morphogenesis and determined that KATANIN promotes the formation of circumferential cortical microtubule arrays in conical cells. Here, we demonstrate that the conserved protein phosphatase PP2A interacts with and dephosphorylates KATANIN to promote the formation of circumferential cortical microtubule arrays in conical cells. KATANIN undergoes cycles of phosphorylation and dephosphorylation. Using co-immunoprecipitation coupled with mass spectrometry, we identified PP2A subunits as KATANIN-interacting proteins. Further biochemical studies showed that PP2A interacts with and dephosphorylates KATANIN to stabilize its cellular abundance. Similar to the katanin mutant, mutants for genes encoding PP2A subunits showed disordered cortical microtubule arrays and defective conical cell shape. Taken together, these findings identify PP2A as a regulator of conical cell shape and suggest that PP2A mediates KATANIN phospho-regulation during plant cell morphogenesis.

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Allele-aware chromosome-scale assembly of the allopolyploid genome of hexaploid Ma bamboo (Dendrocalamus latiflorus Munro)
Yushan Zheng, Deming Yang, Jundong Rong, Liguang Chen, Qiang Zhu, Tianyou He, Lingyan Chen, Jing Ye, Lili Fan, Yubang Gao, Hangxiao Zhang and Lianfeng Gu
J Integr Plant Biol 2022, 64 (3): 649-670.  
doi: 10.1111/jipb.13217
Abstract (Browse 488)  |   Save
Dendrocalamus latiflorus Munro is a woody clumping bamboo with rapid shoot growth. Both genetic transformation and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) gene editing techniques are available for D. latiflorus, enabling reverse genetic approaches. Thus, D. latiflorus has the potential to be a model bamboo species. However, the genome sequence of D. latiflorus has remained unreported due to its polyploidy and large genome size. Here, we sequenced the D. latiflorus genome and assembled it into three allele-aware subgenomes (AABBCC), representing the largest genome of a major bamboo species. We assembled 70 allelic chromosomes (2, 737 Mb) for hexaploid D. latiflorus using both single-molecule sequencing from the Pacific Biosciences (PacBio) Sequel platform and chromosome conformation capture sequencing (Hi-C). Repetitive sequences comprised 52.65% of the D. latiflorus genome. We annotated 135 231 protein-coding genes in the genome based on transcriptomes from eight different tissues. Transcriptome sequencing using RNA-Seq and PacBio single-molecule real-time long-read isoform sequencing revealed highly differential alternative splicing (AS) between non-abortive and abortive shoots, suggesting that AS regulates the abortion rate of bamboo shoots. This high-quality hexaploid genome and comprehensive strand-specific transcriptome datasets for this Poaceae family member will pave the way for bamboo research using D. latiflorus as a model species.
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The direct targets of CBFs: In cold stress response and beyond
Yue Song, Xiaoyan Zhang, Minze Li, Hao Yang, Diyi Fu, Jian Lv, Yanglin Ding, Zhizhong Gong, Yiting Shi and Shuhua Yang
J Integr Plant Biol 2021, 63 (11): 1874-1887.  
DOI: 10.1111/jipb.13161
Abstract (Browse 453)  |   Save
Cold acclimation in Arabidopsis thaliana triggers a significant transcriptional reprogramming altering the expression patterns of thousands of cold-responsive (COR) genes. Essential to this process is the C-repeat binding factor (CBF)-dependent pathway, involving the activity of AP2/ERF (APETALA2/ethylene-responsive factor)-type CBF transcription factors required for plant cold acclimation. In this study, we performed chromatin immunoprecipitation assays followed by deep sequencing (ChIP-seq) to determine the genome-wide binding sites of the CBF transcription factors. Cold-induced CBF proteins specifically bind to the conserved C-repeat (CRT)/dehydration-responsive elements (CRT/DRE; G/ACCGAC) of their target genes. A Gene Ontology enrichment analysis showed that 1,012 genes are targeted by all three CBFs. Combined with a transcriptional analysis of the cbf1,2,3 triple mutant, we define 146 CBF regulons as direct CBF targets. In addition, the CBF-target genes are significantly enriched in functions associated with hormone, light, and circadian rhythm signaling, suggesting that the CBFs act as key integrators of endogenous and external environmental cues. Our findings not only define the genome-wide binding patterns of the CBFs during the early cold response, but also provide insights into the role of the CBFs in regulating multiple biological processes of plants.
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Recent progression and future perspectives in cotton genomic breeding
Zhaoen Yang, Chenxu Gao, Yihao Zhang, Qingdi Yan, Wei Hu, Lan Yang, Zhi Wang and Fuguang Li
J Integr Plant Biol 2023, 65 (2): 548-569.  
doi: 10.1111/jipb.13388
Abstract (Browse 444)  |   Save
Upland cotton is an important global cash crop for its long seed fibers and high edible oil and protein content. Progress in cotton genomics promotes the advancement of cotton genetics, evolutionary studies, functional genetics, and breeding, and has ushered cotton research and breeding into a new era. Here, we summarize high-impact genomics studies for cotton from the last 10 years. The diploid Gossypium arboreum and allotetraploid Gossypium hirsutum are the main focus of most genetic and genomic studies. We next review recent progress in cotton molecular biology and genetics, which builds on cotton genome sequencing efforts, population studies, and functional genomics, to provide insights into the mechanisms shaping abiotic and biotic stress tolerance, plant architecture, seed oil content, and fiber development. We also suggest the application of novel technologies and strategies to facilitate genome-based crop breeding. Explosive growth in the amount of novel genomic data, identified genes, gene modules, and pathways is now enabling researchers to utilize multidisciplinary genomics-enabled breeding strategies to cultivate “super cotton”, synergistically improving multiple traits. These strategies must rise to meet urgent demands for a sustainable cotton industry.
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bZIP71 delays flowering by suppressing Ehd1 expression in rice
Xiufeng Li, Xiaojie Tian, Mingliang He, Xinxin Liu, Zhiyong Li, Jiaqi Tang, Enyang Mei, Min Xu, Yingxiang Liu, Zhenyu Wang, Qingjie Guan, Wei Meng, Jun Fang, Jian Zhang and Qingyun Bu
J Integr Plant Biol 2022, 64 (7): 1352-1363.  
DOI: 10.1111/jipb.13275
Abstract (Browse 432)  |   Save

Flowering time is a fundamental factor determining the global distribution and final yield of rice (Oryza sativa). Although diverse flowering time genes have been reported in this crop, the transcriptional regulation of its key flowering genes are poorly understood. Here, we report that a basic leucine zipper transcription factor, bZIP71, functions as a flowering repressor. The overexpression of bZIP71 delays flowering, while the bzip71 mutant flowers early in both long-day and short-day conditions. A genetic analysis showed that the regulation of flowering by bZIP71 might be independent of Heading date 2 (Hd2), Hd4, and Hd5. Importantly, bZIP71 directly associates with the Early heading date 1 (Ehd1) promoter and represses its transcription, and genetically the function of bZIP71 is impaired in the ehd1 mutant. Moreover, bZIP71 interacts with major components of polycomb repressive complex 2 (PRC2), SET domain group protein 711 (SDG711), and Fertilization independent endosperm 2 (FIE2), through which bZIP71 regulates the H3K27me3 level of Ehd1. Taken together, we present a transcriptional regulatory mechanism in which bZIP71 enhances the H3K27me3 level of Ehd1 and transcriptionally represses its expression, which not only offers a novel insight into a flowering pathway, but also provides a valuable putative target for the genetic engineering and breeding of elite rice cultivars.

