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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 456)  |   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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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 407)  |   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 385)  |   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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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 375)  |   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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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 372)  |   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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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 331)  |   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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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 296)  |   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 282)  |   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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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 265)  |   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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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 258)  |   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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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 256)  |   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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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 255)  |   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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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 251)  |   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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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 247)  |   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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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 237)  |   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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HY5-HDA9 orchestrates the transcription of HsfA2 to modulate salt stress response in Arabidopsis
Jiaheng Yang, Xiao Qu, Tao Li, Yixiang Gao, Haonan Du, Lanjie Zheng, Manchun Ji, Paifeng Zhang, Yan Zhang, Jinxin Hu, Liangyu Liu, Zefu Lu, Zijian Yang, Huiyong Zhang, Jianping Yang, Yongqing Jiao, Xu Zheng
J Integr Plant Biol 2023, 65 (1): 45-63.  
doi: 10.1111/jipb.13372
Abstract (Browse 236)  |   Save
Integration of light signaling and diverse abiotic stress responses contribute to plant survival in a changing environment. Some reports have indicated that light signals contribute a plant's ability to deal with heat, cold, and stress. However, the molecular link between light signaling and the salt-response pathways remains unclear. We demonstrate here that increasing light intensity elevates the salt stress tolerance of plants. Depletion of HY5, a key component of light signaling, causes Arabidopsis thaliana to become salinity sensitive. Interestingly, the small heat shock protein (sHsp) family genes are upregulated in hy5-215 mutant plants, and HsfA2 is commonly involved in the regulation of these sHsps. We found that HY5 directly binds to the G-box motifs in the HsfA2 promoter, with the cooperation of HISTONE DEACETYLASE 9 (HDA9), to repress its expression. Furthermore, the accumulation of HDA9 and the interaction between HY5 and HDA9 are significantly enhanced by salt stress. On the contrary, high temperature triggers HY5 and HDA9 degradation, which leads to dissociation of HY5-HDA9 from the HsfA2 promoter, thereby reducing salt tolerance. Under salt and heat stress conditions, fine tuning of protein accumulation and an interaction between HY5 and HDA9 regulate HsfA2 expression. This implies that HY5, HDA9, and HsfA2 play important roles in the integration of light signaling with salt stress and heat shock response.
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Natural variation in the NAC transcription factor NONRIPENING contributes to melon fruit ripening
Jinfang Wang, Shouwei Tian, Yongtao Yu, Yi Ren, Shaogui Guo, Jie Zhang, Maoying Li, Haiying Zhang, Guoyi Gong, Min Wang and Yong Xu
J Integr Plant Biol 2022, 64 (7): 1448-1461.  
DOI: 10.1111/jipb.13278
Abstract (Browse 235)  |   Save

The NAC transcription factor NONRIPENING (NOR) is a master regulator of climacteric fruit ripening. Melon (Cucumis melo L.) has climacteric and non-climacteric fruit ripening varieties and is an ideal model to study fruit ripening. Two natural CmNAC-NOR variants, the climacteric haplotype CmNAC-NORS,N and the non-climacteric haplotype CmNAC-NORA,S, have effects on fruit ripening; however, their regulatory mechanisms have not been elucidated. Here, we report that a natural mutation in the transcriptional activation domain of CmNAC-NORS,N contributes to climacteric melon fruit ripening. CmNAC-NOR knockout in the climacteric-type melon cultivar “BYJH” completely inhibited fruit ripening, while ripening was delayed by 5–8 d in heterozygous cmnac-nor mutant fruits. CmNAC-NOR directly activated carotenoid, ethylene, and abscisic acid biosynthetic genes to promote fruit coloration and ripening. Furthermore, CmNAC-NOR mediated the transcription of the “CmNAC-NOR-CmNAC73-CmCWINV2” module to enhance flesh sweetness. The transcriptional activation activity of the climacteric haplotype CmNAC-NORS,N on these target genes was significantly higher than that of the non-climacteric haplotype CmNAC-NORA,S. Moreover, CmNAC-NORS,N complementation fully rescued the non-ripening phenotype of the tomato (Solanum lycopersicum) cr-nor mutant, while CmNAC-NORA,S did not. Our results provide insight into the molecular mechanism of climacteric and non-climacteric fruit ripening in melon.

