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The transcriptional control of LcIDL1–LcHSL2 complex by LcARF5 integrates auxin and ethylene signaling for litchi fruitlet abscission
Xingshuai Ma, Zidi He, Ye Yuan, Zhijian Liang, Hang Zhang, Vilde Olsson Lalun, Zhuoyi Liu, Yanqing Zhang, Zhiqiang Huang, Yulian Huang, Jianguo Li and Minglei Zhao
doi:
10.1111/jipb.13646
Version of Record online: 22 March 2024
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A converged ubiquitin‐proteasome pathway for the degradation of TOC and TOM tail‐anchored receptors
Meijing Yang, Shuai Chen, Shey‐Li Lim, Lang Yang, Jia Yi Zhong, Koon Chuen Chan, Zhizhu Zhao, Kam‐Bo Wong, Junqi Wang and Boon Leong Lim
doi:
10.1111/jipb.13645
Version of Record online: 19 March 2024
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ACBP4‐WRKY70‐R
AP2.12
module positively regulates submergence‐induced hypoxia response in
Arabidopsis thaliana
Mengyun Guo, Yingjun Yao, Kangqun Yin, Luna Tan, Meng Liu, Jing Hou, Han Zhang, Ruyun Liang, Xinran Zhang, Heng Yang, Xiaoxiao Chen, Jinrui Tan, Yan Song, Shangling Lou, Liyang Chen, Xuejing Liu, Si Tang, Yongqi Hu, Jin Yan, Wensen Fu, Kai Yang, Ruijia Zhang, Xuerui Li, Yao Liu, Zhen Yan, Wei Liu, Yu Han, Jianquan Liu, Kangshan Mao and Huanhuan Liu
doi:
10.1111/jipb.13647
Version of Record online: 19 March 2024
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Potassium transporter OsHAK9 regulates seed germination under salt stress by preventing gibberellin degradation through mediating
OsGA2ox7
in rice
Peng Zeng, Ting Xie, Jiaxin Shen, Taokai Liang, Lu Yin, Kexin Liu, Ying He, Mingming Chen, Haijuan Tang, Sunlu Chen, Sergey Shabala, Hongsheng Zhang and Jinping Cheng
doi:
10.1111/jipb.13642
Version of Record online: 14 March 2024
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The RING zinc finger protein LbRZF1 promotes salt gland development and salt tolerance in
Limonium bicolor
Zongran Yang, Ziwei Zhang, Ziqi Qiao, Xueying Guo, Yixuan Wen, Yingxue Zhou, Chunliang Yao, Hai Fan, Baoshan Wang and Guoliang Han
doi:
10.1111/jipb.13641
Version of Record online: 13 March 2024
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Expansion and improvement of ChinaMu by MuT-seq and chromosome-level assembly of the
Mu
-starter genome
Lei Liang, Yuancong Wang, Yanbin Han, Yicong Chen, Mengfei Li, Yibo Wu, Zeyang Ma, Han Zhao and Rentao Song
doi:
10.1111/jipb.13637
Version of Record online: 07 March 2024
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SlBEL11 regulates flavonoid biosynthesis, thus fine-tuning auxin efflux to prevent premature fruit drop in tomato
Xiufen Dong, Xianfeng Liu, Lina Cheng, Ruizhen Li, Siqi Ge, Sai Wang, Yue Cai, Yang Liu, Sida Meng, Cai-Zhong Jiang, Chun-Lin Shi, Tianlai Li, Daqi Fu8, Mingfang Qi and Tao Xu
doi:
10.1111/jipb.13627
Version of Record online: 29 February 2024
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Structural insights into the unusual core photocomplex from a triply extremophilic purple bacterium,
Halorhodospira halochloris
Chen-Hui Qi, Guang-Lei Wang, Fang-Fang Wang, Jie Wang, Xiang-Ping Wang, Mei-Juan Zou, Fei Ma, Michael T. Madigan, Yukihiro Kimura, Zheng-Yu Wang-Otomo and Long-Jiang Yu
doi:
10.1111/jipb.13628
Version of Record online: 27 February 2024
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Genomic analysis of
Nypa fruticans
elucidates its intertidal adaptations and early palm evolution
Weihong Wu, Xiao Feng, Nan Wang, Shao Shao, Min Liu, Fa Si, Linhao Chen, Chuanfeng Jin, Shaohua Xu, Zixiao Guo, Cairong Zhong, Suhua Shi and Ziwen He
doi:
10.1111/jipb.13625
Version of Record online: 19 February 2024
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An alfalfa MYB-like transcriptional factor MsMYBH positively regulates alfalfa seedling drought resistance and undergoes MsWAV3-mediated degradation
Kun Shi, Jia Liu, Huan Liang, Hongbin Dong, Jinli Zhang, Yuanhong Wei, Le Zhou, Shaopeng Wang, Jiahao Zhu, Mingshu Cao, Chris S. Jones, Dongmei Ma and Zan Wang
doi:
10.1111/jipb.13626
Version of Record online: 15 February 2024
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CRISPR/CasΦ2-mediated gene editing in wheat and rye
Sanzeng Zhao, Xueying Han, Yachen Zhu, Yuwei Han, Huiyun Liu, Zhen Chen, Huifang Li, Dan Wang, Chaofan Tian, Yuting Yuan, Yajie Guo, Xiaomin Si, Daowen Wang and Xiang Ji
doi:
10.1111/jipb.13624
Version of Record online: 13 February 2024
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Breeding maize of ideal plant architecture for high-density planting tolerance through modulating shade avoidance response and beyond
Fereshteh Jafari, Baobao Wang, Haiyang Wang and Junjie Zou
doi:
10.1111/jipb.13603
Version of Record online: 29 January 2024
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Chromosomal-level genome and metabolome analyses of highly heterozygous allohexaploid
Dendrocalamus brandisii
elucidate shoot quality and developmental characteristics
Jutang Jiang, Zeyu Zhang, Yucong Bai, Xiaojing Wang, Yuping Dou, Ruiman Geng, Chongyang Wu, Hangxiao Zhang, Cunfu Lu, Lianfeng Gu and Jian Gao
doi:
10.1111/jipb.13592
Version of Record online: 12 January 2024
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The dual‐action mechanism of Arabidopsis cryptochromes
Gao‐Ping Qu, Bochen Jiang and Chentao Lin
doi:
10.1111/jipb.13578
Version of Record online: 02 January 2024
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Phase separation of S‐RNase promotes self‐incompatibility in
Petunia hybrida
Huayang Tian, Hongkui Zhang, Huaqiu Huang, Yu'e Zhang and Yongbiao Xue
doi:
10.1111/jipb.13584
Version of Record online: 02 January 2024
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Plant virology in the 21st century in China: Recent advances and future directions
Jianguo Wu, Yongliang Zhang, Fangfang Li, Xiaoming Zhang, Jian Ye, Taiyun Wei, Zhenghe Li, Xiaorong Tao, Feng Cui, Xianbing Wang, Lili Zhang, Fei Yan, Shifang Li, Yule Liu, Dawei Li, Xueping Zhou and Yi Li
J Integr Plant Biol 2024, 66 (3): 579-622.