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Variations in OsSPL10 confer drought tolerance by directly regulating OsNAC2 expression and ROS production in rice
Yingxiu Li, Shichen Han, Xingming Sun, Najeeb Ullah Khan, Qun Zhong, Zhanying Zhang, Hongliang Zhang, Feng Ming, Zichao Li and Jinjie Li
J Integr Plant Biol 2023, 65 (4): 918-933.  
DOI: 10.1111/jipb.13414
Abstract (Browse 423)  |   Save
Drought is a major factor restricting the production of rice (Oryza sativa L.). The identification of natural variants for drought stress‐ related genes is an important step toward developing genetically improved rice varieties. Here, we characterized a member of the SQUAMOSA PROMOTER BINDING PROTEIN‐LIKE (SPL) family, OsSPL10, as a transcription factor involved in the regulation of drought tolerance in rice. OsSPL10 appears to play a vital role in drought tolerance by controlling reactive oxygen species (ROS) production and stomatal movements. Haplotype and allele frequency analyses of OsSPL10 indicated that most upland rice and improved lowland rice varieties harbor the OsSPL10Hap1 allele, whereas the OsSPL10Hap2 allele was mainly present in lowland and landrace rice varieties. Importantly, we demonstrated that the varieties with the OsSPL10Hap1 allele showed low expression levels of OsSPL10 and its downstream gene, OsNAC2, which decreases the expression of OsAP37 and increases the expression of OsCOX11, thus preventing ROS accumulation and programmed cell death (PCD). Furthermore, the knockdown or knockout of OsSPL10 induced fast stomatal closure and prevented water loss, thereby improving drought tolerance in rice. Based on these observations, we propose that OsSPL10 confers drought tolerance by regulating OsNAC2 expression and that OsSPL10Hap1 could be a valuable haplotype for the genetic improvement of drought tolerance in rice.
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Efficient and genotype independent maize transformation using pollen transfected by DNA-coated magnetic nanoparticles
Zuo‐Ping Wang, Zhong‐Bao Zhang, Deng‐Yu Zheng, Tong‐Tong Zhang, Xiang‐Long Li, Chun Zhang, Rong Yu, Jian‐Hua Wei and Zhong‐Yi Wu
J Integr Plant Biol 2022, 64 (6): 1145-1156.  
doi: 10.1111/jipb.13263
Abstract (Browse 407)  |   Save

Current gene delivery methods for maize are limited to specific genotypes and depend on time-consuming and labor-intensive tissue culture techniques. Here, we report a new method to transfect maize that is culture-free and genotype independent. To enhance efficiency of DNA entry and maintain high pollen viability of 32%-55%, transfection was performed at cool temperature using pollen pretreated to open the germination aperture (40%–55%). Magnetic nanoparticles (MNPs) coated with DNA encoding either red fluorescent protein (RFP), β-glucuronidase gene (GUS), enhanced green fluorescent protein (EGFP) or bialaphos resistance (bar) was delivered into pollen grains, and female florets of maize inbred lines were pollinated. Red fluorescence was detected in 22% transfected pollen grains, and GUS stained 55% embryos at 18 d after pollination. Green fluorescence was detected in both silk filaments and immature kernels. The T1 generation of six inbred lines showed considerable EGFP or GUS transcripts (29%–74%) quantitated by polymerase chain reaction, and 5%–16% of the T1 seedlings showed immunologically active EGFP or GUS protein. Moreover, 1.41% of the bar transfected T1 plants were glufosinate resistant, and heritable bar gene was integrated into the maize genome effectively as verified by DNA hybridization. These results demonstrate that exogenous DNA could be delivered efficiently into elite maize inbred lines recalcitrant to tissue culture-mediated transformation and expressed normally through our genotype-independent pollen transfection system.

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GmPIN1-mediated auxin asymmetry regulates leaf petiole angle and plant architecture in soybean
Zhongqin Zhang, Le Gao, Meiyu Ke, Zhen Gao, Tianli Tu, Laimei Huang, Jiaomei Chen, Yuefeng Guan, Xi Huang and Xu Chen
J Integr Plant Biol 2022, 64 (7): 1325-1338.  
doi: 10.1111/jipb.13269
Abstract (Browse 402)  |   Save

Crop breeding during the Green Revolution resulted in high yields largely due to the creation of plants with semi-dwarf architectures that could tolerate high-density planting. Although semi-dwarf varieties have been developed in rice, wheat and maize, none was reported in soybean (Glycine max), and few genes controlling plant architecture have been characterized in soybean. Here, we demonstrate that the auxin efflux transporter PINFORMED1 (GmPIN1), which determines polar auxin transport, regulates the leaf petiole angle in soybean. CRISPR-Cas9-induced Gmpin1abc and Gmpin1bc multiple mutants displayed a compact architecture with a smaller petiole angle than wild-type plants. GmPIN1 transcripts and auxin were distributed asymmetrically in the petiole base, with high levels of GmPIN1a/c transcript and auxin in the lower cells, which resulted in asymmetric cell expansion. By contrast, the (iso)flavonoid content was greater in the upper petiole cells than in the lower cells. Our results suggest that (iso)flavonoids inhibit GmPIN1a/c expression to regulate the petiole angle. Overall, our study demonstrates that a signal cascade that integrates (iso)flavonoid biosynthesis, GmPIN1a/c expression, auxin accumulation, and cell expansion in an asymmetric manner creates a desirable petiole curvature in soybean. This study provides a genetic resource for improving soybean plant architecture.

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Circadian clock in plants: Linking timing to fitness
Xiaodong Xu, Li Yuan, Xin Yang, Xiao Zhang, Lei Wang and Qiguang Xie
J Integr Plant Biol 2022, 64 (4): 792-811.  
doi: 10.1111/jipb.13230
Abstract (Browse 385)  |   Save
Endogenous circadian clock integrates cyclic signals of environment and daily and seasonal behaviors of organisms to achieve spatiotemporal synchronization, which greatly improves genetic diversity and fitness of species. This review addresses recent studies on the plant circadian system in the field of chronobiology, covering topics on molecular mechanisms, internal and external Zeitgebers, and hierarchical regulation of physiological outputs. The architecture of the circadian clock involves the autoregulatory transcriptional feedback loops, post-translational modifications of core oscillators, and epigenetic modifications of DNA and histones. Here, light, temperature, humidity, and internal elemental nutrients are summarized to illustrate the sensitivity of the circadian clock to timing cues. In addition, the circadian clock runs cell-autonomously, driving independent circadian rhythms in various tissues. The core oscillators responds to each other with biochemical factors including calcium ions, mineral nutrients, photosynthetic products, and hormones. We describe clock components sequentially expressed during a 24-h day that regulate rhythmic growth, aging, immune response, and resistance to biotic and abiotic stresses. Notably, more data have suggested the circadian clock links chrono-culture to key agronomic traits in crops.
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CmNF-YB8 affects drought resistance in chrysanthemum by altering stomatal status and leaf cuticle thickness
Tianle Wang, Qian Wei, Zhiling Wang, Wenwen Liu, Xin Zhao, Chao Ma, Junping Gao, Yanjie Xu and Bo Hong
J Integr Plant Biol 2022, 64 (3): 741-755.  
DOI: 10.1111/jipb.13201
Abstract (Browse 384)  |   Save

