J Integr Plant Biol

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PanGraphRNA: An efficient and flexible bioinformatics platform for graph pangenome-based RNA-seq data analysis

Yifan Bu, Zhixu Qiu, Wen Sun, Yishui Han, Yifan Liu, Jing Yang, Minggui Song, Zenglin Li, Songyu Liu, Yuzhou Zhang, Chuang Ma

doi: 10.1111/jipb.70231

Version of Record online: 19 March 2026

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Pentatricopeptide repeat proteins in crops: Advances in functional mechanisms and breeding applications

Mingming Wu, Maohong Cai, Rongrong Zhai, Jing Ye, Guofu Zhu, Faming Yu, Shenghai Ye, Xiaoming Zhang

doi: 10.1111/jipb.70217

Version of Record online: 19 March 2026

Pentatricopeptide repeat proteins coordinate nucleus-organelle communication by modulating RNA metabolism within chloroplasts and mitochondria. This review highlights how they control critical processes like photosynthesis, seed development, fertility restoration, and stress survival in crops, and explores their potential as programmable tools for RNA manipulation in organelles.

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Convergence and parallelism in the evolution of plant metabolism

Federico Scossa, Mustafa Bulut, Thomas Naake, John C. D'Auria, Alisdair R. Fernie

doi: 10.1111/jipb.70236

Version of Record online: 19 March 2026

Similar traits in different organisms may originate from shared ancestry or evolve independently. The terminology used to define phenotypic similarity is often confusing. This review attempts to clarify the definitions and present examples from plant domestication and specialized metabolism to explain how complex traits evolve repeatedly in plants.

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Metabolite‐mediated plant immunity: From traditional defensors to artificial elicitors

Jiajun Tang, Weiwei Xie, Yunjiang Cheng, Alisdair R. Fernie, Feng Zhu

DOI: 10.1111/jipb.70225

Version of Record online: 17 March 2026

This review summarizes the roles of plant metabolites in immunity and pathogen-induced reprogramming; it also explores nanoscience, de novo domestication, and artificial intelligence for the development of next-generation elicitors.

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Unlocking the genetic basis of quantitative hybrid sterility in rice

Xin Gou, Ruiying Liu, Yaoguang Liu, Yongyao Xie

doi: 10.1111/jipb.70229

Version of Record online: 17 March 2026

This commentary summarizes hybrid sterility models in plants, with an emphasis on a recent study that addresses the genetic basis of the RIS/RIA-RID-RIR system underlying S44-mediated hybrid sterility between Oryza longistaminata and indica rice, revealing a novel killer-protector-target model integrated with modifiers that regulate reproductive isolation.

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An efficient transformation and gene editing system for Lilium species

Yajie Zhao, Yixuan Li, Jinxin Shi, Yutong Chen, Jingwei Wei, Jinlong Li, Yiqing Wang, Dingyi Liu, Dong Jing, Shuo Long, Manman Zhang, Junwei Tang, Jian Wu

doi: 10.1111/jipb.70237

Version of Record online: 17 March 2026

A transformation system exploits lily bulb scale propagation and de novo formation of bulblets, integrating tissue culture with non-tissue culture approaches. Through optimized scale propagation and disinfection treatments, it achieves efficient stable gene overexpression and editing in lily.

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Transcriptional adapter ADA2 regulates yield and end‐use quality through liquid–liquid phase separation in wheat

Xiaobang Zhang, Ruijie Zhang, Yuhan Zhang, Tao Yang, Longfei Wu, Yuan Cao, Jun Xiao, Jigang Li, Xin Gao, Xinyou Cao, Jie Liu, Mingming Xin, Yuan Zong, Zhongfu Ni, Qixin Sun, Yingyin Yao

doi: 10.1111/jipb.70227

Version of Record online: 16 March 2026

The transcriptional adapter ADA2 interacts with the histone acetyltransferase GCN5 to regulate starch and storage protein content in wheat grains through histone acetylation. ADA2 undergoes phase separation and is modulated by GCN5, affecting histone acetyltransferase activity and gene transcription. An elite ADA2-B haplotype correlates with improved grain size.