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A cost-effective tsCUT&Tag method for profiling transcription factor binding landscape
Leiming Wu, Zi Luo, Yanni Shi, Yizhe Jiang, Ruonan Li, Xinxin Miao, Fang Yang, Qing Li, Han Zhao, Jiquan Xue, Shutu Xu, Tifu Zhang and Lin Li
J Integr Plant Biol 2022, 64 (11): 2033-2038.  
doi: 10.1111/jipb.13354
Abstract (Browse 234)  |   Save

Knowledge of the transcription factor binding landscape (TFBL) is necessary to analyze gene regulatory networks for important agronomic traits. However, a low-cost and high-throughput in vivo chromatin profiling method is still lacking in plants. Here, we developed a transient and simplified cleavage under targets and tagmentation (tsCUT&Tag) that combines transient expression of transcription factor proteins in protoplasts with a simplified CUT&Tag without nucleus extraction. Our tsCUT&Tag method provided higher data quality and signal resolution with lower sequencing depth compared with traditional ChIP-seq. Furthermore, we developed a strategy combining tsCUT&Tag with machine learning, which has great potential for profiling the TFBL across plant development.

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UBA domain protein SUF1 interacts with NatA-complex subunit NAA15 to regulate thermotolerance in Arabidopsis
Ze‐Ting Song, Xiao‐Jie Chen, Ling Luo, Feifei Yu, Jian‐Xiang Liu and Jia‐Jia Han
J Integr Plant Biol 2022, 64 (7): 1297-1302.  
doi: 10.1111/jipb.13273
Abstract (Browse 232)  |   Save
During recovery from heat stress, plants clear away the heat-stress-induced misfolded proteins through the ubiquitin-proteasome system (UPS). In the UPS, the recognition of substrate proteins by E3 ligase can be regulated by the N-terminal acetyltransferase A (NatA) complex. Here, we determined that Arabidopsis STRESS-RELATED UBIQUITIN-ASSOCIATED-DOMAIN PROTEIN FACTOR 1 (SUF1) interacts with the NatA complex core subunit NAA15 and positively regulates NAA15. The suf1 and naa15 mutants are sensitive to heat stress; the NatA substrate NSNC1 is stabilized in suf1 mutant plants during heat stress recovery. Therefore, SUF1 and its interactor NAA15 play important roles in basal thermotolerance in Arabidopsis.
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Starch phosphorylase 2 is essential for cellular carbohydrate partitioning in maize
Yao Qin, Ziyi Xiao, Hailiang Zhao, Jing Wang, Yuanru Wang and Fazhan Qiu
J Integr Plant Biol 2022, 64 (9): 1755-1769.  
DOI: 10.1111/jipb.13328
Abstract (Browse 226)  |   Save

Carbohydrate partitioning is essential for plant growth and development, and its hindrance will result in excess accumulation of carbohydrates in source tissues. Most of the related mutants in maize (Zea mays L.) display impaired whole-plant sucrose transport, but other mechanisms affecting carbohydrate partitioning have seldom been reported. Here, we characterized chlorotic leaf3 (chl3), a recessive mutation causing leaf chlorosis with starch accumulation excessively in bundle sheath chloroplasts, suggesting that chl3 is defective in carbohydrate partitioning. Positional cloning revealed that the chl3 phenotype results from a frameshift mutation in ZmPHOH, which encodes starch phosphorylase 2. Two mutants in ZmPHOH exhibited the same phenotype as chl3, and both alleles failed to complement the chl3 mutant phenotype in an allelism test. Inactivation of ZmPHOH in chl3 leaves reduced the efficiency of transitory starch conversion, resulting in increased leaf starch contents and altered carbohydrate metabolism patterns. RNA-seq revealed the transcriptional downregulation of genes related to photosynthesis and carbohydrate metabolism in chl3 leaves compared to the wild type. Our results demonstrate that transitory starch remobilization is very important for cellular carbohydrate partitioning in maize, in which ZmPHOH plays an indispensable role.

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Transcriptional regulation of fleshy fruit texture
Yanna Shi, Bai‐Jun Li, Guanqing Su, Mengxue Zhang, Donald Grierson and Kun‐Song Chen
J Integr Plant Biol 2022, 64 (9): 1649-1672.  
doi: 10.1111/jipb.13316
Abstract (Browse 225)  |   Save

Fleshy fruit texture is a critically important quality characteristic of ripe fruit. Softening is an irreversible process which operates in most fleshy fruits during ripening which, together with changes in color and taste, contributes to improvements in mouthfeel and general attractiveness. Softening results mainly from the expression of genes encoding enzymes responsible for cell wall modifications but starch degradation and high levels of flavonoids can also contribute to texture change. Some fleshy fruit undergo lignification during development and post-harvest, which negatively affects eating quality. Excessive softening can also lead to physical damage and infection, particularly during transport and storage which causes severe supply chain losses. Many transcription factors (TFs) that regulate fruit texture by controlling the expression of genes involved in cell wall and starch metabolism have been characterized. Some TFs directly regulate cell wall targets, while others act as part of a broader regulatory program governing several aspects of the ripening process. In this review, we focus on advances in our understanding of the transcriptional regulatory mechanisms governing fruit textural change during fruit development, ripening and post-harvest. Potential targets for breeding and future research directions for the control of texture and quality improvement are discussed.