Drought is a major abiotic stress that limits plant growth and development. Adaptive mechanisms have evolved to mitigate drought stress, including the capacity to adjust water loss rate and to modify the morphology and structure of the epidermis. Here, we show that the expression of CmNF-YB8, encoding a nuclear factor Y (NF-Y) B-type subunit, is lower under drought conditions in chrysanthemum (Chrysanthemum morifolium). Transgenic chrysanthemum lines in which transcript levels of CmNF-YB8 were reduced by RNA interference (CmNF-YB8-RNAi) exhibited enhanced drought resistance relative to control lines, whereas lines overexpressing CmNF-YB8 (CmNF-YB8-OX) were less tolerant to drought. Compared to wild type (WT), CmNF-YB8-RNAi plants showed reduced stomatal opening and a thicker epidermal cuticle that correlated with their water loss rate. We also identified genes involved in stomatal adjustment (CBL-interacting protein kinase 6, CmCIPK6) and cuticle biosynthesis (CmSHN3) that are more highly expressed in CmNF-YB8-RNAi lines than in WT, CmCIPK6 being a direct downstream target of CmNF-YB8. Virus-induced gene silencing of CmCIPK6 or CmSHN3 in the CmNF-YB8-RNAi background abolished the effects of CmNF-YB8-RNAi on stomatal closure and cuticle deposition, respectively. CmNF-YB8 thus regulates CmCIPK6 and CmSHN3 expression to alter stomatal movement and cuticle thickness in the leaf epidermis, thereby affecting drought resistance.

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Integration of light and temperature signaling pathways in plants
Lijuan Qi, Yiting Shi, William Terzaghi, Shuhua Yang and Jigang Li
J Integr Plant Biol 2022, 64 (2): 393-411.  
doi: 10.1111/jipb.13216
Abstract (Browse 371)  |   Save
As two of the most important environmental factors, light and temperature regulate almost all aspects of plant growth and development. Under natural conditions, light is accompanied by warm temperatures and darkness by cooler temperatures, suggesting that light and temperature are tightly associated signals for plants. Indeed, accumulating evidence shows that plants have evolved a wide range of mechanisms to simultaneously perceive and respond to dynamic changes in light and temperature. Notably, the photoreceptor phytochrome B (phyB) was recently shown to function as a thermosensor, thus reinforcing the notion that light and temperature signaling pathways are tightly associated in plants. In this review, we summarize and discuss the current understanding of the molecular mechanisms integrating light and temperature signaling pathways in plants, with the emphasis on recent progress in temperature sensing, light control of plant freezing tolerance, and thermomorphogenesis. We also discuss the questions that are crucial for a further understanding of the interactions between light and temperature signaling pathways in plants.
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The root microbiome: Community assembly and its contributions to plant fitness
Bo Bai, Weidong Liu, Xingyu Qiu, Jie Zhang, Jingying Zhang and Yang Bai
J Integr Plant Biol 2022, 64 (2): 230-243.  
doi: 10.1111/jipb.13226
Abstract (Browse 364)  |   Save
The root microbiome refers to the community of microbes living in association with a plant's roots, and includes mutualists, pathogens, and commensals. Here we focus on recent advances in the study of root commensal community which is the major research object of microbiome-related researches. With the rapid development of new technologies, plant–commensal interactions can be explored with unprecedented breadth and depth. Both the soil environment and the host plant drive commensal community assembly. The bulk soil is the seed bank of potential commensals, and plants use root exudates and immune responses to build healthy microbial communities from the available microbes. The plant microbiome extends the functional system of plants by participating in a variety of processes, including nutrient absorption, growth promotion, and resistance to biotic and abiotic stresses. Plants and their microbiomes have evolved adaptation strategies over time. However, there is still a huge gap in our understanding of the regulatory mechanisms of plant–commensal interactions. In this review, we summarize recent research on the assembly of root microbial communities and the effects of these communities on plant growth and development, and look at the prospects for promoting sustainable agricultural development through the study of the root microbiome.
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Nitrate transporter NRT1.1 and anion channel SLAH3 form a functional unit to regulate nitrate-dependent alleviation of ammonium toxicity
Chengbin Xiao, Doudou Sun, Beibei Liu, Xianming Fang, Pengcheng Li, Yao Jiang, Mingming He, Jia Li, Sheng Luan and Kai He
J Integr Plant Biol 2022, 64 (4): 942-957.  
doi: 10.1111/jipb.13239
Abstract (Browse 355)  |   Save

Ammonium (NH4+) and nitrate (NO3) are major inorganic nitrogen (N) sources for plants. When serving as the sole or dominant N supply, NH4+ often causes root inhibition and shoot chlorosis in plants, known as ammonium toxicity. NO3 usually causes no toxicity and can mitigate ammonium toxicity even at low concentrations, referred to as nitrate-dependent alleviation of ammonium toxicity. Our previous studies indicated a NO3 efflux channel SLAH3 is involved in this process. However, whether additional components contribute to NO3-mediated NH4+ detoxification is unknown. Previously, mutations in NO3 transporter NRT1.1 were shown to cause enhanced resistance to high concentrations of NH4+. Whereas, in this study, we found when the high-NH4+ medium was supplemented with low concentrations of NO3, nrt1.1 mutant plants showed hyper-sensitive phenotype instead. Furthermore, mutation in NRT1.1 caused enhanced medium acidification under high-NH4+/low-NO3 condition, suggesting NRT1.1 regulates ammonium toxicity by facilitating H+ uptake. Moreover, NRT1.1 was shown to interact with SLAH3 to form a transporter-channel complex. Interestingly, SLAH3 appeared to affect NO3 influx while NRT1.1 influenced NO3 efflux, suggesting NRT1.1 and SLAH3 regulate each other at protein and/or gene expression levels. Our study thus revealed NRT1.1 and SLAH3 form a functional unit to regulate nitrate-dependent alleviation of ammonium toxicity through regulating NO3 transport and balancing rhizosphere acidification.

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The divergence of brassinosteroid sensitivity between rice subspecies involves natural variation conferring altered internal auto-binding of OsBSK2
Wenchao Yin, Lulu Li, Zhikun Yu, Fan Zhang, Dapu Liu, Hongkai Wu, Mei Niu, Wenjing Meng, Xiaoxing Zhang, Nana Dong, Yanzhao Yang, Jihong Liu, Yongqiang Liu, Guoxia Zhang, Jianlong Xu, Shimei Wang, Chengcai Chu, Qian Qian and Hongning Tong
J Integr Plant Biol 2022, 64 (8): 1614-1630.  
doi: 10.1111/jipb.13322
Abstract (Browse 353)  |   Save

Japonica/geng and indica/xian are two major rice (Oryza sativa) subspecies with multiple divergent traits, but how these traits are related and interact within each subspecies remains elusive. Brassinosteroids (BRs) are a class of steroid phytohormones that modulate many important agronomic traits in rice. Here, using different physiological assays, we revealed that japonica rice exhibits an overall lower BR sensitivity than indica. Extensive screening of BR signaling genes led to the identification of a set of genes distributed throughout the primary BR signaling pathway with divergent polymorphisms. Among these, we demonstrate that the C38/T variant in BR Signaling Kinase2 (OsBSK2), causing the amino acid change P13L, plays a central role in mediating differential BR signaling in japonica and indica rice. OsBSK2L13 in indica plays a greater role in BR signaling than OsBSK2P13 in japonica by affecting the auto-binding and protein accumulation of OsBSK2. Finally, we determined that OsBSK2 is involved in a number of divergent traits in japonica relative to indica rice, including grain shape, tiller number, cold adaptation, and nitrogen-use efficiency. Our study suggests that the natural variation in OsBSK2 plays a key role in the divergence of BR signaling, which underlies multiple divergent traits between japonica and indica.