doi:
10.1111/jipb.13580
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Plant viruses are a group of intracellular pathogens that persistently threaten global food security. Significant advances in plant virology have been achieved by Chinese scientists over the last 20 years, including basic research and technologies for preventing and controlling plant viral diseases. Here, we review these milestones and advances, including the identification of new crop-infecting viruses, dissection of pathogenic mechanisms of multiple viruses, examination of multilayered interactions among viruses, their host plants, and virus-transmitting arthropod vectors, and in-depth interrogation of plant-encoded resistance and susceptibility determinants. Notably, various plant virus-based vectors have also been successfully developed for gene function studies and target gene expression in plants. We also recommend future plant virology studies in China.
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Wood of trees: Cellular structure, molecular formation, and genetic engineering
Yingying Zhu and Laigeng Li
J Integr Plant Biol 2024, 66 (3): 443-467.
doi:
10.1111/jipb.13589
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Wood is an invaluable asset to human society due to its renewable nature, making it suitable for both sustainable energy production and material manufacturing. Additionally, wood derived from forest trees plays a crucial role in sequestering a significant portion of the carbon dioxide fixed during photosynthesis by terrestrial plants. Nevertheless, with the expansion of the global population and ongoing industrialization, forest coverage has been substantially decreased, resulting in significant challenges for wood production and supply. Wood production practices have changed away from natural forests toward plantation forests. Thus, understanding the underlying genetic mechanisms of wood formation is the foundation for developing high-quality, fast-growing plantation trees. Breeding ideal forest trees for wood production using genetic technologies has attracted the interest of many. Tremendous studies have been carried out in recent years on the molecular, genetic, and cell-biological mechanisms of wood formation, and considerable progress and findings have been achieved. These studies and findings indicate enormous possibilities and prospects for tree improvement. This review will outline and assess the cellular and molecular mechanisms of wood formation, as well as studies on genetically improving forest trees, and address future development prospects.
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A historical review of hybrid rice breeding
Xiaoming Zheng, Fei Wei, Cheng Cheng and Qian Qian
J Integr Plant Biol 2024, 66 (3): 532-545.
doi:
10.1111/jipb.13598
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The development of germplasm resources and advances in breeding methods have led to steady increases in yield and quality of rice (
Oryza sativa
L.). Three milestones in the recent history of rice breeding have contributed to these increases: dwarf rice breeding, hybrid rice breeding, and super rice breeding. On the 50th anniversary of the success of three-line hybrid rice, we highlight important scientific discoveries in rice breeding that were made by Chinese scientists and summarize the broader history of the field. We discuss the strategies that could be used in the future to optimize rice breeding further in the hope that China will continue to play a leading role in international rice breeding.
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Reactive oxygen species: Multidimensional regulators of plant adaptation to abiotic stress and development
Pengtao Wang, Wen‐Cheng Liu, Chao Han, Situ Wang, Ming‐Yi Bai and Chun‐Peng Song
J Integr Plant Biol 2024, 66 (3): 330-367.
doi:
10.1111/jipb.13601
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Reactive oxygen species (ROS) are produced as undesirable by-products of metabolism in various cellular compartments, especially in response to unfavorable environmental conditions, throughout the life cycle of plants. Stress-induced ROS production disrupts normal cellular function and leads to oxidative damage. To cope with excessive ROS, plants are equipped with a sophisticated antioxidative defense system consisting of enzymatic and non-enzymatic components that scavenge ROS or inhibit their harmful effects on biomolecules. Nonetheless, when maintained at relatively low levels, ROS act as signaling molecules that regulate plant growth, development, and adaptation to adverse conditions. Here, we provide an overview of current approaches for detecting ROS. We also discuss recent advances in understanding ROS signaling, ROS metabolism, and the roles of ROS in plant growth and responses to various abiotic stresses.
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Nuclear phylogenomics of angiosperms and insights into their relationships and evolution
Guojin Zhang and Hong Ma
J Integr Plant Biol 2024, 66 (3): 546-578.
doi:
10.1111/jipb.13609
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Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the “abominable mystery,” hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of
Amborella
,
Nymphaea
,
Chloranthus
,
Ceratophyllum
, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.