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OsCPN10a, cooperating with OsCPN20 and OsHSP60‐3B negatively regulate ABA signaling and enhance seed storability in rice

Sufeng Liao, Yidong Wei, Yongsheng Zhu, Kunyang Li, Ting Chen, Shuai Zhao, Fangxi Wu, Jinlan Wang, Pengbo Yu, Hongguang Xie, Liping Chen, Qiuhua Cai, Huaan Xie, Jianfu Zhang

doi: 10.1111/jipb.70230

Version of Record online: 16 March 2026

Abscisic acid signaling homeostasis is essential for seed storability. The molecular chaperone OsCPN10a enhances rice seed storability by forming a trimeric chaperone complex with OsCPN20-OsHSP60-3B that attenuates abscisic acid signaling via direct interaction with OsPYL10-OsABIL1, thereby maintaining starch integrity and offering a promising target for crop improvement.

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Developing a robust multiplex CRISPR/Cas12i3‐5M system for trait stacking in soybean

Wenxin Lin, Haijie Wu, Huaqin Kuang, Xiangchi Feng, Mengyan Bai, Fanghui He, Ruixuan Liang, Yizhi Zeng, Meina Li, Fanjiang Kong, Baohui Liu, Yuefeng Guan

doi: 10.1111/jipb.70233

Version of Record online: 16 March 2026

The high-efficiency multiplex gene editing technology based CRISPR-Cas12i3-5M is capable of simultaneously editing 13 target sites in soybean, and was used to generate germplasm with high oleic acid content and no beany flavor.

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Constitution and function of intergenic genome regions in cultivated versus annual wild soybean in China

Xiaoshuai Hao, Xinyang Hu, Yongpeng Pan, Qi Zhang, Ran Ou, Fenfen Jiang, Fangdong Liu, Jiaoping Zhang, Wubin Wang, Guangnan Xing, Junyi Gai, Jianbo He

doi: 10.1111/jipb.70223

Version of Record online: 16 March 2026

Three-case restricted two-stage multi-locus multi-allele genome-wide association study identified main-effect genes and detected the regulatory effects of intergenic loci on genes, enabling comprehensive dissection of the genic-intergenic genetic system for quantitative traits and providing a strategy for studying their genetic basis.

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Functional characterization of two O-methyltransferases and a glycosyltransferase catalyzing the last two steps of phillyrin biosynthesis in Forsythia suspensa

Zhiyao Wang, Naichao Zhang, Peimin Wu, Fei Chen, Ying Cao, Jing Wang, Yiming Qin, Wenhui Zheng, Yinghua Sheng, Shuai Chen, Baojing Li, Lei Wei, Junli Zhang, Yuqing Liu, Ninghua Tan, Wei Wang, Min Chen

DOI: 10.1111/jipb.70216

Version of Record online: 15 March 2026

The O-methyltransferases FsE4MT01 and FsE4MT02, and the and glycosyltransferase FsP4′GT catalyze the terminal methylation and glycosylation steps in biosynthesis of the unique antiviral lignan phillyrin in Forsythia suspensa; these enzymes may enable metabolic engineering for enhanced phillyrin production.

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Correction to “The miR172a–ERF416/413 module regulates soybean seed traits”

DOI: 10.1111/jipb.70228

Version of Record online: 15 March 2026

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Synergistic engineering of Casδ nuclease for robust genome editing

Fanghui Ge, Chenchen Peng, Yang Du, Ying Chen, Zilong Zhao, Meixia Yu, Huairu Feng, Yuyang Xie, Siwei Sun, Shengnan Liu, Beibei Xin, Haiming Zhao, Sen Wu, Chao Bian, Zhijia Yang, Jinsheng Lai, Jian Chen

doi: 10.1111/jipb.70222

Version of Record online: 15 March 2026

A hierarchical engineering strategy was used to enhance the editing activity of Casδ, yielding an optimized variant termed enCasδ. This variant enables robust genome editing in animal cells and plants, with overall editing performance comparable to that of SpCas9 and other Cas12 nucleases.