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OsRLR4 binds to the OsAUX1 promoter to negatively regulate primary root development in rice
Chendong Sun, Dongming Li, Zhenyu Gao, Lei Gao, Lianguang Shang, Mei Wang, Jiyue Qiao, Shilin Ding, Chuanyou Li, Markus Geisler, Dean Jiang, Yanhua Qi and Qian Qian
J Integr Plant Biol 2022, 64 (1): 118-134.  
doi: 10.1111/jipb.13183
Abstract (Browse 353)  |   Save
Root architecture is one of the most important agronomic traits that determines rice crop yield. The primary root (PR) absorbs mineral nutrients and provides mechanical support; however, the molecular mechanisms of PR elongation remain unclear in rice. Here, the two loss-of-function T-DNA insertion mutants of root length regulator 4 (OsRLR4), osrlr4-1 and osrlr4-2 with longer PR, and three OsRLR4 overexpression lines, OE-OsRLR4-1/-2/-3 with shorter PR compared to the wild type/Hwayoung (WT/HY), were identified. OsRLR4 is one of five members of the PRAF subfamily of the regulator chromosome condensation 1 (RCC1) family. Phylogenetic analysis of OsRLR4 from wild and cultivated rice indicated that it is under selective sweeps, suggesting its potential role in domestication. OsRLR4 controls PR development by regulating auxin accumulation in the PR tip and thus the root apical meristem activity. A series of biochemical and genetic analyses demonstrated that OsRLR4 functions directly upstream of the auxin transporter OsAUX1. Moreover, OsRLR4 interacts with the TRITHORAX-like protein OsTrx1 to promote H3K4me3 deposition at the OsAUX1 promoter, thus altering its transcription level. This work provides insight into the cooperation of auxin and epigenetic modifications in regulating root architecture and provides a genetic resource for plant architecture breeding.
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Ascorbate peroxidase 1 confers resistance to southern corn leaf blight in maize
Jinghua Zhang, Xingmeng Jia, Guan‐Feng Wang, Shijun Ma, Shunxi Wang, Qin Yang, Xueyan Chen, Yuqian Zhang, Yajing Lyu, Xiaoxu Wang, Jiawei Shi, Yangtao Zhao, Yanhui Chen and Liuji Wu
J Integr Plant Biol 2022, 64 (6): 1196-1211.  
DOI: 10.1111/jipb.13254
Abstract (Browse 352)  |   Save

Southern corn leaf blight (SCLB), caused by Bipolaris maydis, is one of the most devastating diseases affecting maize production. However, only one SLCB resistance gene, conferring partial resistance, is currently known, underscoring the importance of isolating new SCLB resistance-related genes. Here, we performed a comparative proteomic analysis and identified 258 proteins showing differential abundance during the maize response to B. maydis. These proteins included an ascorbate peroxidase (Zea mays ascorbate peroxidase 1 (ZmAPX1)) encoded by a gene located within the mapping interval of a previously identified quantitative trait locus associated with SCLB resistance. ZmAPX1 overexpression resulted in lower H2O2 accumulation and enhanced resistance against B. maydis. Jasmonic acid (JA) contents and transcript levels for JA biosynthesis and responsive genes increased in ZmAPX1-overexpressing plants infected with B. maydis, whereas Zmapx1 mutants showed the opposite effects. We further determined that low levels of H2O2 are accompanied by an accumulation of JA that enhances SCLB resistance. These results demonstrate that ZmAPX1 positively regulates SCLB resistance by decreasing H2O2 accumulation and activating the JA-mediated defense signaling pathway. This study identified ZmAPX1 as a potentially useful gene for increasing SCLB resistance. Furthermore, the generated data may be relevant for clarifying the functions of plant APXs.

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Creation of fragrant sorghum by CRISPR/Cas9
Dan Zhang, Sanyuan Tang, Peng Xie, Dekai Yang, Yaorong Wu, Shujing Cheng, Kai Du, Peiyong Xin, Jinfang Chu, Feifei Yu and Qi Xie
J Integr Plant Biol 2022, 64 (5): 961-964.  
doi: 10.1111/jipb.13232
Abstract (Browse 342)  |   Save

Sorghum, the fifth largest cereal crop, has high value as a staple food and raw material for liquor and vinegar brewing. Due to its high biomass and quality, it is also used as the second most planted silage resource. No fragrant sorghums are currently on the market. Through CRISPR/Cas9-mediated knockout of SbBADH2, we obtained sorghum lines with extraordinary aromatic smell in both seeds and leaves. Animal feeding experiments showed that fragrant sorghum leaves were attractable. We believe this advantage will produce great value in the sorghum market for both grain and whole biomass forage.

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Mitogen-activated protein kinase cascades in plant signaling
Mengmeng Zhang and Shuqun Zhang
J Integr Plant Biol 2022, 64 (2): 301-341.  
doi: 10.1111/jipb.13215
Abstract (Browse 339)  |   Save
Mitogen-activated protein kinase (MAPK) cascades are key signaling modules downstream of receptors/sensors that perceive either endogenously produced stimuli such as peptide ligands and damage-associated molecular patterns (DAMPs) or exogenously originated stimuli such as pathogen/microbe-associated molecular patterns (P/MAMPs), pathogen-derived effectors, and environmental factors. In this review, we provide a historic view of plant MAPK research and summarize recent advances in the establishment of MAPK cascades as essential components in plant immunity, response to environmental stresses, and normal growth and development. Each tier of the MAPK cascades is encoded by a small gene family, and multiple members can function redundantly in an MAPK cascade. Yet, they carry out a diverse array of biological functions in plants. How the signaling specificity is achieved has become an interesting topic of MAPK research. Future investigations into the molecular mechanism(s) underlying the regulation of MAPK activation including the activation kinetics and magnitude in response to a stimulus, the spatiotemporal expression patterns of all the components in the signaling pathway, and functional characterization of novel MAPK substrates are central to our understanding of MAPK functions and signaling specificity in plants.
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The MIEL1-ABI5/MYB30 regulatory module fine tunes abscisic acid signaling during seed germination
Kaili Nie, Hongyun Zhao, Xiaopei Wang, Yanli Niu, Huapeng Zhou and Yuan Zheng
J Integr Plant Biol 2022, 64 (4): 930-941.  
DOI: 10.1111/jipb.13234
Abstract (Browse 336)  |   Save

The transcription factor ABSCISIC ACID INSENSITIVE5 (ABI5) plays a crucial role in abscisic acid (ABA) signaling during seed germination. However, how ABI5 is regulated during this process is poorly understood. Here, we report that the ubiquitin E3 ligase MIEL1 and its target transcription factor MYB30 modulate ABA responses in Arabidopsis thaliana during seed germination and seedling establishment via the precise regulation of ABI5. MIEL1 interacts with and ubiquitinates ABI5 to facilitate its degradation during germination. The transcription factor MYB30, whose turnover is mediated by MIEL1 during seed germination, also interacts with ABI5 to interfere with its transcriptional activity. MYB30 functions downstream of MIEL1 in the ABA response, and both are epistatic to ABI5 in ABA-mediated inhibition of seed germination and postgerminative growth. ABA treatment induces the degradation of MIEL1 and represses the interaction between MIEL1 and ABI5/MYB30, thus releasing both ABI5 and MYB30. Our results demonstrate that MIEL1 directly mediates the proteasomal degradation of ABI5 and inhibits its activity via the release of its target protein MYB30, thus ensuring precise ABA signaling during seed germination and seedling establishment.