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A centromere map based on super pan-genome highlights the structure and function of rice centromeres
Yang Lv, Congcong Liu, Xiaoxia Li, Yueying Wang, Huiying He, Wenchuang He, Wu Chen, Longbo Yang, Xiaofan Dai, Xinglan Cao, Xiaoman Yu, Jiajia Liu, Bin Zhang, Hua Wei, Hong Zhang, Hongge Qian, Chuanlin Shi, Yue Leng, Xiangpei Liu, Mingliang Guo, Xianmeng Wang, Zhipeng Zhang, Tianyi Wang, Bintao Zhang, Qiang Xu, Yan Cui, Qianqian Zhang, Qiaoling Yuan, Noushin Jahan, Jie Ma, Xiaoming Zheng, Yongfeng Zhou, Qian Qian, Longbiao Guo and Lianguang Shang
J Integr Plant Biol 2024, 66 (2): 196-207.
doi:
10.1111/jipb.13607
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Rice (
Oryza sativa
) is a significant crop worldwide with a genome shaped by various evolutionary factors. Rice centromeres are crucial for chromosome segregation, and contain some unreported genes. Due to the diverse and complex centromere region, a comprehensive understanding of rice centromere structure and function at the population level is needed. We constructed a high-quality centromere map based on the rice super pan-genome consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice. We showed that rice centromeres have diverse satellite repeat CentO, which vary across chromosomes and subpopulations, reflecting their distinct evolutionary patterns. We also revealed that long terminal repeats (LTRs), especially young Gypsy-type LTRs, are abundant in the peripheral CentO-enriched regions and drive rice centromere expansion and evolution. Furthermore, high-quality genome assembly and complete telomere-to-telomere (T2T) reference genome enable us to obtain more centromeric genome information despite mapping and cloning of centromere genes being challenging. We investigated the association between structural variations and gene expression in the rice centromere. A centromere gene,
OsMAB
, which positively regulates rice tiller number, was further confirmed by expression quantitative trait loci, haplotype analysis and clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 methods. By revealing the new insights into the evolutionary patterns and biological roles of rice centromeres, our finding will facilitate future research on centromere biology and crop improvement.
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Angiosperm-wide analysis of fruit and ovary evolution aided by a new nuclear phylogeny supports association of the same ovary type with both dry and fleshy fruits
Yezi Xiang, Taikui Zhang, Yiyong Zhao, Hongjin Dong, Hongyi Chen, Yi Hu, Chien‐Hsun Huang, Jun Xiang and Hong Ma
J Integr Plant Biol 2024, 66 (2): 228-251.
doi:
10.1111/jipb.13618
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21
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Fruit functions in seed protection and dispersal and belongs to many dry and fleshy types, yet their evolutionary pattern remains unclear in part due to uncertainties in the phylogenetic relationships among several orders and families. Thus we used nuclear genes of 502 angiosperm species representing 231 families to reconstruct a well supported phylogeny, with resolved relationships for orders and families with previously uncertain placements. Using this phylogeny as a framework, molecular dating supports a Triassic origin of the crown angiosperms, followed by the emergence of most orders in the Jurassic and Cretaceous and their rise to ecological dominance during the Cretaceous Terrestrial Revolution. The robust phylogeny allowed an examination of the evolutionary pattern of fruit and ovary types, revealing a trend of parallel carpel fusions during early diversifications in eudicots, monocots, and magnoliids. Moreover, taxa in the same order or family with the same ovary type can develop either dry or fleshy fruits with strong correlations between specific types of dry and fleshy fruits; such associations of ovary, dry and fleshy fruits define several ovary-fruit “modules” each found in multiple families. One of the frequent modules has an ovary containing multiple ovules, capsules and berries, and another with an ovary having one or two ovules, achenes (or other single-seeded dry fruits) and drupes. This new perspective of relationships among fruit types highlights the closeness of specific dry and fleshy fruit types, such as capsule and berry, that develop from the same ovary type and belong to the same module relative to dry and fleshy fruits of other modules (such as achenes and drupes). Further analyses of gene families containing known genes for ovary and fruit development identified phylogenetic nodes with multiple gene duplications, supporting a possible role of whole-genome duplications, in combination with climate changes and animal behaviors, in angiosperm fruit and ovary diversification.
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Increased long-distance and homo-trans interactions related to H3K27me3 in
Arabidopsis
hybrids
Zhaoxu Gao, Yanning Su, Le Chang, Guanzhong Jiao, Yang Ou, Mei Yang, Chao Xu, Pengtao Liu, Zejia Wang, Zewen Qi, Wenwen Liu, Linhua Sun, Guangming He, Xing Wang Deng and Hang He
J Integr Plant Biol 2024, 66 (2): 208-227.
doi:
10.1111/jipb.13620
Abstract
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In plants, the genome structure of hybrids changes compared with their parents, but the effects of these changes in hybrids remain elusive. Comparing reciprocal crosses between Col×C24 and C24×Col in
Arabidopsis
using high-throughput chromosome conformation capture assay (Hi-C) analysis, we found that hybrid three-dimensional (3D) chromatin organization had more long-distance interactions relative to parents, and this was mainly located in promoter regions and enriched in genes with heterosis-related pathways. The interactions between euchromatin and heterochromatin were increased, and the compartment strength decreased in hybrids. In compartment domain (CD) boundaries, the distal interactions were more in hybrids than their parents. In the hybrids of
CURLY LEAF
(
clf
) mutants
clf
Col
×
clf
C24
and
clf
C24
×
clf
Col
, the heterosis phenotype was damaged, and the long-distance interactions in hybrids were fewer than in their parents with lower H3K27me3. ChIP-seq data revealed higher levels of H3K27me3 in the region adjacent to the CD boundary and the same interactional homo-trans sites in the wild-type (WT) hybrids, which may have led to more long-distance interactions. In addition, the differentially expressed genes (DEGs) located in the boundaries of CDs and loop regions changed obviously in WT, and the functional enrichment for DEGs was different between WT and
clf
in the long-distance interactions and loop regions. Our findings may therefore propose a new epigenetic explanation of heterosis in the
Arabidopsis
hybrids and provide new insights into crop breeding and yield increase.