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Cultivated hawthorn (Crataegus pinnatifida var. major) genome sheds light on the evolution of Maleae (apple tribe)
Ticao Zhang, Qin Qiao, Xiao Du, Xiao Zhang, Yali Hou, Xin Wei, Chao Sun, Rengang Zhang, Quanzheng Yun, M. James C. Crabbe, Yves Van de Peer and Wenxuan Dong
J Integr Plant Biol 2022, 64 (8): 1487-1501.  
doi: 10.1111/jipb.13318
Abstract (Browse 224)  |   Save

Cultivated hawthorn (Crataegus pinnatifida var. major) is an important medicinal and edible plant with a long history of use for health protection in China. Herein, we provide a de novo chromosome-level genome sequence of the hawthorn cultivar “Qiu Jinxing.” We assembled an 823.41 Mb genome encoding 40 571 genes and further anchored the 779.24 Mb sequence into 17 pseudo-chromosomes, which account for 94.64% of the assembled genome. Phylogenomic analyses revealed that cultivated hawthorn diverged from other species within the Maleae (apple tribe) at approximately 35.4 Mya. Notably, genes involved in the flavonoid and triterpenoid biosynthetic pathways have been significantly amplified in the hawthorn genome. In addition, our results indicated that the Maleae share a unique ancient tetraploidization event; however, no recent independent whole-genome duplication event was specifically detected in hawthorn. The amplification of non-specific long terminal repeat retrotransposons contributed the most to the expansion of the hawthorn genome. Furthermore, we identified two paleo-sub-genomes in extant species of Maleae and found that these two sub-genomes showed different rearrangement mechanisms. We also reconstructed the ancestral chromosomes of Rosaceae and discussed two possible paleo-polyploid origin patterns (autopolyploidization or allopolyploidization) of Maleae. Overall, our study provides an improved context for understanding the evolution of Maleae species, and this new high-quality reference genome provides a useful resource for the horticultural improvement of hawthorn.

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Rapid responses: Receptor-like kinases directly regulate the functions of membrane transport proteins in plants
Xiaopeng Li, Jingjie Zhang, Hongyong Shi, Bo Li and Jia Li
J Integr Plant Biol 2022, 64 (7): 1303-1309.  
DOI: 10.1111/jipb.13274
Abstract (Browse 224)  |   Save
Receptor-like kinases (RLKs) are a large group of plant-specific transmembrane proteins mainly acting as receptors or co-receptors of various extracellular signals. They usually turn extracellular signals into intracellular responses via altering gene expression profiles. However, recent studies confirmed that many RLKs can physically interact with diverse membrane-localized transport proteins and regulate their activities for speedy responses in limited tissues or cells. In this minireview, we highlight recent discoveries regarding how RLKs can work with membrane transport proteins collaboratively and thereby trigger cellular responses in a precise and rapid manner. It is anticipated that such regulation broadly presents in plants and more examples will be gradually revealed when in-depth analyses are conducted for the functions of RLKs.
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Rapid improvement of rice eating and cooking quality through gene editing toward glutelin as target
Yihao Yang, Ziyan Shen, Youguang Li, Chenda Xu, Han Xia, Hao Zhuang, Shengyuan Sun, Min Guo and Changjie Yan
J Integr Plant Biol 2022, 64 (10): 1860-1865.  
doi: 10.1111/jipb.13334
Abstract (Browse 223)  |   Save
Rice eating and cooking quality (ECQ) is a major concern of breeders and consumers, determining market competitiveness worldwide. Rice grain protein content (GPC) is negatively related to ECQ, making it possible to improve ECQ by manipulating GPC. However, GPC is genetically complex and sensitive to environmental conditions; therefore, little progress has been made in traditional breeding for ECQ. Here, we report that CRISPR/Cas9-mediated knockout of genes encoding the grain storage protein glutelin rapidly produced lines with downregulated GPC and improved ECQ. Our finding provides a new strategy for improving rice ECQ.
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A bZIP transcription factor (CiFD) regulates drought- and low-temperature-induced flowering by alternative splicing in citrus
Li-Xia Ye, Yan-Mei Wu, Jin-Xia Zhang, Jin-Xin Zhang, Huan Zhou, Ren-Fang Zeng, Wei-Xuan Zheng, Mei-Qi Qiu, Jing-Jing Zhou, Zong-Zhou Xie, Chun-Gen Hu and Jin-Zhi Zhang
J Integr Plant Biol 2023, 65 (3): 674-691.  
DOI: 10.1111/jipb.13390
Abstract (Browse 221)  |   Save
Drought and low temperature are two key environmental factors that induce adult citrus flowering. However, the underlying regulation mechanism is poorly understood. The bZIP transcription factor FD is a key component of the florigen activation complex (FAC) which is composed of FLOWERING LOCUS T (FT), FD, and 14-3-3 proteins. In this study, isolation and characterization of CiFD in citrus found that there was alternative splicing (AS) of CiFD, forming two different proteins (CiFDα and CiFDβ). Further investigation found that their expression patterns were similar in different tissues of citrus, but the subcellular localization and transcriptional activity were different. Overexpression of the CiFD DNA sequence (CiFD-DNA), CiFDα, or CiFDβ in tobacco and citrus showed early flowering, and CiFD-DNA transgenic plants were the earliest, followed by CiFDβ and CiFDα. Interestingly, CiFDα and CiFDβ were induced by low temperature and drought, respectively. Further analysis showed that CiFDα can form a FAC complex with CiFT, Ci14-3-3, and then bind to the citrus APETALA1 (CiAP1) promoter and promote its expression. However, CiFDβ can directly bind to the CiAP1 promoter independently of CiFT and Ci14-3-3. These results showed that CiFDβ can form a more direct and simplified pathway that is independent of the FAC complex to regulate drought-induced flowering through AS. In addition, a bHLH transcription factor (CibHLH96) binds to CiFD promoter and promotes the expression of CiFD under drought condition. Transgenic analysis found that CibHLH96 can promote flowering in transgenic tobacco. These results suggest that CiFD is involved in drought- and low-temperature-induced citrus flowering through different regulatory patterns.
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Quantitative proteomics reveals redox-based functional regulation of photosynthesis under fluctuating light in plants
Qi Chen, Yixian Xiao, Yu Ming, Rong Peng, Jiliang Hu, Hong‐Bin Wang and Hong‐Lei Jin
J Integr Plant Biol 2022, 64 (11): 2168-2186.  
doi: 10.1111/jipb.13348
Abstract (Browse 219)  |   Save