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BAK1 plays contrasting roles in regulating abscisic acid-induced stomatal closure and abscisic acid-inhibited primary root growth in Arabidopsis
Jinping Deng, Lingyao Kong, Yinhua Zhu, Dan Pei, Xuexue Chen, Yu Wang, Junsheng Qi, Chunpeng Song, Shuhua Yang and Zhizhong Gong
J Integr Plant Biol 2022, 64 (6): 1264-1280.  
DOI: 10.1111/jipb.13257
Abstract (Browse 327)  |   Save

The mechanisms that balance plant growth and stress responses are poorly understood, but they appear to involve abscisic acid (ABA) signaling mediated by protein kinases. Here, to explore these mechanisms, we examined the responses of Arabidopsis thaliana protein kinase mutants to ABA treatment. We found that mutants of BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED RECEPTOR KINASE 1 (BAK1) were hypersensitive to the effects of ABA on both seed germination and primary root growth. The kinase OPEN STOMATA 1 (OST1) was more highly activated by ABA in bak1 mutant than the wild type. BAK1 was not activated by ABA treatment in the dominant negative mutant abi1-1 or the pyr1 pyl4 pyl5 pyl8 quadruple mutant, but it was more highly activated by this treatment in the abi1-2 abi2-2 hab1-1 loss-of-function triple mutant than the wild type. BAK1 phosphorylates OST1 T146 and inhibits its activity. Genetic analyses suggested that BAK1 acts at or upstream of core components in the ABA signaling pathway, including PYLs, PP2Cs, and SnRK2s, during seed germination and primary root growth. Although the upstream brassinosteroid (BR) signaling components BAK1 and BR INSENSITIVE 1 (BRI1) positively regulate ABA-induced stomatal closure, mutations affecting downstream components of BR signaling, including BRASSINOSTEROID-SIGNALING KINASEs (BSKs) and BRASSINOSTEROID-INSENSITIVE 2 (BIN2), did not affect ABA-mediated stomatal movement. Thus, our study uncovered an important role of BAK1 in negatively regulating ABA signaling during seed germination and primary root growth, but positively modulating ABA-induced stomatal closure, thus optimizing the plant growth under drought stress.

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Highly efficient, genotype-independent transformation and gene editing in watermelon (Citrullus lanatus) using a chimeric ClGRF4-GIF1 gene
Qin Feng, Ling Xiao, Yizhen He, Man Liu, Jiafa Wang, Shujuan Tian, Xian Zhang and Li Yuan
J Integr Plant Biol 2021, 63 (12): 2038-2042.  
doi: 10.1111/jipb.13199
Abstract (Browse 327)  |   Save
Efficient genetic transformation has the potential to advance research and breeding in watermelon (Citrullus lanatus), but regeneration from tissue culture remains challenging. Previous work showed that expressing a fusion of two interacting transcription factors, GROWTH-REGULATING FACTOR4 (GRF4) and GRF-INTERACTING FACTOR1 (GIF1), improved regeneration in wheat (Triticum aestivum). By overexpressing a chimeric fusion of ClGRF4 and ClGIF1, we achieved highly efficient transformation in watermelon. Mutating the mi396 microRNA target site in ClGRF further boosted the transformation efficiency up to 67.27% in a genotype-independent manner. ClGRF4-GIF1 can also be combined with clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) genome editing tools to achieve highly efficient gene editing in watermelon, which we used to successfully create diploid seedless watermelon. This research thus puts forward a powerful transformation tool for future watermelon research and breeding.
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Exploring key developmental phases and phase-specific genes across the entirety of anther development in maize
Yingjia Han, Mingjian Hu, Xuxu Ma, Ge Yan, Chunyu Wang, Siqi Jiang, Jinsheng Lai and Mei Zhang
J Integr Plant Biol 2022, 64 (7): 1394-1410.  
DOI: 10.1111/jipb.13276
Abstract (Browse 323)  |   Save

Anther development from stamen primordium to pollen dispersal is complex and essential to sexual reproduction. How this highly dynamic and complex developmental process is controlled genetically is not well understood, especially for genes involved in specific key developmental phases. Here we generated RNA sequencing libraries spanning 10 key stages across the entirety of anther development in maize (Zea mays). Global transcriptome analyses revealed distinct phases of cell division and expansion, meiosis, pollen maturation, and mature pollen, for which we detected 50, 245, 42, and 414 phase-specific marker genes, respectively. Phase-specific transcription factor genes were significantly enriched in the phase of meiosis. The phase-specific expression of these marker genes was highly conserved among the maize lines Chang7-2 and W23, indicating they might have important roles in anther development. We explored a desiccation-related protein gene, ZmDRP1, which was exclusively expressed in the tapetum from the tetrad to the uninucleate microspore stage, by generating knockout mutants. Notably, mutants in ZmDRP1 were completely male-sterile, with abnormal Ubisch bodies and defective pollen exine. Our work provides a glimpse into the gene expression dynamics and a valuable resource for exploring the roles of key phase-specific genes that regulate anther development.