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SlGRF1 mediates gibberellin signaling to control cut‐budding in tomato

Yaping Xu, Yinhuan Xie, Huimin Jia, Qianqian Li, Xinqin Liu, Ting Ma, Zhaobo Lang, Qingfeng Niu

doi: 10.1111/jipb.70219

Version of Record online: 15 March 2026

Upon wounding, cytokinin increases to initiate callus formation. Gibberellin enhances this, but later blocks bud formation by suppressing SlGRF1. Wounding-induced protein SlGRF1 triggers buds via NAM1, EPF4, and ER2. Hormonal shifts control cut-budding phases.

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GSK3 regulates DOG1L4 to enhance pre‐harvest sprouting resistance in wheat

Huixue Dong, Danning Yang, Yu He, Qian Chen, Xiaojiang Guo, Mengping Cheng, Maolian Li, Zhongwei Yuan, Jirui Wang

doi: 10.1111/jipb.70234

Version of Record online: 15 March 2026

GLYCOGEN SYNTHASE KINASE 3 (GSK3), a negative regulator of brassinosteroid signaling, phosphorylates and stabilizes the seed dormancy protein DOG1L4, which in turn activates ABSCISIC ACID INSENSITIVE 5 (ABI5) to enhance seed dormancy. GSK3 also phosphorylates ABI5. This dual-target mechanism suggests a strategy for controlling seed dormancy and germination in crops.

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Two mycorrhiza-responsive MADS transcription factors, OsMADS61 and OsMADS26, regulate both direct and mycorrhizal nitrate transport pathways

Yuhan Ren, Congfan Yang, Haoyan Ji, Kun Xie, Haoran Mao, Dechao Zeng, Lingxiao Wang, Shuangshuang Wang, Guohua Xu, Aiqun Chen

DOI: 10.1111/jipb.70224

Version of Record online: 12 March 2026

In rice, the transcription factors OsMADS26 and OsMADS61 orchestrate direct and symbiotic nitrate uptake pathways via transcriptionally activating the nitrate transporter genes OsNPF4.5 and OsNAR2.1/NRT2.2 by recognizing the CrAG cis-element in their promoters, consequently enhancing nitrogen acquisition and utilization efficiencies during arbuscular mycorrhizal symbiosis.

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LpMPK6 regulates leaf color in perennial ryegrass by inhibiting LpMYBR1-modulated transcription of LpNRT1.5

Liaoliao Ye, Xiuhua Tang, Zhijian Cao, Cun Wang, Jinwei Yang, Zhiquan Qiang, Tao Qin

DOI: 10.1111/jipb.70226

Version of Record online: 12 March 2026

In perennial ryegrass, the MAP kinase LpMPK6 phosphorylates the transcription factor LpMYBR1 to suppress transcription of the nitrate transporter gene LpNRT1.5, thereby inhibiting root-to-shoot nitrate transport and causing leaf chlorosis under nitrogen deficiency.

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SlARF11–SlGATA5 stimulates tomato leaf angle by feedback regulation with brassinosteroid signaling

Qihui Wang, Ruoxuan Wang, Xi Wang, Junfeng Luo, Qiongqiong Zhang, Xin Liu, Jing Jiang

DOI: 10.1111/jipb.70215

Version of Record online: 12 March 2026

Leaf angle in tomato is regulated by a regulatory module involving the non-canonical auxin response factor SlARF11, which interacts with SlGATA5, facilitating SlGATA5 binding to the promoters of genes involved in brassinosteroid signaling, cell elongation, and lignin deposition.

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CasY7: An optimized Cas12i system for enhanced genome editing in monocot crops

Dating Zhong, Yanxiao Dong, Hong Pan, Yanan Fu, Yining Zhao, Shuting Ruan, Wencong Yu, Yiwen Wang, Qianlan Yin, Yanfei Zhang, Yisen Huang, Jiaqi Shen, Hongling Zhang, Yuxuan Wu, Jieting Xu, Yuming Lu

DOI: 10.1111/jipb.70181

Version of Record online: 11 March 2026

The Cas12i-derived nuclease CasY7 system achieved high editing efficiency in rice, maize, and wheat, notably enabling multiplex editing. This establishes CasY7 as a robust CRISPR tool for crop improvement.