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The Ti-TAN plasmid toolbox for TurboID-based proximity labeling assays in
Nicotiana benthamiana
Huang Tan, Yu Zhou, Erik Dinius and Rosa Lozano‐Durán
J Integr Plant Biol 2024, 66 (2): 166-168.
doi:
10.1111/jipb.13610
Abstract
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IbNIEL-mediated degradation of IbNAC087 regulates jasmonic acid-dependent salt and drought tolerance in sweet potato
Xu Li, Zhen Wang, Sifan Sun, Zhuoru Dai, Jun Zhang, Wenbin Wang, Kui Peng, Wenhao Geng, Shuanghong Xia, Qingchang Liu, Hong Zhai, Shaopei Gao, Ning Zhao, Feng Tian, Huan Zhang and Shaozhen He
J Integr Plant Biol 2024, 66 (2): 176-195.
doi:
10.1111/jipb.13612
Abstract
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) |
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Sweet potato (
Ipomoea batatas
[L.] Lam.) is a crucial staple and bioenergy crop. Its abiotic stress tolerance holds significant importance in fully utilizing marginal lands. Transcriptional processes regulate abiotic stress responses, yet the molecular regulatory mechanisms in sweet potato remain unclear. In this study, a NAC (NAM, ATAF1/2, and CUC2) transcription factor,
IbNAC087
, was identified, which is commonly upregulated in salt- and drought-tolerant germplasms. Overexpression of
IbNAC087
increased salt and drought tolerance by increasing jasmonic acid (JA) accumulation and activating reactive oxygen species (ROS) scavenging, whereas silencing this gene resulted in opposite phenotypes. JA-rich
IbNAC087
-OE (overexpression) plants exhibited more stomatal closure than wild-type (WT) and
IbNAC087
-Ri plants under NaCl, polyethylene glycol, and methyl jasmonate treatments. IbNAC087 functions as a nuclear transcriptional activator and directly activates the expression of the key JA biosynthesis-related genes
lipoxygenase
(
IbLOX
) and
allene oxide synthase
(
IbAOS
). Moreover, IbNAC087 physically interacted with a RING-type E3 ubiquitin ligase NAC087-INTERACTING E3 LIGASE (IbNIEL), negatively regulating salt and drought tolerance in sweet potato. IbNIEL ubiquitinated IbNAC087 to promote 26S proteasome degradation, which weakened its activation on
IbLOX
and
IbAOS
. The findings provide insights into the mechanism underlying the IbNIEL-IbNAC087 module regulation of JA-dependent salt and drought response in sweet potato and provide candidate genes for improving abiotic stress tolerance in crops.
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Post-transcriptional regulation of grain weight and shape by the RBP-A-J-K complex in rice
Ding Ren, Hui Liu, Xuejun Sun, Fan Zhang, Ling Jiang, Ying Wang, Ning Jiang, Peiwen Yan, Jinhao Cui, Jinshui Yang, Zhikang Li, Pingli Lu and Xiaojin Luo
J Integr Plant Biol 2024, 66 (1): 66-85.
doi:
10.1111/jipb.13583
Abstract
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124
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RNA-binding proteins (RBPs) are components of the post-transcriptional regulatory system, but their regulatory effects on complex traits remain unknown. Using an integrated strategy involving map-based cloning, functional characterizations, and transcriptomic and population genomic analyses, we revealed that
RBP-K
(
LOC
_
Os08g23120
),
RBP-A
(
LOC
_
Os11g41890
), and
RBP-J
(
LOC
_
Os10g33230
) encode proteins that form an RBP-A-J-K complex that negatively regulates rice yield-related traits. Examinations of the RBP-A-J-K complex indicated RBP-K functions as a relatively non-specific RBP chaperone that enables RBP-A and RBP-J to function normally. Additionally, RBP-J most likely affects GA pathways, resulting in considerable increases in grain and panicle lengths, but decreases in grain width and thickness. In contrast, RBP-A negatively regulates the expression of genes most likely involved in auxin-regulated pathways controlling cell wall elongation and carbohydrate transport, with substantial effects on the rice grain filling process as well as grain length and weight. Evolutionarily,
RBP-K
is relatively ancient and highly conserved, whereas
RBP-J
and
RBP-A
are more diverse. Thus, the RBP-A-J-K complex may represent a typical functional model for many RBPs and protein complexes that function at transcriptional and post-transcriptional levels in plants and animals for increased functional consistency, efficiency, and versatility, as well as increased evolutionary potential. Our results clearly demonstrate the importance of RBP-mediated post-transcriptional regulation for the diversity of complex traits. Furthermore, rice grain yield and quality may be enhanced by introducing various complete or partial loss-of-function mutations to specific RBP genes using clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 technology and by exploiting desirable natural tri-genic allelic combinations at the loci encoding the components of the RBP-A-J-K complex through marker-assisted selection.
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Trade-offs between the accumulation of cuticular wax and jasmonic acid-mediated herbivory resistance in maize
Jiong Liu, Lu Li, Zhilong Xiong, Christelle A.M. Robert, Baozhu Li, Shan He, Wenjie Chen, Jiasheng Bi, Guanqing Zhai, Siyi Guo, Hui Zhang, Jieping Li, Shutang Zhou, Xi Zhang and Chun‐Peng Song
J Integr Plant Biol 2024, 66 (1): 143-159.
doi:
10.1111/jipb.13586
Abstract
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Plants have evolved complex physical and chemical defense systems that allow them to withstand herbivory infestation. Composed of a complex mixture of very-long-chain fatty acids (VLCFAs) and their derivatives, cuticular wax constitutes the first physical line of defense against herbivores. Here, we report the function of
Glossy 8
(
ZmGL8
), which encodes a 3-ketoacyl reductase belonging to the fatty acid elongase complex, in orchestrating wax production and jasmonic acid (JA)-mediated defenses against herbivores in maize (
Zea mays
). The mutation of
GL8
enhanced chemical defenses by activating the JA-dependent pathway. We observed a trade-off between wax accumulation and JA levels across maize
glossy
mutants and 24 globally collected maize inbred lines. In addition, we demonstrated that mutants defective in cuticular wax biosynthesis in
Arabidopsis thaliana
and maize exhibit enhanced chemical defenses. Comprehensive transcriptomic and lipidomic analyses indicated that the
gl8
mutant confers chemical resistance to herbivores by remodeling VLCFA-related lipid metabolism and subsequent JA biosynthesis and signaling. These results suggest that VLCFA-related lipid metabolism has a critical role in regulating the trade-offs between cuticular wax and JA-mediated chemical defenses.