Photosynthesis involves a series of redox reactions and is the major source of reactive oxygen species in plant cells. Fluctuating light (FL) levels, which occur commonly in natural environments, affect photosynthesis; however, little is known about the specific effects of FL on the redox regulation of photosynthesis. Here, we performed global quantitative mapping of the Arabidopsis thaliana cysteine thiol redox proteome under constant light and FL conditions. We identified 8857 redox-switched thiols in 4350 proteins, and 1501 proteins that are differentially modified depending on light conditions. Notably, proteins related to photosynthesis, especially photosystem I (PSI), are operational thiol-switching hotspots. Exposure of wild-type A. thaliana to FL resulted in decreased PSI abundance, stability, and activity. Interestingly, in response to PSI photodamage, more of the PSI assembly factor PSA3 dynamically switches to the reduced state. Furthermore, the Cys199 and Cys200 sites in PSA3 are necessary for its full function. Moreover, thioredoxin m (Trx m) proteins play roles in redox switching of PSA3, and are required for PSI activity and photosynthesis. This study thus reveals a mechanism for redox-based regulation of PSI under FL, and provides insight into the dynamic acclimation of photosynthesis in a changing environment.

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Vitamin B1 THIAMIN REQUIRING1 synthase mediates the maintenance of chloroplast function by regulating sugar and fatty acid metabolism in rice
Yanshen Nie, Li Yu, Lianlian Mao, Wenxuan Zou, Xiufeng Zhang and Jie Zhao
J Integr Plant Biol 2022, 64 (8): 1575-1595.  
DOI: 10.1111/jipb.13283
Abstract (Browse 217)  |   Save

Vitamin B1 (VB1), including thiamin, thiamin monophosphate (TMP), and thiamin pyrophosphate (TPP), is an essential micronutrient for all living organisms. Nevertheless, the precise function of VB1 in rice remains unclear. Here, we described a VB1 auxotrophic mutant, chlorotic lethal seedling (cles) from the mutation of OsTH1, which displayed collapsed chloroplast membrane system and decreased pigment content. OsTH1 encoded a phosphomethylpyrimidine kinase/thiamin-phosphate pyrophosphorylase, and was expressed in various tissues, especially in seedlings, leaves, and young panicles. The VB1 content in cles was markedly reduced, despite an increase in the expression of VB1 synthesis genes. The decreased TPP content affected the tricarboxylic acid cycle, pentose phosphate pathway, and de novo fatty acid synthesis, leading to a reduction in fatty acids (C16:0 and C18:0) and sugars (sucrose and glucose) of cles. Additionally, irregular expression of chloroplast membrane synthesis genes led to membrane collapse. We also found that alternative splicing and translation allowed OsTH1 to be localized to both chloroplast and cytosol. Our study revealed that OsTH1 was an essential enzyme in VB1 biosynthesis and played crucial roles in seedling growth and development by participating in fatty acid and sugar metabolism, providing new perspectives on VB1 function in rice.