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HSP101-encoding NEO-TETRAPLOID RICE FERTILITY GENE 1 regulates tapetum development through interaction with SAPK2 in polyploid rice

Lichong Cao, Weicong Huang, Hang Yu, Sanglin Liu, Jianmin Yin, Zijun Lu, Jinwen Wu, Xiangdong Liu

doi: 10.1111/jipb.70218

Version of Record online: 11 March 2026

In neo-tetraploid rice, the NTRF1–SAPK2 heat shock protein–kinase module coordinates abscisic acid signaling with reactive oxygen species homeostasis to ensure timely tapetal programmed cell death and subsequent pollen maturation, providing a resource for the genetic improvement of polyploid rice.

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The SAG101–NRG1 branch of TIR signaling activates phenylalanine-derived SA biosynthesis in Nicotiana benthamiana

Lu Xu, Mingsong Wu, Yanan Liu, Xin Li, Yuelin Zhang

DOI: 10.1111/jipb.70214

Version of Record online: 11 March 2026

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Transcriptome-wide association study identifies the ZmbZIP89–ZmSAUR21 module as a key regulator of root growth and drought tolerance in maize

Tianze Zhu, Houmiao Wang, Yunyun Wang, Xiaoyi Yang, Shuai Fang, Wei Li, Wenye Rui, Baoqing Wang, Yimei Tian, Dan Sun, Haoxin Gao, Zefeng Yang, Chenwu Xu, Pengcheng Li

DOI: 10.1111/jipb.70220

Version of Record online: 11 March 2026

The maize Small Auxin-Up RNA gene ZmSAUR21 is activated by the transcription factor ZmbZIP89 and regulates root development, providing a direct target for breeding maize with stronger, deeper root systems, that are more resilient to drought.

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Efficient CRISPR/Cas‐SF01 genome editing tools with high editing efficiency in allotetraploid oilseed rape

Mengyu Hao, Meili Zhou, Fei Pan, Tiantian Liu, Yilin Li, Nan Su, Ayub Ashfaq, Miaoying Song, Hui Wang, Wenxiang Wang, Jia Liu, Chao Li, Li Fu, Ping He, Qiong Hu, Desheng Mei, Hongtao Cheng

DOI: 10.1111/jipb.70221

Version of Record online: 09 March 2026

An efficient protoplast system was used to test gene editing and Cas-SF01 was developed for gene editing in oilseed rape and used to create plants with multilocular siliques and male sterility, with high precision and no off-target edits. Cas-SF01 recognizes more flexible DNA targets than CRISPR-Cas9.

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Plant strategies against herbivorous insects

Liuhong Zhu, Hanchi Yang, Peixuan Li, Lina Dong, Shang Zhao, Honghao Lv, Neil Crickmore, Xuguo Zhou, Youjun Zhang, Zhaojiang Guo

DOI: 10.1111/jipb.70209

Version of Record online: 08 March 2026

This review summarizes two centuries of research on plant resistance to herbivorous insects and proposes a unified framework encompassing physical, chemical, ecological modulation, and behavioral defenses. It highlights their coordination, key resistance genes, and breeding applications, offering new perspectives for sustainable pest management and crop improvement.

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Recent advances in genetic control of fiber length in upland cotton

Gangling Li, Tao Wang, Shuqian Yao, Haoliang Yan, Juwu Gong, Youlu Yuan, Haihong Shang

DOI: 10.1111/jipb.70213

Version of Record online: 08 March 2026

Construction of genetic regulatory networks affecting cotton fiber length and an interaction network among different hormones that affect cotton fiber length provides insight on the application of these genes in breeding and suggests potential issues that may arise during breeding applications.

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Exploration of diverse glycosyltransferases in Dracocephalum moldavica and engineering the production of bioactive flavonoid glycosides

Dan-Dan Xu, Ni-Hong Du, Jia-Hui Li, Jiang-Nan Li, Jie Fu, Ming-Xin Cui, Rong Ni, Jiao-Zhen Zhang, Ying Lu, Ping Xu, Hong-Xiang Lou, Ai-Xia Cheng

DOI: 10.1111/jipb.70212

Version of Record online: 04 March 2026

Identification of key enzymes in Dracocephalum moldavica that produce valuable flavonoid glycosides, then engineering these enzymes and optimizing sugar supply in Escherichia coli, resulted in efficient microbial production of scutellarin and phloretin di-C-glycoside.