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Unveiling a half-century mystery of molecular bases for three-line hybrid rice breeding system
Xiaoming Zheng and Qian Qian
J Integr Plant Biol 2024, 66 (1): 3-6.
doi:
10.1111/jipb.13590
Abstract
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93
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Low temperature-mediated repression and far-red light-mediated induction determine morning
FLOWERING LOCUS T
expression levels
Hayeon Kim, Hye Won Kang, Dae Yeon Hwang, Nayoung Lee, Akane Kubota, Takato Imaizumi and Young Hun Song
J Integr Plant Biol 2024, 66 (1): 103-120.
doi:
10.1111/jipb.13595
Abstract
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In order to flower in the appropriate season, plants monitor light and temperature changes and alter downstream pathways that regulate florigen genes such as Arabidopsis (
Arabidopsis thaliana
)
FLOWERING LOCUS T
(
FT
). In Arabidopsis,
FT
messenger RNA levels peak in the morning and evening under natural long-day conditions (LDs). However, the regulatory mechanisms governing morning
FT
induction remain poorly understood. The morning
FT
peak is absent in typical laboratory LDs characterized by high red:far-red light (R:FR) ratios and constant temperatures. Here, we demonstrate that ZEITLUPE (ZTL) interacts with the
FT
repressors TARGET OF EATs (TOEs), thereby repressing morning
FT
expression in natural environments. Under LDs with simulated sunlight (R:FR = 1.0) and daily temperature cycles, which are natural LD-mimicking environmental conditions,
FT
transcript levels in the
ztl
mutant were high specifically in the morning, a pattern that was mirrored in the
toe1 toe2
double mutant. Low night-to-morning temperatures increased the inhibitory effect of ZTL on morning
FT
expression by increasing ZTL protein levels early in the morning. Far-red light counteracted ZTL activity by decreasing its abundance (possibly via phytochrome A (phyA)) while increasing GIGANTEA (GI) levels and negatively affecting the formation of the ZTL–GI complex in the morning. Therefore, the phyA-mediated high-irradiance response and GI play pivotal roles in morning
FT
induction. Our findings suggest that the delicate balance between low temperature-mediated ZTL activity and the far-red light-mediated functions of phyA and GI offers plants flexibility in fine-tuning their flowering time by controlling
FT
expression in the morning.
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The advantages of crosstalk during the evolution of the BZR1-ARF6-PIF4 (BAP) module
Runjie Diao, Mengru Zhao, Yannan Liu, Zhenhua Zhang and Bojian Zhong
J Integr Plant Biol 2023, 65 (12): 2631-2644.
doi:
10.1111/jipb.13554
Abstract
(Browse
136
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The BAP module, comprising BRASSINAZOLE RESISTANT 1 (BZR1), AUXIN RESPONSE FACTOR 6 (ARF6), and PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), functions as a molecular hub to orchestrate plant growth and development. In
Arabidopsis thaliana
, components of the BAP module physically interact to form a complex system that integrates light, brassinosteroid (BR), and auxin signals. Little is known about the origin and evolution of the BAP module. Here, we conducted comparative genomic and transcriptomic analyses to investigate the evolution and functional diversification of the BAP module. Our results suggest that the BAP module originated in land plants and that the ζ, ε, and γ whole-genome duplication/triplication events contributed to the expansion of BAP module components in seed plants. Comparative transcriptomic analysis suggested that the prototype BAP module arose in
Marchantia polymorpha
, experienced stepwise evolution, and became established as a mature regulatory system in seed plants. We developed a formula to calculate the signal transduction productivity of the BAP module and demonstrate that more crosstalk among components enables higher signal transduction efficiency. Our results reveal the evolutionary history of the BAP module and provide insights into the evolution of plant signaling networks and the strategies employed by plants to integrate environmental and endogenous signals.
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Identification of natural allelic variation in TTL1 controlling thermotolerance and grain size by a rice super pan-genome
Yarong Lin, Yiwang Zhu, Yuchao Cui, Hongge Qian, Qiaoling Yuan, Rui Chen, Yan Lin, Jianmin Chen, Xishi Zhou, Chuanlin Shi, Huiying He, Taijiao Hu, Chenbo Gu, Xiaoman Yu, Xiying Zhu, Yuexing Wang, Qian Qian, Cuijun Zhang, Feng Wang and Lianguang Shang
J Integr Plant Biol 2023, 65 (12): 2541-2551.
doi:
10.1111/jipb.13568
Abstract
(Browse
153
) |
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Continuously increasing global temperatures present great challenges to food security. Grain size, one of the critical components determining grain yield in rice (
Oryza sativa
L.), is a prime target for genetic breeding. Thus, there is an immediate need for genetic improvement in rice to maintain grain yield under heat stress. However, quantitative trait loci (QTLs) endowing heat stress tolerance and grain size in rice are extremely rare. Here, we identified a novel negative regulator with pleiotropic effects,
Thermo-Tolerance and grain Length 1
(
TTL1
), from the super pan-genomic and transcriptomic data. Loss-of-function mutations in
TTL1
enhanced heat tolerance, and caused an increase in grain size by coordinating cell expansion and proliferation. TTL1 was shown to function as a transcriptional regulator and localized to the nucleus and cell membrane. Furthermore, haplotype analysis showed that
hap
L
and
hap
S
of
TTL1
were obviously correlated with variations of thermotolerance and grain size in a core collection of cultivars. Genome evolution analysis of available rice germplasms suggested that
TTL1
was selected during domestication of the
indica
and
japonica
rice subspecies, but still had much breeding potential for increasing grain length and thermotolerance. These findings provide insights into
TTL1
as a novel potential target for the development of high-yield and thermotolerant rice varieties.