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Base editing-mediated targeted evolution of ACCase for herbicide-resistant rice mutants
Hongzhi Wang, Yuxin He, Yingying Wang, Zuren Li, Jiannan Hao, Yijiao Song, Mugui Wang and Jian‐Kang Zhu
J Integr Plant Biol 2022, 64 (11): 2029-2032.  
doi: 10.1111/jipb.13352
Abstract (Browse 211)  |   Save
Improved cytosine and adenine base editors and an efficient dual editor were applied in targeted evolution of ACETYL COA CARBOXYLASE in rice, resulting in the generation of dozens of herbicide-resistant mutations, at least three of which, W2125L, W2125Q and C2186H, have not been reported previously.
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Genome-wide binding analysis of transcription factor Rice Indeterminate 1 reveals a complex network controlling rice floral transition
Shuo Zhang, Li Deng, Lun Zhao and Changyin Wu
J Integr Plant Biol 2022, 64 (9): 1690-1705.  
DOI: 10.1111/jipb.13325
Abstract (Browse 210)  |   Save

RICE INDETERMINATE 1 (RID1) plays a critical role in controlling floral transition in rice (Oryza sativa). However, the molecular basis for this effect, particularly the target genes and regulatory specificity, remains largely unclear. Here, we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) in young leaves at the pre-floral-transition stage to identify the target genes of RID1, identifying 2,680 genes associated with RID1 binding sites genome-wide. RID1 binding peaks were highly enriched for TTTGTC, the direct binding motif of the INDETERMINATE DOMAIN protein family that includes RID1. Interestingly, CACGTG and GTGGGCCC, two previously uncharacterized indirect binding motifs, were enriched through the interactions of RID1 with the novel flowering-promoting proteins OsPIL12 and OsTCP11, respectively. Moreover, the ChIP-seq data demonstrated that RID1 bound to numerous rice heading-date genes, such as HEADING DATE 1 (HD1) and FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (OsFKF1). Notably, transcriptome sequencing (RNA-seq) analysis revealed roles of RID1 in diverse developmental pathways. Genetic analysis combined with genome-wide ChIP-seq and RNA-seq results showed that RID1 directly binds to the promoter of OsERF#136 (a repressor of rice flowering) and negatively regulates its expression. Overall, our findings provide new insights into the molecular and genetic mechanisms underlying rice floral transition and characterize OsERF#136 as a previously unrecognized direct target of RID1.

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The Phytophthora effector Avh94 manipulates host jasmonic acid signaling to promote infection
Yao Zhao, Bo Yang, Huawei Xu, Jinbin Wu, Zhiyang Xu and Yuanchao Wang
J Integr Plant Biol 2022, 64 (11): 2199-2210.  
DOI: 10.1111/jipb.13358
Abstract (Browse 205)  |   Save

The oomycete pathogen Phytophthora sojae is a causal agent of soybean root rot. Upon colonization of soybeans, P. sojae secretes various RXLR effectors to suppress host immune responses, supporting successful infection. Previous research has demonstrated that the RXLR effector Avh94 functions as a virulence effector, but the molecular mechanism underlying its role in virulence remains unknown. Here, we demonstrate that Avh94 overexpression in plants and pathogens promotes Phytophthora infection. Avh94 interacts with soybean JAZ1/2, which is a repressor of jasmonic acid (JA) signaling. Avh94 stabilizes JAZ1/2 to inhibit JA signaling and silencing of JAZ1/2 enhances soybean resistance against P. sojae. Moreover, P. sojae lines overexpressing Avh94 inhibit JA signaling. Furthermore, exogenous application of methyl jasmonate improves plant resistance to Phytophthora. Taken together, these findings suggest that P. sojae employs an RXLR effector to hijack JA signaling and thereby promote infection.

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DEAP1 encodes a fasciclin-like arabinogalactan protein required for male fertility in rice
Dan Zhou, Ting Zou, Kaixuan Zhang, Pingping Xiong, Fuxing Zhou, Hao Chen, Gongwen Li, Kaiyou Zheng, Yuhao Han, Kun Peng, Xu Zhang, Shangyu Yang, Qiming Deng, Shiquan Wang, Jun Zhu, Yueyang Liang, Changhui Sun, Xiumei Yu, Huainian Liu, Lingxia Wang, Ping Li and Shuangcheng Li
J Integr Plant Biol 2022, 64 (7): 1430-1447.  
DOI: 10.1111/jipb.13271
Abstract (Browse 205)  |   Save

Arabinogalactan proteins (AGPs) are widely distributed in plant cells. Fasciclin-like AGPs (FLAs) belong to a subclass of AGPs that play important roles in plant growth and development. However, little is known about the biological functions of rice FLA. Herein, we report the identification of a male-sterile mutant of DEFECTIVE EXINE AND APERTURE PATTERNING1 (DEAP1) in rice. The deap1 mutant anthers produced aberrant pollen grains with defective exine formation and a flattened aperture annulus and exhibited slightly delayed tapetum degradation. DEAP1 encodes a plasma membrane-associated member of group III plant FLAs and is specifically and temporally expressed in reproductive cells and the tapetum layer during male development. Gene expression studies revealed reduced transcript accumulation of genes related to exine formation, aperture patterning, and tapetum development in deap1 mutants. Moreover, DEAP1 may interact with two rice D6 PROTEIN KINASE-LIKE3s (OsD6PKL3s), homologs of a known Arabidopsis aperture protein, to affect rice pollen aperture development. Our findings suggested that DEAP1 is involved in male reproductive development and may affect exine formation and aperture patterning, thereby providing new insights into the molecular functions of plant FLAs in male fertility.

