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CIPK9–PP2C39 module modulates the trade-off between abscisic acid-dependent drought tolerance and plant growth in Brassica napus L. CIPK9-PP2C39模块调控甘蓝型油菜脱落酸依赖抗旱性与植株生长之间的平衡。
IF 5.7 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2026-02-05 DOI: 10.1111/tpj.70713
Nan Wang, Jiaming Mai, Chao He, Xianfei Hou, Donghai Jia, Tingdong Fu, Jing Wen, Lun Zhao, Jitao Zou, Yuanguo Gu, Jinxiong Shen

Drought poses a critical threat to global agriculture, food security, and livestock sustainability. In Brassica napus L. (B. napus), a major oilseed crop, yield losses under water deficit underscore the urgent need for breeding strategies that improve water-use efficiency. Here, this study demonstrates that CIPK9 loss-of-function lines of B. napus displayed enhanced drought tolerance compared with the wild-type (WT). Yeast two-hybrid, split-luciferase complementation (LCI), and bimolecular fluorescence complementation (BiFC) assays showed that BnaCIPK9 physically interacts with PP2C39 both in vivo and in vitro. Transcript analysis and enzymatic assays further revealed that CIPK9 functioned in an abscisic acid (ABA)-dependent pathway regulating ABA biosynthesis and enhanced antioxidant capacity by promoting reactive oxygen species (ROS) scavenging. In Arabidopsis, both pp2c39 and cipk9 mutants exhibited stronger drought tolerance than WT plants. Notably, cipk9 mutants showed greater detoxification capacity, resulting in reduced ROS accumulation, higher stomatal conductance, and increased growth, whereas pp2c39 mutants triggered hyperactive stress signaling, leading to elevated ROS levels, lower stomatal conductance, and growth inhibition. These findings highlight a dual drought-response strategy that balances stress defense with cellular homeostasis to sustain growth. Specifically, PP2C39 mediates ABA-induced stress signaling, while the PP2C39–CIPK9 module mitigates its cytotoxic consequences, and their interaction links two distinct pathways to maintain equilibrium between defense and growth. This work provides mechanistic insights for breeding, suggesting that exploiting functional redundancy can reduce excessive self-regulation to improve stress resilience while avoiding modifications that overactivate stress responses and compromise plant development.

干旱对全球农业、粮食安全和畜牧业可持续性构成严重威胁。甘蓝型油菜(Brassica napus L., B. napus)是一种主要的油籽作物,在缺水条件下产量损失突出表明迫切需要提高水分利用效率的育种策略。本研究表明,与野生型(WT)相比,甘蓝型油菜CIPK9功能缺失系表现出更强的耐旱性。酵母双杂交、分裂荧光素酶互补(LCI)和双分子荧光互补(BiFC)实验表明,BnaCIPK9在体内和体外均与PP2C39发生物理相互作用。转录分析和酶促实验进一步表明,CIPK9在ABA依赖通路中发挥作用,通过促进活性氧(ROS)清除来调节ABA的生物合成和增强抗氧化能力。在拟南芥中,pp2c39和cipk9突变体均表现出比WT更强的耐旱性。值得注意的是,cipk9突变体表现出更强的解毒能力,导致ROS积累减少,气孔导度提高,生长加快,而pp2c39突变体引发过度活跃的胁迫信号,导致ROS水平升高,气孔导度降低,生长抑制。这些发现强调了一种双重干旱响应策略,即平衡应激防御和细胞稳态以维持生长。具体来说,PP2C39介导aba诱导的应激信号,而PP2C39- cipk9模块减轻其细胞毒性后果,它们的相互作用将两个不同的途径联系起来,以维持防御和生长之间的平衡。这项工作为育种提供了机制上的见解,表明利用功能冗余可以减少过度的自我调节,以提高应激恢复能力,同时避免过度激活应激反应和损害植物发育的修饰。
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引用次数: 0
CBL1/9–CIPK6 complex negatively regulates Respiratory burst oxidase homolog D in Arabidopsis thaliana CBL1/9-CIPK6复合物负调控拟南芥呼吸爆发氧化酶同源物D。
IF 5.7 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2026-02-04 DOI: 10.1111/tpj.70700
Niraj Kumar Vishwakarma, Shalini Yadav, Atish Sardar, Megha Choudhary, Debasis Chattopadhyay