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Paternally imprinted
LATE-FLOWERING2
transcription factor contributes to paternal-excess interploidy hybridization barriers in wheat
Guanghui Yang, Man Feng, Kuohai Yu, Guangxian Cui, Yan Zhou, Lv Sun, Lulu Gao, Yumei Zhang, Huiru Peng, Yingyin Yao, Zhaorong Hu, Vincenzo Rossi, Ive De Smet, Zhongfu Ni, Qixin Sun and Mingming Xin
J Integr Plant Biol 2023, 65 (12): 2587-2603.
doi:
10.1111/jipb.13574
Abstract
(Browse
92
) |
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Interploidy hybridization between hexaploid and tetraploid genotypes occurred repeatedly during genomic introgression events throughout wheat evolution, and is commonly employed in wheat breeding programs. Hexaploid wheat usually serves as maternal parent because the reciprocal cross generates progeny with severe defects and poor seed germination, but the underlying mechanism is poorly understood. Here, we performed detailed analysis of phenotypic variation in endosperm between two interploidy reciprocal crosses arising from tetraploid (
Triticum durum
, AABB) and hexaploid wheat (
Triticum aestivum
, AABBDD). In the paternal- versus the maternal-excess cross, the timing of endosperm cellularization was delayed and starch granule accumulation in the endosperm was repressed, causing reduced germination percentage. The expression profiles of genes involved in nutrient metabolism differed strongly between these endosperm types. Furthermore, expression patterns of parental alleles were dramatically disturbed in interploidy versus intraploidy crosses, leading to increased number of imprinted genes. The endosperm-specific
TaLFL2
showed a paternally imprinted expression pattern in interploidy crosses partially due to allele-specific DNA methylation. Paternal TaLFL2 binds to and represses a nutrient accumulation regulator
TaNAC019
, leading to reduced storage protein and starch accumulation during endosperm development in paternal-excess cross, as confirmed by interploidy crosses between tetraploid wild-type and clustered regularly interspaced palindromic repeats (CRISPR)-CRISPR-associated protein 9 generated hexaploid mutants. These findings reveal a contribution of genomic imprinting to paternal-excess interploidy hybridization barriers during wheat evolution history and explains why experienced breeders preferentially exploit maternal-excess interploidy crosses in wheat breeding programs.
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Enhancing maize's nitrogen-fixing potential through
ZmSBT3
, a gene suppressing mucilage secretion
Jingyang Gao, Peijiang Feng, Jingli Zhang, Chaopei Dong, Zhao Wang, Mingxiang Chen, Zhongliang Yu, Bowen Zhao, Xin Hou, Huijuan Wang, Zhaokun Wu, Razia Sultana Jemim, Haidong Yu, Doudou Sun, Pei Jing, Jiafa Chen, Weibin Song, Xuecai Zhang, Zijian Zhou and Jianyu Wu,
J Integr Plant Biol 2023, 65 (12): 2645-2659.
doi:
10.1111/jipb.13581
Abstract
(Browse
128
) |
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Maize (
Zea mays
) requires substantial amounts of nitrogen, posing a challenge for its cultivation. Recent work discovered that some ancient Mexican maize landraces harbored diazotrophic bacteria in mucilage secreted by their aerial roots. To see if this trait is retained in modern maize, we conducted a field study of aerial root mucilage (ARM) in 258 inbred lines. We observed that ARM secretion is common in modern maize, but the amount significantly varies, and only a few lines have retained the nitrogen-fixing traits found in ancient landraces. The mucilage of the high-ARM inbred line HN5-724 had high nitrogen-fixing enzyme activity and abundant diazotrophic bacteria. Our genome-wide association study identified 17 candidate genes associated with ARM across three environments. Knockouts of one candidate gene, the subtilase family gene
ZmSBT3
, confirmed that it negatively regulates ARM secretion. Notably, the
ZmSBT3
knockout lines had increased biomass and total nitrogen accumulation under nitrogen-free culture conditions. High ARM was associated with three
ZmSBT3
haplotypes that were gradually lost during maize domestication, being retained in only a few modern inbred lines such as HN5-724. In summary, our results identify
ZmSBT3
as a potential tool for enhancing ARM, and thus nitrogen fixation, in maize.
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SD-RLK28 positively regulates pollen hydration on stigmas as a PCP-Bβ receptor in
Arabidopsis thaliana
Li Guo, Ziya Huang, Xingyu Chen, Min Yang, Miaomiao Yang, Ziwei Liu, Xuejie Han, Xiangjie Ma, Xiaoli Wang and Qiguo Gao
J Integr Plant Biol 2023, 65 (10): 2395-2406.
doi:
10.1111/jipb.13547
Abstract
(Browse
156
) |
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Pollen hydration on dry stigmas is strictly regulated by pollen–stigma interactions in Brassicaceae. Although several related molecular events have been described, the molecular mechanism underlying pollen hydration remains elusive. Multiple B-class pollen coat proteins (PCP-Bs) are involved in pollen hydration. Here, by analyzing the interactions of two PCP-Bs with three
Arabidopsis thaliana
stigmas strongly expressing
S
-domain receptor kinase (SD-RLK), we determined that SD-RLK28 directly interacts with PCP-Bβ. We investigated pollen hydration, pollen germination, pollen tube growth, and stigma receptivity in the
sd-rlk28
and
pcp-b
β mutants. PCP-Bβ acts in the pollen to regulate pollen hydration on stigmas. Loss of SD-RLK28 had no effect on pollen viability, and
sd-rlk28
plants had normal life cycles without obvious defects. However, pollen hydration on
sd-rlk28
stigmas was impaired and pollen tube growth in
sd-rlk28
pistils was delayed. The defect in pollen hydration on
sd-rlk28
stigmas was independent of changes in reactive oxygen species levels in stigmas. These results indicate that SD-RLK28 functions in the stigma as a PCP-Bβ receptor to positively regulate pollen hydration on dry stigmas.