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Efficient genotype-independent cotton genetic transformation and genome editing
Xiaoyang Ge, Jieting Xu, Zhaoen Yang, Xiaofeng Yang, Ye Wang, Yanli Chen, Peng Wang and Fuguang Li
J Integr Plant Biol 2023, 65 (4): 907-917.  
doi: 10.1111/jipb.13427
Abstract (Browse 317)  |   Save
Cotton (Gossypium spp.) is one of the most important fiber crops worldwide. In the last two decades, transgenesis and genome editing have played important roles in cotton improvement. However, genotype dependence is one of the key bottlenecks in generating transgenic and gene‐edited cotton plants through either particle bombardment or Agrobacterium‐mediated transformation. Here, we developed a shoot apical meristem (SAM) cell‐ mediated transformation system (SAMT) that allowed the transformation of recalcitrant cotton genotypes including widely grown upland cotton (Gossypium hirsutum), Sea island cotton (Gossypium barbadense), and Asiatic cotton (Gossypium arboreum). Through SAMT, we successfully introduced two foreign genes, GFP and RUBY, into SAM cells of some recalcitrant cotton genotypes. Within 2–3 months, transgenic adventitious shoots generated from the axillary meristem zone could be recovered and grown into whole cotton plants. The GFP fluorescent signal and betalain accumulation could be observed in various tissues in GFP‐ and RUBY‐positive plants, as well as in their progenies, indicating that the transgenes were stably integrated into the genome and transmitted to the next generation. Furthermore, using SAMT, we successfully generated edited cotton plants with inheritable targeted mutagenesis in the GhPGF and GhRCD1 genes through CRISPR/Cas9‐mediated genome editing. In summary, the established SAMT transformation system here in this study bypasses the embryogenesis process during tissue culture in a conventional transformation procedure and significantly accelerates the generation of transgenic and gene‐edited plants for genetic improvement of recalcitrant cotton varieties.
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OsMKKK70 regulates grain size and leaf angle in rice through the OsMKK4-OsMAPK6-OsWRKY53 signaling pathway
Zhiqi Liu, Enyang Mei, Xiaojie Tian, Mingliang He, Jiaqi Tang, Min Xu, Jiali Liu, Lu Song, Xiufeng Li, Zhenyu Wang, Qingjie Guan, Qijiang Xu and Qingyun Bu
J Integr Plant Biol 2021, 63 (12): 2043-2057.  
DOI: 10.1111/jipb.13174
Abstract (Browse 315)  |   Save
Grain size and leaf angle are key agronomic traits that determine final yields in rice. However, the underlying molecular mechanisms are not well understood. Here we demonstrate that the Oryza sativa Mitogen Activated Protein Kinase Kinase Kinase OsMKKK70 regulates grain size and leaf angle in rice. Overexpressing OsMKKK70 caused plants to produce longer seeds. The osmkkk62/70 double mutant and the osmkkk55/62/70 triple mutant displayed significantly smaller seeds and a more erect leaf angle compared to the wild type, indicating that OsMKKK70 functions redundantly with its homologs OsMKKK62 and OsMKKK55. Biochemical analysis demonstrated that OsMKKK70 is an active kinase and that OsMKKK70 interacts with OsMKK4 and promotes OsMAPK6 phosphorylation. In addition, the osmkkk62/70 double mutant showed reduced sensitivity to Brassinosteroids (BRs). Finally, overexpressing constitutively active OsMKK4, OsMAPK6, and OsWRKY53 can partially complement the smaller seed size, erect leaf, and BR hyposensitivity of the osmkkk62/70 double mutant. Taken together, these findings suggest that OsMKKK70 might regulate grain size and leaf angle in rice by activating OsMAPK6 and that OsMKKK70, OsMKK4, OsMAPK6, and OsWRKY53 function in a common signaling pathway that controls grain shape and leaf angle.
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Versatile effectors of phytopathogenic fungi target host immunity
Muhammad Tariqjaveed, Abdul Mateen, Shanzhi Wang, Shanshan Qiu, Xinhang Zheng, Jie Zhang, Vijai Bhadauria and Wenxian Sun
J Integr Plant Biol 2021, 63 (11): 1856-1873.  
DOI: 10.1111/jipb.13162
Abstract (Browse 315)  |   Save
Phytopathogenic fungi secrete a large arsenal of effector molecules, including proteinaceous effectors, small RNAs, phytohormones and derivatives thereof. The pathogenicity of fungal pathogens is primarily determined by these effectors that are secreted into host cells to undermine innate immunity, as well as to facilitate the acquisition of nutrients for their in planta growth and proliferation. After conventional and non-conventional secretion, fungal effectors are translocated into different subcellular compartments of the host cells to interfere with various biological processes. In extracellular spaces, apoplastic effectors cope with physical and chemical barriers to break the first line of plant defenses. Intracellular effectors target essential immune components on the plasma membrane, in the cytosol, including cytosolic organelles, and in the nucleus to suppress host immunity and reprogram host physiology, favoring pathogen colonization. In this review, we comprehensively summarize the recent advances in fungal effector biology, with a focus on the versatile virulence functions of fungal effectors in promoting pathogen infection and colonization. A perspective of future research on fungal effector biology is also discussed.
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Phase separation in plants: New insights into cellular compartmentalization
Xiumei Xu, Canhui Zheng, Dandan Lu, Chun‐Peng Song and Lixin Zhang
J Integr Plant Biol 2021, 63 (11): 1835-1855.  
doi: 10.1111/jipb.13152
Abstract (Browse 313)  |   Save
A fundamental challenge for cells is how to coordinate various biochemical reactions in space and time. To achieve spatiotemporal control, cells have developed organelles that are surrounded by lipid bilayer membranes. Further, membraneless compartmentalization, a process induced by dynamic physical association of biomolecules through phase transition offers another efficient mechanism for intracellular organization. While our understanding of phase separation was predominantly dependent on yeast and animal models, recent findings have provided compelling evidence for emerging roles of phase separation in plants. In this review, we first provide an overview of the current knowledge of phase separation, including its definition, biophysical principles, molecular features and regulatory mechanisms. Then we summarize plant-specific phase separation phenomena and describe their functions in plant biological processes in great detail. Moreover, we propose that phase separation is an evolutionarily conserved and efficient mechanism for cellular compartmentalization which allows for distinct metabolic processes and signaling pathways, and is especially beneficial for the sessile lifestyle of plants to quickly and efficiently respond to the changing environment.
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GmFtsH25 overexpression increases soybean seed yield by enhancing photosynthesis and photosynthates
Li Wang, Yuming Yang, Zhongyi Yang, Wenlong Li, Dezhou Hu, Huilian Yu, Xiao Li, Hao Cheng, Guizhen Kan, Zhijun Che, Dan Zhang, Hengyou Zhang, Hui Wang, Fang Huang and Deyue Yu
J Integr Plant Biol 2023, 65 (4): 1026-1040.  
DOI: 10.1111/jipb.13405
Abstract (Browse 310)  |   Save
Increasing plant photosynthetic capacity is a promising approach to boost yields, but it is particularly challenging in C3 crops, such as soybean (Glycine max (L.) Merr.). Here, we identified GmFtsH25, encoding a member of the filamentation temperature‐sensitive protein H protease family, as a major gene involved in soybean photosynthesis, using linkage mapping and a genome‐wide association study. Overexpressing GmFtsH25 resulted in more grana thylakoid stacks in chloroplasts and increased photosynthetic efficiency and starch content, while knocking out GmFtsH25 produced the opposite phenotypes. GmFtsH25 interacted with photosystem I light harvesting complex 2 (GmLHCa2), and this interaction may contribute to the observed enhanced photosynthesis. GmFtsH25 overexpression lines had superior yield traits, such as yield per plant, compared to the wild type and knockout lines. Additionally, we identified an elite haplotype of GmFtsH25, generated by natural mutations, which appears to have been selected during soybean domestication. Our study sheds light on the molecular mechanism by which GmFtsH25 modulates photosynthesis and provides a promising strategy for improving the yields of soybean and other crops.
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The miR157-SPL-CNR module acts upstream of bHLH101 to negatively regulate iron deficiency responses in tomato
Huihui Zhu, Jiayi Wang, Dan Jiang, Yiguo Hong, Jiming Xu, Shaojian Zheng, Jianli Yang and Weiwei Chen
J Integr Plant Biol 2022, 64 (5): 1059-1075.  
DOI: 10.1111/jipb.13251
Abstract (Browse 299)  |   Save