Plant innate immune response is a well-balanced process with positive and negative regulations for the plants to survive. Calcium signaling is essential for pathogen-associated molecular pattern (PAMP)-driven respiratory burst oxidase homolog D (RBOHD)-mediated reactive oxygen species (ROS) burst. We show that calcium sensors calcineurin B like protein 1 (CBL1) and CBL9 and their interacting protein kinase CIPK6 negatively regulate RBOHD activity and immune response in Arabidopsis thaliana. Arabidopsis mutant cbl1cbl9, like cipk6, exhibited enhanced resistance and ROS production when infected with the bacterial pathogen Pseudomonas syringae pv. tomato (Pst). CBL1 and CBL9 enhanced kinase activity of CIPK6. CBL1/9-CIPK6 module interacts with RBOHD at the plasma membrane. CIPK6 along with CBL1 reduces RBOHD activity in planta. CIPK6 phosphorylates the N-terminal cytoplasmic domain of RBOHD at a non-conserved (S33) and a conserved (S39) serine residue. While S39 phosphorylation increased RBOHD activity, S33 phosphorylation drastically reduced it and superseded the effect of S39 phosphorylation. We propose a model that CIPK6 phosphorylates RBOHD at S33 to suppress its activity to balance ROS generation in post-PTI situation in Arabidopsis. Our study reports a direct mechanism of negative regulation of ROS production and plant immune response by a calcium-signaling module in Arabidopsis thaliana.

植物的先天免疫反应是一个平衡的过程,有正负调节,以维持植物的生存。钙信号是病原体相关分子模式(PAMP)驱动的呼吸爆发氧化酶同源物D (RBOHD)介导的活性氧(ROS)爆发所必需的。我们发现钙传感器钙调神经磷酸酶B样蛋白1 (CBL1)和CBL9及其相互作用的蛋白激酶CIPK6负调控拟南芥RBOHD活性和免疫应答。拟南芥突变体cbl1cbl9与cipk6一样,在感染丁香假单胞菌pv后表现出增强的抗性和ROS的产生。番茄(Pst)。CBL1和CBL9增强了CIPK6的激酶活性。CBL1/9-CIPK6模块在质膜上与RBOHD相互作用。CIPK6和CBL1可降低植物RBOHD活性。CIPK6在非保守(S33)和保守(S39)丝氨酸残基上磷酸化RBOHD的n端胞质结构域。S39磷酸化可提高RBOHD活性,而S33磷酸化可显著降低RBOHD活性,并取代S39磷酸化的作用。我们提出了一个模型,CIPK6在S33位点磷酸化RBOHD,抑制其活性,以平衡pti后拟南芥中ROS的产生。我们的研究报告了拟南芥钙信号模块负调控ROS产生和植物免疫应答的直接机制。
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引用次数: 0
Sex-specific ethylene responses drive floral sexual plasticity in Cannabis sativa 性别特异性乙烯反应驱动大麻花的性可塑性。
IF 5.7 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2026-02-04 DOI: 10.1111/tpj.70721
Adrian S. Monthony, Julien Roy, Maxime de Ronne, Olivia Carlson, Susan J. Murch, Davoud Torkamaneh

Cannabis sativa L. exhibits pronounced sexual plasticity in which both XX and XY plants can undergo floral phenotypic sex reversal in response to ethylene modulation, yet the underlying molecular mechanisms remain poorly defined. Here, we present the most extensive multi-omic analysis of ethylene-induced sex change in C. sativa to date, integrating over 130 RNA-seq libraries, ethylene pathway metabolite quantification, and whole-genome sequencing across three XX and XY genotypes. Treatments with silver thiosulfate and ethephon induced more than 80% phenotypic conversion, but transcriptomic responses diverged sharply between XX and XY plants. Profiling 47 ERGs revealed 14 high-confidence candidates, including CsACS1, CsACO5, CsERF1, and CsMTN, with sex-specific and temporal expression patterns that show dynamic ethylene mediation of plasticity. Early transcriptional activation occurred prior to the emergence of flowers, within 18 h of sex-change treatments and the photoperiod-induced transition to flowering. As opposite-sex floral tissues emerged, ethylene-related gene expression shifted accordingly within developing floral organs, with distinct sets of genes stabilizing the opposite-sex phenotype in XX and XY plants. Several candidates were located in non-recombining regions of the X chromosome or were absent from the Y chromosome, and most exhibited low nucleotide diversity, consistent with functional constraint. These results provide a high-resolution view of ethylene-responsive sexual plasticity in cannabis and show that the shared capacity for sex reversal in XX and XY plants is implemented through distinct regulatory trajectories that produce opposite-sex floral phenotypes. This work expands the mechanistic understanding of sex expression in dioecious species and identifies candidate genes relevant to the development of sex-stable cultivars.