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The aquaporin MePIP2;7 improves MeMGT9-mediated Mg
2+
acquisition in cassava
Qiuxiang Ma, Yancai Feng, Shu Luo, Lu Cheng, Weijing Tong, Xinlu Lu, Youzhi Li and Peng Zhang
J Integr Plant Biol 2023, 65 (10): 2349-2367.
doi:
10.1111/jipb.13552
Abstract
(Browse
131
) |
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Aquaporins are important transmembrane water transport proteins which transport water and several neutral molecules. However, how aquaporins are involved in the synergistic transport of Mg
2+
and water remains poorly understood. Here, we found that the cassava aquaporin MePIP2;7 was involved in Mg
2+
transport through interaction with MeMGT9, a lower affinity magnesium transporter protein. Knockdown of
MePIP2;7
in cassava led to magnesium deficiency in basal mature leaves with chlorosis and necrotic spots on their edges and starch over-accumulation. Mg
2+
content was significantly decreased in leaves and roots of
MePIP2;7
-RNA interference (PIP-Ri) plants grown in both field and Mg
2+
-free hydroponic solution.
Xenopus
oocyte injection analysis verified that MePIP2;7 possessed the ability to transport water only and MeMGT9 was responsible for Mg
2+
efflux. More importantly, MePIP2;7 improved the transportability of Mg
2+
via MeMGT9 as verified using the CM66 mutant complementation assay and
Xenopus
oocytes expressing system. Yeast two-hybrid, bimolecular fluorescence complementation, co-localization, and co-immunoprecipitation assays demonstrated the direct protein–protein interaction between MePIP2;7 and MeMGT9
in vivo
. Mg
2+
flux was significantly elevated in
MePIP2;7
-overexpressing lines in hydroponic solution through non-invasive micro-test technique analysis. Under Mg
2+
-free condition, the retarded growth of PIP-Ri transgenic plants could be recovered with Mg
2+
supplementation. Taken together, our results demonstrated the synergistic effect of the MePIP2;7 and MeMGT9 interaction in regulating water and Mg
2+
absorption and transport in cassava.
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MaBEL1 regulates banana fruit ripening by activating cell wall and starch degradation-related genes
Zunyang Song, Xiaoyang Zhu, Xiuhua Lai, Hangcong Chen, Lihua Wang, Yulin Yao, Weixin Chen and Xueping Li
J Integr Plant Biol 2023, 65 (9): 2036-2055.
doi:
10.1111/jipb.13506
Abstract
(Browse
181
) |
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Banana is a typical subtropical fruit, sensitive to chilling injuries and prone to softening disorder. However, the underlying regulatory mechanisms of the softening disorder caused by cold stress remain obscure. Herein, we found that BEL1-LIKE HOMEODOMAIN transcription factor 1 (MaBEL1) and its associated proteins regulate the fruit softening and ripening process. The transcript and protein levels of MaBEL1 were up-regulated with fruit ripening but severely repressed by the chilling stress. Moreover, the MaBEL1 protein interacted directly with the promoters of the cell wall and starch degradation-related genes, such as
MaAMY3
,
MaXYL32
, and
MaEXP-A8
. The transient overexpression of
MaBEL1
alleviated fruit chilling injury and ripening disorder caused by cold stress and promoted fruit softening and ripening of “Fenjiao” banana by inducing ethylene production and starch and cell wall degradation. The accelerated ripening was also validated by the ectopic overexpression in tomatoes. Conversely,
MaBEL1
-silencing aggravated the chilling injury and ripening disorder and repressed fruit softening and ripening by inhibiting ethylene production and starch and cell wall degradation. MaABI5-like and MaEBF1, the two positive regulators of the fruit softening process, interacted with MaBEL1 to enhance the promoter activity of the starch and cell wall degradation-related genes. Moreover, the F-box protein MaEBF1 does not modulate the degradation of MaBEL1, which regulates the transcription of
MaABI5-like
protein. Overall, we report a novel MaBEL1-MaEBF1-MaABI5-like complex system that mediates the fruit softening and ripening disorder in “Fenjiao” bananas caused by cold stress.
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Fusarium
-produced vitamin B
6
promotes the evasion of soybean resistance by
Phytophthora sojae
Shuchen Wang, Xiaoyi Zhang, Zhichao Zhang, Yun Chen, Qing Tian, Dandan Zeng, Miao Xu, Yan Wang, Suomeng Dong, Zhonghua Ma, Yuanchao Wang, Xiaobo Zheng and Wenwu Ye
J Integr Plant Biol 2023, 65 (9): 2204-2217.
doi:
10.1111/jipb.13505
Abstract
(Browse
129
) |
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Plants can be infected by multiple pathogens concurrently in natural systems. However, pathogen–pathogen interactions have rarely been studied. In addition to the oomycete
Phytophthora sojae
, fungi such as
Fusarium
spp. also cause soybean root rot. In a 3-year field investigation, we discovered that
P. sojae
and
Fusarium
spp. frequently coexisted in diseased soybean roots. Out of 336
P. sojae
–soybean–
Fusarium
combinations, more than 80% aggravated disease. Different
Fusarium
species all enhanced
P. sojae
infection when co-inoculated on soybean. Treatment with
Fusarium
secreted non-proteinaceous metabolites had an effect equal to the direct pathogen co-inoculation. By screening a
Fusarium graminearum
mutant library, we identified
Fusarium
promoting factor of
Phytophthora sojae
infection 1 (
Fpp1
), encoding a zinc alcohol dehydrogenase.
Fpp1
is functionally conserved in
Fusarium
and contributes to metabolite-mediated infection promotion, in which vitamin B
6
(VB6) produced by
Fusarium
is key. Transcriptional and functional analyses revealed that Fpp1 regulates two VB6 metabolism genes, and VB6 suppresses expression of soybean disease resistance-related genes. These results reveal that co-infection with
Fusarium
promotes loss of
P. sojae
resistance in soybean, information that will inform the sustainable use of disease-resistant crop varieties and provide new strategies to control soybean root rot.