Iron (Fe) homeostasis is critical for plant growth, development, and stress responses. Fe levels are tightly controlled by intricate regulatory networks in which transcription factors (TFs) play a central role. A series of basic helix-loop-helix (bHLH) TFs have been shown to contribute to Fe homeostasis, but the regulatory layers beyond bHLH TFs remain largely unclear. Here, we demonstrate that the SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL) TF SlSPL-CNR negatively regulates Fe-deficiency responses in tomato (Solanum lycopersicum) roots. Fe deficiency rapidly repressed the expression of SlSPL-CNR, and Fe deficiency responses were intensified in two clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9-generated SlSPL-CNR knock-out lines compared to the wild-type. Comparative transcriptome analysis identified 47 Fe deficiency-responsive genes the expression of which is negatively regulated by SlSPL-CNR, one of which, SlbHLH101, helps regulate Fe uptake genes. SlSPL-CNR localizes the nucleus and interacts with the GTAC and BOX 4 (ATTAAT) motifs in the SlbHLH101 promoter to repress its expression. Inhibition of SlSPL-CNR expression in response to Fe deficiency was well correlated with the expression of the microRNA SlymiR157. SlymiR157-overexpressing tomato lines displayed enhanced Fe deficiency responses, as did SlSPL-CNR loss-of-function mutants. We propose that the SlymiR157-SlSPL-CNR module represents a novel pathway that acts upstream of SlbHLH101 to regulate Fe homeostasis in tomato roots.

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The multi-omics basis of potato heterosis
Dawei Li, Xiaoyue Lu, Yanhui Zhu, Jun Pan, Shaoqun Zhou, Xinyan Zhang, Guangtao Zhu, Yi Shang, Sanwen Huang and Chunzhi Zhang
J Integr Plant Biol 2022, 64 (3): 671-687.  
doi: 10.1111/jipb.13211
Abstract (Browse 298)  |   Save

Heterosis is a fundamental biological phenomenon characterized by the superior performance of hybrids over their parents. Although tremendous progress has been reported in seed crops, the molecular mechanisms underlying heterosis in clonally propagated crops are largely unknown. Potato (Solanum tuberosum L.) is the most important tuber crop and an ongoing revolution is transforming potato from a clonally propagated tetraploid crop into a seed-propagated diploid hybrid potato. In our previous study, we developed the first generation of highly homozygous inbred lines of potato and hybrids with strong heterosis. Here, we integrated transcriptome, metabolome, and DNA methylation data to explore the genetic and molecular basis of potato heterosis at three developmental stages. We found that the initial establishment of heterosis in diploid potato was mainly due to dominant complementation. Flower color, male fertility, and starch and sucrose metabolism showed obvious gene dominant complementation in hybrids, and hybrids devoted more energy to primary metabolism for rapid growth. In addition, we identified ~2 700 allele-specific expression genes at each stage, which likely function in potato heterosis and might be regulated by CHH allele-specific methylation level. Our multi-omics analysis provides insight into heterosis in potato and facilitates the exploitation of heterosis in potato breeding.

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Ca2+ signaling in plant responses to abiotic stresses
Qiuyan Dong, Lukas Wallrad, Bader O. Almutairi and Jörg Kudla
J Integr Plant Biol 2022, 64 (2): 287-300.  
doi: 10.1111/jipb.13228
Abstract (Browse 295)  |   Save
Adverse variations of abiotic environmental cues that deviate from an optimal range impose stresses to plants. Abiotic stresses severely impede plant physiology and development. Consequently, such stresses dramatically reduce crop yield and negatively impact on ecosystem stability and composition. Physical components of abiotic stresses can be, for example, suboptimal temperature and osmotic perturbations, while representative chemical facets of abiotic stresses can be toxic ions or suboptimal nutrient availability. The sheer complexity of abiotic stresses causes a multitude of diverse components and mechanisms for their sensing and signal transduction. Ca2+, as a versatile second messenger, plays multifaceted roles in almost all abiotic stress responses in that, for a certain abiotic stress, Ca2+ is not only reciprocally connected with its perception, but also multifunctionally ensures subsequent signal transduction. Here, we will focus on salt/osmotic stress and responses to altered nutrient availability as model cases to detail novel insights into the identity of components that link stress perception to Ca2+ signal formation as well as on new insights into mechanisms of Ca2+ signal implementation. Finally, we will deduce emerging conceptual consequences of these novel insights and outline arising avenues of future research on the role of Ca2+ signaling in abiotic stress responses in plants.
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Cas12a-based on-site, rapid detection of genetically modified crops
Zhiqiang Duan, Xiaoliang Yang, Xingkun Ji, Ying Chen, Xiaomu Niu, Anping Guo, Jian‐Kang Zhu, Feng Li, Zhaobo Lang and Hui Zhao
J Integr Plant Biol 2022, 64 (10): 1856-1859.  
doi: 10.1111/jipb.13342
Abstract (Browse 290)  |   Save
A CRISPR/LbCas12a-based nucleic acid detection method that uses crude leaf extracts as samples and is rapid (≤40 min for a full run) and highly sensitive (0.01%) can be used to monitor genetically modified organisms in the field.
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The Larix kaempferi genome reveals new insights into wood properties
Chao Sun, Yun‐Hui Xie, Zhen Li, Yan‐Jing Liu, Xiao‐Mei Sun, Jing‐Jing Li, Wei‐Peng Quan, Qing‐Yin Zeng, Yves Van de Peer and Shou‐Gong Zhang
J Integr Plant Biol 2022, 64 (7): 1364-1373.  
doi: 10.1111/jipb.13265
Abstract (Browse 289)  |   Save

Here, through single-molecule real-time sequencing, we present a high-quality genome sequence of the Japanese larch (Larix kaempferi), a conifer species with great value for wood production and ecological afforestation. The assembled genome is 10.97 Gb in size, harboring 45,828 protein-coding genes. Of the genome, 66.8% consists of repeat sequences, of which long terminal repeat retrotransposons are dominant and make up 69.86%. We find that tandem duplications have been responsible for the expansion of genes involved in transcriptional regulation and stress responses, unveiling their crucial roles in adaptive evolution. Population transcriptome analysis reveals that lignin content in L. kaempferi is mainly determined by the process of monolignol polymerization. The expression values of six genes (LkCOMT7, LkCOMT8, LkLAC23, LkLAC102, LkPRX148, and LkPRX166) have significantly positive correlations with lignin content. These results indicated that the increased expression of these six genes might be responsible for the high lignin content of the larches' wood. Overall, this study provides new genome resources for investigating the evolution and biological function of conifer trees, and also offers new insights into wood properties of larches.