大麻(Cannabis sativa L.)表现出明显的性别可塑性,其中XX和XY植物都可以在乙烯调节下发生花表型性别逆转,但潜在的分子机制尚未明确。在这里,我们介绍了迄今为止最广泛的乙烯诱导的sativa性别变化的多组学分析,整合了超过130个RNA-seq文库,乙烯途径代谢物量化和三种XX和XY基因型的全基因组测序。硫代硫酸银和乙烯利处理诱导了80%以上的表型转化,但转录组反应在XX和XY植株之间存在明显差异。对47个ERGs进行分析,发现了14个高可信度候选基因,包括CsACS1、CsACO5、CsERF1和CsMTN,它们具有性别特异性和时间特异性表达模式,显示乙烯对可塑性的动态调节。早期的转录激活发生在花的出现之前,在变性处理和光周期诱导的开花过渡的18小时内。随着异性花组织的出现,发育中的花器官内乙烯相关基因的表达也发生了相应的变化,XX和XY植物中有不同的基因组稳定异性表型。一些候选基因位于X染色体的非重组区或不存在于Y染色体上,并且大多数表现出低核苷酸多样性,符合功能限制。这些结果提供了大麻中乙烯响应性可塑性的高分辨率视图,并表明XX和XY植物的性别逆转共享能力是通过产生异性花表型的不同调节轨迹实现的。这项工作扩大了对雌雄异株物种性别表达机制的理解,并确定了与性稳定品种发育相关的候选基因。
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引用次数: 0
Pohsphorylation of MAP4K1 and MAP4K2 by OST1 is required for drought tolerance OST1对MAP4K1和MAP4K2的磷酸化是抗旱性所必需的。
IF 5.7 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2026-02-04 DOI: 10.1111/tpj.70723
Pengcheng Hu, Lipeng Zheng, Lan Chen, Yiming Zhou, Yuxin Wang, Tongtong huang, He Zhang, Yong Ding

Protein phosphorylation has pivotal roles in ABA and dehydration stress signaling in higher plants. However, little is known about MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE KINASE (MAP4K) in dehydration tolerance. Here, we report MAP4K1 and MAP4K2 are involved in dehydration tolerance. Mutations in MAP4K1 or MAP4K2 did not show obvious phenotype whereas map4k1 map4k2 double mutant exhibited the dwarf phenotype and low dehydration tolerance with hyposensitivity to exogenous abscisic acid. MAP4K1 and MAP4K2 interacted with SnRK2.2, SnRK2.3, and OST1 in vitro and in vivo. OST1, but not SnRK2.2 or SnRK2.3, phosphorylated MAP4K1 and MAP4K2. Mass spectrometry and phosphorylation activity assay revealed that OST1 phosphorylated MAP4K1 on serine 487 and MAP4K2 on serine 488, respectively. MAP4K1 and MAP4K2 as well as OST1 act in the same dehydration stress pathway, with OST1 acting downstream of MAP4K1 and MAP4K2. Together, we identified MAP4K1 and MAP4K2 as new substrates of OST1, and MAP4K1 and MAP4K2 are redundant in dehydration tolerance.

蛋白质磷酸化在高等植物ABA和脱水胁迫信号传导中起着关键作用。然而,对丝裂原活化蛋白激酶激酶激酶激酶(MAP4K)在脱水耐受性中的作用知之甚少。在这里,我们报道MAP4K1和MAP4K2参与脱水耐受性。MAP4K1和MAP4K2双突变体表现为矮化表型和低脱水耐受性,对外源脱落酸不敏感。在体外和体内,MAP4K1和MAP4K2与SnRK2.2、SnRK2.3和OST1相互作用。OST1磷酸化MAP4K1和MAP4K2,而SnRK2.2和SnRK2.3不磷酸化。质谱分析和磷酸化活性分析显示,OST1分别磷酸化MAP4K1的丝氨酸487和MAP4K2的丝氨酸488。MAP4K1和MAP4K2以及OST1在相同的脱水应激途径中起作用,其中OST1作用于MAP4K1和MAP4K2的下游。总之,我们确定了MAP4K1和MAP4K2是OST1的新底物,MAP4K1和MAP4K2在脱水耐受性中是多余的。
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引用次数: 0
The transcription factor NO TRANSMITTING TRACT/WIP2 modulates cytokinin homeostasis in Arabidopsis 转录因子NO传输通道/WIP2调节拟南芥细胞分裂素稳态。
IF 5.7 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2026-02-03 DOI: 10.1111/tpj.70715
David Díaz-Ramírez, Edgar Demesa-Arevalo, Yolanda Durán-Medina, Rosa E. Becerra-García, José E. Cruz-Valderrama, Beatriz E. Ruiz-Cortés, Humberto Herrera-Ubaldo, Ricardo A. Chávez Montes, Maurizio Di Marzo, Clelia De la Peña, Lucia Colombo, Martin Sagasser, Rüdiger Simon, Ondrej Novak, Stefan de Folter, Nayelli Marsch-Martinez