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Arabidopsis ROOT ELONGATION RECEPTOR KINASES negatively regulate root growth putatively via altering cell wall remodeling gene expression
Yanze Wang, Weiyue Chen, Yang Ou, Yingying Zhu and Jia Li
J Integr Plant Biol 2022, 64 (8): 1502-1513.  
DOI: 10.1111/jipb.13282
Abstract (Browse 203)  |   Save

Receptor-like kinases (RLKs) play key roles in regulating various physiological aspects in plant growth and development. In Arabidopsis thaliana, there are at least 223 leucine-rich repeat (LRR) RLKs. The functions of the majority of RLKs in the LRR XI subfamily were previously revealed. Only three RLKs were not characterized. Here we report that two independent triple mutants of these RLKs, named ROOT ELONGATION RECEPTOR KINASES (REKs), exhibit increased cell numbers in the root apical meristem and enhanced cell size in the elongation and maturation zones. The promoter activities of a number of Quiescent Center marker genes are significantly up-regulated in the triple mutant. However, the promoter activities of several marker genes known to control root stem cell niche activities are not altered. RNA-seq analysis revealed that a number of cell wall remodeling genes are significantly up-regulated in the triple mutant. Our results suggest that these REKs play key roles in regulating root development likely via negatively regulating the expression of a number of key cell wall remodeling genes.

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The NAC transcription factor ONAC083 negatively regulates rice immunity against Magnaporthe oryzae by directly activating transcription of the RING-H2 gene OsRFPH2-6
Yan Bi, Hui Wang, Xi Yuan, Yuqing Yan, Dayong Li and Fengming Song
J Integr Plant Biol 2023, 65 (3): 854-875.  
DOI: 10.1111/jipb.13399
Abstract (Browse 199)  |   Save
NAC transcription factors (TFs) play critical roles in plant immunity by modulating the expression of downstream genes via binding to specific cis-elements in promoters. Here, we report the function and regulatory network of a pathogen- and defense phytohormone-inducible NAC TF gene, ONAC083, in rice (Oryza sativa) immunity. ONAC083 localizes to the nucleus and exhibits transcriptional activation activity that depends on its C-terminal region. Knockout of ONAC083 enhances rice immunity against Magnaporthe oryzae, strengthening pathogen-induced defense responses, and boosting chitin-induced pattern-triggered immunity (PTI), whereas ONAC083 overexpression has opposite effects. We identified ONAC083-binding sites in the promoters of 82 genes, and showed that ONAC083 specifically binds to a conserved element with the core sequence ACGCAA. ONAC083 activated the transcription of the genes OsRFPH2-6, OsTrx1, and OsPUP4 by directly binding to the ACGCAA element. OsRFPH2-6, encoding a RING-H2 protein with an N-terminal transmembrane region and a C-terminal typical RING domain, negatively regulated rice immunity against M. oryzae and chitin-triggered PTI. These data demonstrate that ONAC083 negatively contributes to rice immunity against M. oryzae by directly activating the transcription of OsRFPH2-6 through the ACGCAA element in its promoter. Overall, our study provides new insight into the molecular regulatory network of NAC TFs in rice immunity.
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Brassinosteroid signaling positively regulates abscisic acid biosynthesis in response to chilling stress in tomato
Shengmin An, Yue Liu, Kangqi Sang, Ting Wang, Jingquan Yu, Yanhong Zhou, Xiaojian Xia
J Integr Plant Biol 2023, 65 (1): 10-24.  
doi: 10.1111/jipb.13356
Abstract (Browse 198)  |   Save
Brassinosteroids (BRs) and abscisic acid (ABA) are essential regulators of plant growth and stress tolerance. Although the antagonistic interaction of BRs and ABA is proposed to ensure the balance between growth and defense in model plants, the crosstalk between BRs and ABA in response to chilling in tomato (Solanum lycopersicum), a warm-climate horticultural crop, is unclear. Here, we determined that overexpression of the BR biosynthesis gene DWARF (DWF) or the key BR signaling gene BRASSINAZOLE-RESISTANT1 (BZR1) increases ABA levels in response to chilling stress via positively regulating the expression of the ABA biosynthesis gene 9-CIS-EPOXYCAROTENOID DIOXYGENASE1 (NCED1). BR-induced chilling tolerance was mostly dependent on ABA biosynthesis. Chilling stress or high BR levels decreased the abundance of BRASSINOSTEROID-INSENSITIVE2 (BIN2), a negative regulator of BR signaling. Moreover, we observed that chilling stress increases BR levels and results in the accumulation of BZR1. BIN2 negatively regulated both the accumulation of BZR1 protein and chilling tolerance by suppressing ABA biosynthesis. Our results demonstrate that BR signaling positively regulates chilling tolerance via ABA biosynthesis in tomato. The study has implications in production of warm-climate crops in horticulture.
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CHH methylation of genes associated with fatty acid and jasmonate biosynthesis contributes to cold tolerance in autotetraploids of Poncirus trifoliata
Yue Wang, Lanlan Zuo, Tonglu Wei, Yu Zhang, Yang Zhang, Ruhong Ming, Daharo Bachar, Wei Xiao, Khan Madiha, Chuanwu Chen, Qijun Fan, Chunlong Li, Ji-Hong Liu
J Integr Plant Biol 2022, 64 (12): 2327-2343.  
doi: 10.1111/jipb.13379
Abstract (Browse 198)  |   Save