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Functional characterization of plant UGT93s producing prenylated phenolic glycosides

Hong-Ye Li, Jian-Lin Zou, Bao Nie, Zi-Long Wang, Meng Zhang, Chun-Xue Zhao, Yan-Fang Yang, Xi-Ran Zhang, Xin-Yue Zhan, Li Wang, Min Ye

DOI: 10.1111/jipb.70202

Version of Record online: 04 March 2026

Characterization of 31 plant UGT93 glycosyltransferases and their ancestral enzyme showed a catalytic preference for prenylated phenolics and that aromatic and hydrophobic residues in the substrate binding domain are significant for this catalytic preference.

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A leucine-rich-repeat receptor-like kinase SERL1 phosphorylates and stabilizes OsALDH2B1 to promote alkaline tolerance and grain size in rice

Zemin Ma, Xuanlin Gao, Shuaizu An, Mengyuan Chen, Biaoming Zhang, Lei Zhou, Shengyuan Sun, Ming Li, Feng Yu, Shiyou Lü, Zhaohui Chu, Aiqing You, Yinggen Ke, Pingfang Yang

doi: 10.1111/jipb.70210

Version of Record online: 04 March 2026

The rice aldehyde dehydrogenase OsALDH2B1 enhances grain size and tolerance to alkaline soil by repressing GRAIN SIZE 3 and activating catalases. SERL1-mediated phosphorylation stabilizes OsALDH2B1 under stress, establishing a signaling axis that overcomes growth-defense trade-offs and provides a direct target for breeding high-yield, alkaline-resilient rice.

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Unlocking plant abiotic stress resilience through biostimulants and omics-driven innovations

Muhammad Ateeq, Shariq Mahmood Alam, Muhammad Mohsin Kaleem, Shah Fahad, Muhammad Atiq Ashraf, Muhammad Asim, Kaijie Zhu, Fareeha Shireen, Junwei Liu, Hanzi He

DOI: 10.1111/jipb.70205

Version of Record online: 04 March 2026

This review discusses how biostimulants protect plants from climate stress by activating natural defenses. To design targeted biostimulants, microbes, key protective genes, and metabolites are identified using AI networks, multi-omics, and metabolic engineering. This approach boosts crop resilience without yield loss, supporting sustainable agriculture.

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Key metabolites secreted by Chlorella vulgaris alleviate salt stress in soybean seedlings

Yunyi Shi, Ruitong Chen, Kai Jiang, Aijuan Jiang, Jianchao Yang, Hongli Cui, Min Chen

doi: 10.1111/jipb.70207

Version of Record online: 04 March 2026

Chlorella vulgaris secretes exosome-derived linolenic acid and inosine, which alleviate salt stress and enhance salt tolerance in soybean seedlings by activating stress-responsive signaling networks.

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De novo stolon organogenesis in potato leaf callus elicited by Agrobacterium tumefaciens stimulus

Seung Yong Shin, Su-Jin Park, Ji-Sun Park, Ki-Beom Moon, Jae Sun Moon, Hye Sun Cho, Hyun-Soon Kim, Hyo-Jun Lee

DOI: 10.1111/jipb.70203

Version of Record online: 01 March 2026

Agrobacterium tumefaciens triggers stolon regeneration from potato leaf callus independent of T-DNA insertion, suggesting a strategy to reprogram callus identity and expand the potential of tissue regeneration.

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Atypical NLR pairs in wheat: Sensor–helper NLRs conferring disease resistance

Yanbin Guan, Xuening Zhang, Zabta Khan Shinwari, Jian Chen, Guang Qi, Fengquan Liu, Huan Chen

DOI: 10.1111/jipb.70208

Version of Record online: 01 March 2026

This commentary discusses new research showing that six structurally and functionally atypical NLR pairs in wheat confer disease resistance via a sensor NLR-helper NLR module. The functional mechanisms of some NLR pairs differ from the classical NLR pair model, revealing the complexity and diversity of the wheat immune system.