The transcription factor WIP2/NO TRANSMITTING TRACT (WIP2/NTT) belongs to the WIP zinc finger family. Loss of WIP/NTT function in Arabidopsis thaliana causes alterations in specific tissues in the gynoecium. It also impairs root development, but only when combined with the loss of WIP4 and WIP5 function, due to redundancy. Certain mutant loss-of-function phenotypes can be recovered by cytokinin application, NTT interacts with cytokinin signaling components, and the phenotypes displayed by plants with increased WIP2/NTT expression also suggest a possible interaction with this pathway. Therefore, the objective of this study was to investigate the relationship between WIP2/NTT and the cytokinin pathway. To overcome the issue of genetic redundancy, we used a commonly used inducible system. We found that WIP2/NTT induction alters cytokinin levels and signaling in a tissue-specific manner, as shown by cytokinin content measurements and TCSn::GFP reporter analysis. Transcriptome analyses revealed candidate target genes related to the cytokinin pathway. Yeast one-hybrid and transactivation assays demonstrated direct NTT binding to regulatory regions of the cytokinin genes ISOPENTENYL TRANSFERASE 5 (IPT5), ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 6 (AHP6), and CYTOKININ OXIDASE/DEHYDROGENASE 7 (CKX7) involved in cytokinin biosynthesis, signaling, and degradation, respectively. Moreover, immunolocalization assays revealed that cytokinin distribution was altered in loss of function mutants and after NTT induction. The results of this work indicate that WIP2/NTT modulates cytokinin homeostasis.

转录因子WIP2/NO传输道(WIP2/NTT)属于WIP锌指家族。在拟南芥中,WIP/NTT功能的丧失会导致雌蕊中特定组织的改变。它也会损害根的发育,但只有在与WIP4和WIP5功能的丧失相结合时,由于冗余。某些突变体丧失功能的表型可以通过细胞分裂素的应用恢复,NTT与细胞分裂素信号组分相互作用,WIP2/NTT表达增加的植物所显示的表型也表明可能与该途径相互作用。因此,本研究的目的是探讨WIP2/NTT与细胞分裂素通路的关系。为了克服遗传冗余的问题,我们使用了一种常用的诱导系统。我们发现WIP2/NTT诱导以组织特异性的方式改变细胞分裂素水平和信号传导,如细胞分裂素含量测量和TCSn::GFP报告者分析所示。转录组分析揭示了与细胞分裂素途径相关的候选靶基因。酵母单杂交和转激活实验表明,NTT直接结合细胞分裂素基因异戊烯基转移酶5 (IPT5)、拟南芥组氨酸磷酸转移蛋白6 (AHP6)和细胞分裂素氧化酶/脱氢酶7 (CKX7)的调控区域,分别参与细胞分裂素的生物合成、信号传导和降解。此外,免疫定位分析显示,细胞分裂素分布在功能丧失突变体和NTT诱导后发生了改变。这项工作的结果表明,WIP2/NTT调节细胞分裂素的稳态。
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引用次数: 0
A novel domain of unknown function 707 protein coordinates root growth and drought tolerance 一个功能未知的707蛋白新结构域协调根系生长和耐旱性。
IF 5.7 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2026-02-02 DOI: 10.1111/tpj.70710
Qi Yan, Yunyue Xiao, Xue Li, Shengsheng Wang, Jiyu Zhang

A well-developed root system is one of the morphological mechanisms through which xerophytes adapt to drought. However, the molecular mechanisms underlying root growth are not completely known. In this work, two domain of unknown function 707 (DUF707) proteins were identified as hub genes for the response of roots to drought stress in Lespedeza potaninii, a xerophytic subshrub. We found that angiosperm DUF707 proteins can be divided into two subfamilies. LpDUF707-1 expression was strongly induced under drought stress and abscisic acid (ABA) treatment in the roots of L. potaninii, and its promoter activity in the roots was significantly induced by drought stress and mannitol treatments. The overexpression of LpDUF707-1 significantly improved root growth and drought tolerance, whereas the silencing of LpDUF707-1 inhibited root growth and reduced drought tolerance. We further revealed that the LpOBP3.1 transcription factor directly binds to the promoter region of LpDUF707-1, thereby repressing its activity. LpOBP3.1 expression was strongly suppressed under drought stress and ABA treatment in the roots of L. potaninii. The overexpression of LpOBP3.1 significantly inhibited root growth and decreased drought tolerance, whereas LpOBP3.1-RNAi lines presented the opposite pattern. Collectively, our results demonstrated that this novel module regulates root growth and drought tolerance in L. potaninii, thus providing gene targets for the development of elite crop varieties with well-developed root-mediated drought tolerance.