Polyploids have elevated stress tolerance, but the underlying mechanisms remain largely elusive. In this study, we showed that naturally occurring tetraploid plants of trifoliate orange (Poncirus trifoliata (L.) Raf.) exhibited enhanced cold tolerance relative to their diploid progenitors. Transcriptome analysis revealed that whole-genome duplication was associated with higher expression levels of a range of well-characterized cold stress-responsive genes. Global DNA methylation profiling demonstrated that the tetraploids underwent more extensive DNA demethylation in comparison with the diploids under cold stress. CHH methylation in the promoters was associated with up-regulation of related genes, whereas CG, CHG, and CHH methylation in the 3'-regions was relevant to gene down-regulation. Of note, genes involved in unsaturated fatty acids (UFAs) and jasmonate (JA) biosynthesis in the tetraploids displayed different CHH methylation in the gene flanking regions and were prominently up-regulated, consistent with greater accumulation of UFAs and JA when exposed to the cold stress. Collectively, our findings explored the difference in cold stress response between diploids and tetraploids at both transcriptional and epigenetic levels, and gained new insight into the molecular mechanisms underlying enhanced cold tolerance of the tetraploid. These results contribute to uncovering a novel regulatory role of DNA methylation in better cold tolerance of polyploids.

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Making small molecules in plants: A chassis for synthetic biology-based production of plant natural products
Xinyu Liu, Peijun Zhang, Qiao Zhao and Ancheng C. Huang
J Integr Plant Biol 2023, 65 (2): 417-443.  
doi: 10.1111/jipb.13330
Abstract (Browse 194)  |   Save
Plant natural products have been extensively exploited in food, medicine, flavor, cosmetic, renewable fuel, and other industrial sectors. Synthetic biology has recently emerged as a promising means for the cost-effective and sustainable production of natural products. Compared with engineering microbes for the production of plant natural products, the potential of plants as chassis for producing these compounds is underestimated, largely due to challenges encountered in engineering plants. Knowledge in plant engineering is instrumental for enabling the effective and efficient production of valuable phytochemicals in plants, and also paves the way for a more sustainable future agriculture. In this manuscript, we briefly recap the biosynthesis of plant natural products, focusing primarily on industrially important terpenoids, alkaloids, and phenylpropanoids. We further summarize the plant hosts and strategies that have been used to engineer the production of natural products. The challenges and opportunities of using plant synthetic biology to achieve rapid and scalable production of high-value plant natural products are also discussed.
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SICKLE represses photomorphogenic development of Arabidopsis seedlings via HY5- and PIF4-mediated signaling
Tao Li, Haojie Li, Hongmei Lian, Pengyu Song, Yulong Wang, Jie Duan, Zhaoqing Song, Yan Cao, Dongqing Xu, Jigang Li and Huiyong Zhang
J Integr Plant Biol 2022, 64 (9): 1706-1723.  
doi: 10.1111/jipb.13329
Abstract (Browse 191)  |   Save

Arabidopsis CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1) and PHYTOCHROME INTERACTING FACTORs (PIFs) are negative regulators, and ELONGATED HYPOCOTYL5 (HY5) is a positive regulator of seedling photomorphogenic development. Here, we report that SICKLE (SIC), a proline rich protein, acts as a novel negative regulator of photomorphogenesis. HY5 directly binds the SIC promoter and activates SIC expression in response to light. In turn, SIC physically interacts with HY5 and interferes with its transcriptional regulation of downstream target genes. Moreover, SIC interacts with PIF4 and promotes PIF4-activated transcription of itself. Interestingly, SIC is targeted by COP1 for 26S proteasome-mediated degradation in the dark. Collectively, our data demonstrate that light-induced SIC functions as a brake to prevent exaggerated light response via mediating HY5 and PIF4 signaling, and its degradation by COP1 in the dark avoid too strong inhibition on photomorphogenesis at the beginning of light exposure.