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A prolific and robust whole-genome genotyping method using PCR amplification via primer-template mismatched annealing
Sheng Zhao, Cuicui Zhang, Liqun Wang, Minxuan Luo, Peng Zhang, Yue Wang, Waqar Afzal Malik, Yue Wang, Peng Chen, Xianjin Qiu, Chongrong Wang, Hong Lu, Yong Xiang, Yuwen Liu, Jue Ruan, Qian Qian, Haijian Zhi and Yuxiao Chang
J Integr Plant Biol 2023, 65 (3): 633-645.  
doi: 10.1111/jipb.13395
Abstract (Browse 288)  |   Save
Whole-genome genotyping methods are important for breeding. However, it has been challenging to develop a robust method for simultaneous foreground and background genotyping that can easily be adapted to different genes and species. In our study, we accidently discovered that in adapter ligation-mediated PCR, the amplification by primer-template mismatched annealing (PTMA) along the genome could generate thousands of stable PCR products. Based on this observation, we consequently developed a novel method for simultaneous foreground and background integrated genotyping by sequencing (FBI-seq) using one specific primer, in which foreground genotyping is performed by primer-template perfect annealing (PTPA), while background genotyping employs PTMA. Unlike DNA arrays, multiple PCR, or genome target enrichments, FBI-seq requires little preliminary work for primer design and synthesis, and it is easily adaptable to different foreground genes and species. FBI-seq therefore provides a prolific, robust, and accurate method for simultaneous foreground and background genotyping to facilitate breeding in the post-genomics era.
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OsCPL3 is involved in brassinosteroid signaling by regulating OsGSK2 stability
Luping Gong, Shenghao Liao, Wen Duan, Yongqiang Liu, Dongmei Zhu, Xiaosheng Zhou, Baoping Xue, Chengcai Chu and Yun‐Kuan Liang
J Integr Plant Biol 2022, 64 (8): 1560-1574.  
DOI: 10.1111/jipb.13311
Abstract (Browse 288)  |   Save

Glycogen synthase kinase 3 (GSK3) proteins play key roles in brassinosteroid (BR) signaling during plant growth and development by phosphorylating various substrates. However, how GSK3 protein stability and activity are themselves modulated is not well understood. Here, we demonstrate in vitro and in vivo that C-TERMINAL DOMAIN PHOSPHATASE-LIKE 3 (OsCPL3), a member of the RNA Pol II CTD phosphatase-like family, physically interacts with OsGSK2 in rice (Oryza sativa). OsCPL3 expression was widely detected in various tissues and organs including roots, leaves and lamina joints, and was induced by exogenous BR treatment. OsCPL3 localized to the nucleus, where it dephosphorylated OsGSK2 at the Ser-222 and Thr-284 residues to modulate its protein turnover and kinase activity, in turn affecting the degradation of BRASSINAZOLE-RESISTANT 1 (BZR1) and BR signaling. Loss of OsCPL3 function resulted in higher OsGSK2 abundance and lower OsBZR1 levels, leading to decreased BR responsiveness and alterations in plant morphology including semi-dwarfism, leaf erectness and grain size, which are of fundamental importance to crop productivity. These results reveal a previously unrecognized role for OsCPL3 and add another layer of complexity to the tightly controlled BR signaling pathway in plants.

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From molecular basics to agronomic benefits: Insights into noncoding RNA-mediated gene regulation in plants
Yuqiu Wang, Xing Wang Deng and Danmeng Zhu
J Integr Plant Biol 2022, 64 (12): 2290-2308.  
doi: 10.1111/jipb.13420
Abstract (Browse 287)  |   Save

The development of plants is largely dependent on their growth environment. To better adapt to a particular habitat, plants have evolved various subtle regulatory mechanisms for altering gene expression. Non coding RNAs (ncRNAs) constitute a major portion of the transcriptomes of eukaryotes. Various ncRNAs have been recognized as important regulators of the expression of genes involved in essential biological processes throughout the whole life cycles of plants. In this review, we summarize the current understanding of the biogenesis and contributions of small nucle olar RNA (snoRNA)- and regulatory long non coding RNA (lncRNA)-mediated gene regulation in plant development and environmental responses. Many regulatory ncRNAs appear to be associated with increased yield, quality and disease resistance of various species and cultivars. These ncRNAs may potentially be used as genetic resources for improving agronomic traits and for molecular breeding. The challenges in understanding plant ncRNA biology and the possibilities to make better use of these valuable gene resources in the future are discussed in this review.

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Ribonuclease H-like gene SMALL GRAIN2 regulates grain size in rice through brassinosteroid signaling pathway
Yunshuai Huang, Hui Dong, Changling Mou, Ping Wang, Qixian Hao, Min Zhang, Hongmin Wu, Fulin Zhang, Tengfei Ma, Rong Miao, Kai Fu, Yaping Chen, Ziyan Zhu, Cheng Chen, Qikai Tong, Zhuoran Wang, Shirong Zhou, Xi Liu, Shijia Liu, Yunlu Tian, Ling Jiang and Jianmin Wan
J Integr Plant Biol 2022, 64 (10): 1883-1900.  
DOI: 10.1111/jipb.13333
Abstract (Browse 284)  |   Save
Grain size is a key agronomic trait that determines the yield in plants. Regulation of grain size by brassinosteroids (BRs) in rice has been widely reported. However, the relationship between the BR signaling pathway and grain size still requires further study. Here, we isolated a rice mutant, named small grain2 (sg2), which displayed smaller grain and a semi-dwarf phenotype. The decreased grain size was caused by repressed cell expansion in spikelet hulls of the sg2 mutant. Using map-based cloning combined with a MutMap approach, we cloned SG2, which encodes a plant-specific protein with a ribonuclease H-like domain. SG2 is a positive regulator downstream of GLYCOGEN SYNTHASE KINASE2 (GSK2) in response to BR signaling, and its mutation causes insensitivity to exogenous BR treatment. Genetical and biochemical analysis showed that GSK2 interacts with and phosphorylates SG2. We further found that BRs enhance the accumulation of SG2 in the nucleus, and subcellular distribution of SG2 is regulated by GSK2 kinase activity. In addition, Oryza sativa OVATE family protein 19 (OsOFP19), a negative regulator of grain shape, interacts with SG2 and plays an antagonistic role with SG2 in controlling gene expression and grain size. Our results indicated that SG2 is a new component of GSK2-related BR signaling response and regulates grain size by interacting with OsOFP19.
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The jasmonate-induced bHLH gene SlJIG functions in terpene biosynthesis and resistance to insects and fungus
Yunyun Cao, Lun Liu, Kangsheng Ma, Wenjing Wang, Hongmei Lv, Ming Gao, Xinman Wang, Xichun Zhang, Shuxin Ren, Na Zhang and Yang‐Dong Guo
J Integr Plant Biol 2022, 64 (5): 1102-1115.  
DOI: 10.1111/jipb.13248
Abstract (Browse 284)  |   Save

Jasmonic acid (JA) is a key regulator of plant defense responses. Although the transcription factor MYC2, the master regulator of the JA signaling pathway, orchestrates a hierarchical transcriptional cascade that regulates the JA responses, only a few transcriptional regulators involved in this cascade have been described. Here, we identified the basic helix-loop-helix (bHLH) transcription factor gene in tomato (Solanum lycopersicum), METHYL JASMONATE (MeJA)-INDUCED GENE (SlJIG), the expression of which was strongly induced by MeJA treatment. Genetic and molecular biology experiments revealed that SlJIG is a direct target of MYC2. SlJIG knockout plants generated by gene editing had lower terpene contents than the wild type from the lower expression of TERPENE SYNTHASE (TPS) genes, rendering them more appealing to cotton bollworm (Helicoverpa armigera). Moreover, SlJIG knockouts exhibited weaker JA-mediated induction of TPSs, suggesting that SlJIG may participate in JA-induced terpene biosynthesis. Knocking out SlJIG also resulted in attenuated expression of JA-responsive defense genes, which may contribute to the observed lower resistance to cotton bollworm and to the fungus Botrytis cinerea. We conclude that SlJIG is a direct target of MYC2, forms a MYC2-SlJIG module, and functions in terpene biosynthesis and resistance against cotton bollworm and B. cinerea.

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Online ISSN: 1744-7909 Print ISSN: 1672-9072 CN: 11-5067/Q