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Rice pollen-specific OsRALF17 and OsRALF19 are essential for pollen tube growth
Eui‐Jung Kim, Ji‐Hyun Kim, Woo‐Jong Hong, Eun Young Kim, Myung‐Hee Kim, Su Kyoung Lee, Cheol Woo Min, Sun Tae Kim, Soon Ki Park, Ki‐Hong Jung and Yu‐Jin Kim
J Integr Plant Biol 2023, 65 (9): 2218-2236.
doi:
10.1111/jipb.13508
Abstract
(Browse
158
) |
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Pollen tube growth is essential for successful double fertilization, which is critical for grain yield in crop plants. Rapid alkalinization factors (RALFs) function as ligands for signal transduction during fertilization. However, functional studies on RALF in monocot plants are lacking. Herein, we functionally characterized two pollen-specific RALFs in rice (
Oryza sativa
) using multiple clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9-induced loss-of-function mutants, peptide treatment, expression analyses, and tag reporter lines. Among the 41 RALF members in rice,
OsRALF17
was specifically expressed at the highest level in pollen and pollen tubes. Exogenously applied OsRALF17 or OsRALF19 peptide inhibited pollen tube germination and elongation at high concentrations but enhanced tube elongation at low concentrations, indicating growth regulation. Double mutants of OsRALF17 and OsRALF19 (
ralf17/19
) exhibited almost full male sterility with defects in pollen hydration, germination, and tube elongation, which was partially recovered by exogenous treatment with OsRALF17 peptide. This study revealed that two partially functionally redundant OsRALF17 and OsRALF19 bind to
Oryza sativa
male-gene transfer defective 2 (OsMTD2) and transmit reactive oxygen species signals for pollen tube germination and integrity maintenance in rice. Transcriptomic analysis confirmed their common downstream genes, in
osmtd2
and
ralf17/19
. This study provides new insights into the role of RALF, expanding our knowledge of the biological role of RALF in regulating rice fertilization.
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Cell type-specific proteomics uncovers a RAF15-SnRK2.6/OST1 kinase cascade in guard cells
Hongliang Wang, Yubei Wang, Tian Sang, Zhen Lin, Rongxia Li, Weiwei Ren, Xin Shen, Bing Zhao, Xiao Wang, Xuebin Zhang, Shaoqun Zhou, Shaojun Dai, Honghong Hu, Chun‐Peng Song and Pengcheng Wang
J Integr Plant Biol 2023, 65 (9): 2122-2137.
doi:
10.1111/jipb.13536
Abstract
(Browse
188
) |
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Multicellular organisms such as plants contain various cell types with specialized functions. Analyzing the characteristics of each cell type reveals specific cell functions and enhances our understanding of organization and function at the organismal level. Guard cells (GCs) are specialized epidermal cells that regulate the movement of the stomata and gaseous exchange, and provide a model genetic system for analyzing cell fate, signaling, and function. Several proteomics analyses of GC are available, but these are limited in depth. Here we used enzymatic isolation and flow cytometry to enrich GC and mesophyll cell protoplasts and perform in-depth proteomics in these two major cell types in
Arabidopsis
leaves. We identified approximately 3,000 proteins not previously found in the GC proteome and more than 600 proteins that may be specific to GC. The depth of our proteomics enabled us to uncover a guard cell-specific kinase cascade whereby Raf15 and Snf1-related kinase2.6 (SnRK2.6)/OST1(open stomata 1) mediate abscisic acid (ABA)-induced stomatal closure. RAF15 directly phosphorylated SnRK2.6/OST1 at the conserved Ser175 residue in its activation loop and was sufficient to reactivate the inactive form of SnRK2.6/OST1. ABA-triggered SnRK2.6/OST1 activation and stomatal closure was impaired in
raf15
mutants. We also showed enrichment of enzymes and flavone metabolism in GC, and consistent, dramatic accumulation of flavone metabolites. Our study answers the long-standing question of how ABA activates SnRK2.6/OST1 in GCs and represents a resource potentially providing further insights into the molecular basis of GC and mesophyll cell development, metabolism, structure, and function.
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Artificial evolution of
OsEPSPS
through an improved dual cytosine and adenine base editor generated a novel allele conferring rice glyphosate tolerance
Chen Zhang, Xue Zhong, Shaoya Li, Lei Yan, Jingying Li, Yubing He, Yong Lin, Yangjun Zhang and Lanqin Xia
J Integr Plant Biol 2023, 65 (9): 2194-2203.
doi:
10.1111/jipb.13543
Abstract
(Browse
186
) |
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Exploiting novel endogenous glyphosate-tolerant alleles is highly desirable and has promising potential for weed control in rice breeding. Here, through fusions of different effective cytosine and adenine deaminases with nCas9-NG, we engineered an effective surrogate two-component composite base editing system, STCBE-2, with improved C-to-T and A-to-G base editing efficiency and expanded the editing window. Furthermore, we targeted a rice endogenous
OsEPSPS
gene for artificial evolution through STCBE-2-mediated near-saturated mutagenesis. After hygromycin and glyphosate selection, we identified a novel
OsEPSPS
allele with an Asp-213-Asn (D213N) mutation (
OsEPSPS
-D213N) in the predicted glyphosate-binding domain, which conferred rice plants reliable glyphosate tolerance and had not been reported or applied in rice breeding. Collectively, we developed a novel dual base editor which will be valuable for artificial evolution of important genes in crops. And the novel glyphosate-tolerant rice germplasm generated in this study will benefit weeds management in rice paddy fields.
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Editorial Office, Journal of Integrative Plant Biology, Institute of Botany, CAS
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Copyright © 2022 by the Institute of Botany, the Chinese Academy of Sciences
Online ISSN: 1744-7909 Print ISSN: 1672-9072 CN: 11-5067/Q
备案号:
京ICP备16067583号-22
Editorial Office, Journal of Integrative Plant Biology, Institute of Botany, CAS
No. 20 Nanxincun, Xiangshan, Beijing 100093, China
Tel: +86 10 6283 6133 Fax: +86 10 8259 2636 E-mail: jipb@ibcas.ac.cn
Copyright © 2022 by the Institute of Botany, the Chinese Academy of Sciences
Online ISSN: 1744-7909 Print ISSN: 1672-9072 CN: 11-5067/Q
网站备案号:京ICP备16067583号-22