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TGA factors promote plant root growth by modulating redox homeostasis or response
Xiaochen Hu, Liyun Yang, Mengfei Ren, Lin Liu, Jing Fu and Hongchang Cui
J Integr Plant Biol 2022, 64 (8): 1543-1559.  
DOI: 10.1111/jipb.13310
Abstract (Browse 187)  |   Save

To identify novel regulators of stem cell renewal, we mined an existing but little explored cell type-specific transcriptome dataset for the Arabidopsis root. A member of the TGA family of transcription factors, TGA8, was found to be specifically expressed in the quiescent center (QC). Mutation in TGA8 caused a subtle root growth phenotype, suggesting functional redundancy with other TGA members. Using a promoter::HGFP transgenic approach, we showed that all TGA factors were expressed in the root, albeit at different levels and with distinct spatial patterns. Mutant analyses revealed that all TGA factors examined contribute to root growth by promoting stem cell renewal, meristem activity, and cell elongation. Combining transcriptome analyses, histochemical assays, and physiological tests, we demonstrated that functional redundancy exists among members of clades II and V or those in clades I and III. These two groups of TGA factors act differently, however, as their mutants responded to oxidative stress differently and quantitative reverse transcription polymerase chain reaction assays showed they regulate different sets of genes that are involved in redox homeostasis. Our study has thus uncovered a previously unrecognized broad role and a mechanistic explanation for TGA factors in root growth and development.

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Structural insight into chitin perception by chitin elicitor receptor kinase 1 of Oryza sativa
Li Xu, Jizong Wang, Yu Xiao, Zhifu Han, Jijie Chai
J Integr Plant Biol 2023, 65 (1): 235-248.  
DOI: 10.1111/jipb.13279
Abstract (Browse 187)  |   Save
Plants have developed innate immune systems to fight against pathogenic fungi by monitoring pathogenic signals known as pathogen-associated molecular patterns (PAMP) and have established endo symbiosis with arbuscular mycorrhizal (AM) fungi through recognition of mycorrhizal (Myc) factors. Chitin elicitor receptor kinase 1 of Oryza sativa subsp. Japonica (OsCERK1) plays a bifunctional role in mediating both chitin-triggered immunity and symbiotic relationships with AM fungi. However, it remains unclear whether OsCERK1 can directly recognize chitin molecules. In this study, we show that OsCERK1 binds to the chitin hexamer ((NAG)6) and tetramer ((NAG)4) directly and determine the crystal structure of the OsCERK1-(NAG)6 complex at 2??. The structure shows that one OsCERK1 is associated with one (NAG)6. Upon recognition, chitin hexamer binds OsCERK1 by interacting with the shallow groove on the surface of LysM2. These structural findings, complemented by mutational analyses, demonstrate that LysM2 is crucial for recognition of both (NAG)6 and (NAG)4. Altogether, these findings provide structural insights into the ability of OsCERK1 in chitin perception, which will lead to a better understanding of the role of OsCERK1 in mediating both immunity and symbiosis in rice.
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EXPLICIT-Kinase: A gene expression predictor for dissecting the functions of the Arabidopsis kinome
Yuming Peng, Wanzhu Zuo, Hui Zhou, Fenfen Miao, Yu Zhang, Yue Qin, Yi Liu, Yu Long and Shisong Ma
J Integr Plant Biol 2022, 64 (7): 1374-1393.  
DOI: 10.1111/jipb.13267
Abstract (Browse 186)  |   Save

Protein kinases regulate virtually all cellular processes, but it remains challenging to determine the functions of all protein kinases, collectively called the “kinome”, in any species. We developed a computational approach called EXPLICIT-Kinase to predict the functions of the Arabidopsis kinome. Because the activities of many kinases can be regulated transcriptionally, their gene expression patterns provide clues to their functions. A universal gene expression predictor for Arabidopsis was constructed to predict the expression of 30,172 non-kinase genes based on the expression of 994 kinases. The model reconstituted highly accurate transcriptomes for diverse Arabidopsis samples. It identified the significant kinases as predictor kinases for predicting the expression of Arabidopsis genes and pathways. Strikingly, these predictor kinases were often regulators of related pathways, as exemplified by those involved in cytokinesis, tissue development, and stress responses. Comparative analyses revealed that portions of these predictor kinases are shared and conserved between Arabidopsis and maize. As an example, we identified a conserved predictor kinase, RAF6, from a stomatal movement module. We verified that RAF6 regulates stomatal closure. It can directly interact with SLAC1, a key anion channel for stomatal closure, and modulate its channel activity. Our approach enables a systematic dissection of the functions of the Arabidopsis kinome.

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