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Dissecting the genetic basis of climatic adaptation in wild relatives (Malus baccata) for climate-resilient apple breeding

Ying Su, Yani Hao, Xuejing Cao, Lin Wang, Zhiqi Xu, Fan Zhang, Zhiyao Ma, Xu Wang, Jiacui Li, Tianrong Fan, Ruoyan Zhao, Zhongqi Liu, Wenrui Wang, Yingchun Zhang, Xuanwen Yang, Sifan Yang, Dajiang Wang, Kun Wang, Simiao Sun, Zichen Li, Wen Tian, Yanming Sun, Zhao Liu, Yanshuai Xu, Hua Xiao, Yanling Peng, Xiaodong Xu, Ruirui Liu, Xinmin Tian, Yongfeng Zhou, Yuan Gao

doi: 10.1111/jipb.70194

Version of Record online: 25 February 2026

This comprehensive map of genetic variation in wild apple (Malus baccata) and set of key genes associated with adaptation to temperature, precipitation, and soil properties establishes a foundation for breeding climate-resilient apple cultivars and conserving the genetic resources of wild crop relatives.

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Correction to “Rice black-streaked dwarf virus-encoded P6 protein impairs OsPelota-mediated antiviral RNA decay defense via promoting OsSCE1b ubiquitination and degradation in rice”

DOI: 10.1111/jipb.70204

Version of Record online: 25 February 2026

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Tandemly duplicated TaERF109 genes confer drought tolerance and post-drought recovery in wheat

Jun Chen, Shang Zhao, Wenjing Li, Chunxiao Wang, Yuan Gao, Zihan Yang, Yongbin Zhou, Ming Chen, Zhaoshi Xu, Youzhi Ma

doi: 10.1111/jipb.70196

Version of Record online: 25 February 2026

Tandemly duplicated TaERF109 transcription factor genes in wheat modulate growth traits and enhance drought tolerance by regulating the TaMADS56 transcription facto gene, cytokinin biosynthesis-related genes, and nicotianamine synthase genes, revealing the critical role of tandemly duplicated genes in the coordination of stress responses and developmental processes in wheat.

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A prominent role of the circadian proteins PRR5 and PRR7 in governing Arabidopsis immunity

Shaoqin Li, Hailin Wang, Zumei Ye, Zhiju Fu, Yanyu Ru, Yongping Yang, Kongfen Wu, Diqiu Yu, Yanjuan Jiang

DOI: 10.1111/jipb.70199

Version of Record online: 25 February 2026

The core clock components PSEUDO-RESPONSE REGULATOR 5 (PRR5) and PRR7 antagonized function of the complex of NONEXPRESSER OF PATHOGENESIS-RELATED GENES 1 with the transcription factor TGA3 to directly inhibit salicylic acid signaling and govern immunity in Arabidopsis.

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Correction to “Endocytosis of the damage-associated molecular pattern receptor PEPR1 is BAK1-dependent”

doi: 10.1111/jipb.70211

Version of Record online: 25 February 2026

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Role of an Arabidopsis mitogen-activated protein kinase kinase kinase in ROS-mediated leaf senescence

Fengbo Yang, Kun Li, José Ramón Botella, Xiaohong Zhu, Yuchen Miao, Yun Zhou, Yuan Li, Dongtao Ren, Chun-Peng Song

DOI: 10.1111/jipb.70191

Version of Record online: 24 February 2026

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SmCPK20 phosphorylates SmWRKY2 to regulate jasmonate-mediated tanshinone synthesis in Salvia miltiorrhiza

Xueying Li, Xiumin Nie, Bolun Li, Xi Han, Xiaona Cai, Qian Yao, Junwen Bu, Jiulin Huang, Bin Zhang, Juane Dong

DOI: 10.1111/jipb.70195

Version of Record online: 24 February 2026

A regulatory module composed of the repressor SmJAZ3, the kinase SmCPK20, and the transcription factor SmWRKY2 integrates jasmonic acid signaling, Ca²⁺ signaling, and CPK-mediated phosphorylation to regulate tanshinone biosynthesis in Salvia miltiorrhiza.

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Correction to “Identifying rubber-related genes through developing a sense/antisense RNA expression mutant library of Taraxacum kok-saghyz Rodin”

DOI: 10.1111/jipb.70206

Version of Record online: 24 February 2026

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