根系发育良好是旱生植物适应干旱的形态机制之一。然而,根系生长的分子机制尚不完全清楚。本研究鉴定了两个未知功能域707 (DUF707)蛋白为旱生亚灌木胡枝子根系响应干旱胁迫的枢纽基因。我们发现被子植物DUF707蛋白可分为两个亚家族。干旱胁迫和ABA处理强烈诱导LpDUF707-1的表达,干旱胁迫和甘露醇处理显著诱导LpDUF707-1的启动子活性。过表达LpDUF707-1显著提高了根的生长和耐旱性,而沉默LpDUF707-1则抑制了根的生长,降低了根的耐旱性。我们进一步发现,LpOBP3.1转录因子直接结合到LpDUF707-1的启动子区域,从而抑制其活性。在干旱胁迫和ABA处理下,LpOBP3.1的表达受到强烈抑制。过表达LpOBP3.1显著抑制了根的生长,降低了根的耐旱性,而过表达LpOBP3.1- rnai则相反。综上所述,我们的研究结果表明,该新模块调节了L. potaninii的根系生长和耐旱性,从而为培育具有良好根系介导耐旱性的优良作物品种提供了基因靶点。
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引用次数: 0
Thermal acclimation of Pinus massoniana to warming depends on water conditions and climate of origin 马尾松对变暖的热适应取决于水条件和原产地气候。
IF 5.7 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2026-02-02 DOI: 10.1111/tpj.70695
Yong Cui, Mingkai Jiang, Ting Wu, Changchang Shao, Danielle A. Way, David T. Tissue, Honglang Duan

Future climatic conditions are projected to become warmer and drier, critically challenging tree growth and survival. Understanding how photosynthesis and respiration of tree seedlings acclimate to warming is pivotal for predicting seedling responses to climate change and tree carbon dynamics. However, the photosynthetic capacity parameters of thermal acclimation remain unresolved; particularly their interaction with water availability constraints and local climate adaptation needs to be fully explored. Here, we grew seedlings of a widely planted timber species in subtropical China, Pinus massoniana, with two provenances from contrasting climates of origin (cooler-drier and warmer-wetter), under three growth temperatures (22°C, 26°C, and 30°C) and two water conditions (well-watered and drought). Temperature responses of gas exchange and nutrient status were investigated, together with a data synthesis of meta-analysis. The experimental results showed that under well-watered conditions, the optimal temperature for photosynthesis (ToptA), the net photosynthetic rate (A25) and dark respiration rate (R25) at 25°C, and respiratory sensitivity parameters (Q10) remained unexpectedly stable under warming for both provenances, contrasting with our hypotheses; however, data synthesis shows that the ToptA from the cooler region increased with warming. Drought reduced ToptA and A25, largely related to the magnitude of warming. Compared to drought-only conditions, warming and drought in combination induced an increase in ToptA and the optimal temperature for photosynthetic electron transport rate (ToptJ) in the provenance from the warmer-wetter region and a reduction in Q10 for both provenances, but did not affect A25 and R25. Collectively, our results indicated that thermal acclimation of photosynthesis and respiration in P. massoniana seedlings was limited under well-watered conditions. However, drought increased the capacity for thermal acclimation in the warmer-wetter provenance compared to the cooler-drier provenance, suggesting that P. massoniana seedlings from warmer-wetter areas may cope better with future warm and dry environments.

预计未来的气候条件将变得更加温暖和干燥,严重挑战树木的生长和生存。了解树木幼苗光合作用和呼吸作用如何适应气候变暖是预测幼苗对气候变化和树木碳动态响应的关键。然而,热驯化的光合能力参数尚未确定;特别是需要充分探索它们与水资源供应限制和当地气候适应的相互作用。在这里,我们在中国亚热带广泛种植的木材树种马尾松(Pinus massoniana)的两种种源下,在三种生长温度(22°C, 26°C和30°C)和两种水分条件(丰水和干旱)下进行了幼苗生长。研究了气体交换和营养状况的温度响应,并对数据进行了meta分析。结果表明,在水分充足的条件下,两种种源的光合作用最佳温度(ToptA)、25°C时的净光合速率(A25)和暗呼吸速率(R25)以及增温条件下的呼吸敏感性参数(Q10)均保持稳定,与我们的假设相反;然而,数据综合表明,来自较冷地区的ToptA随着变暖而增加。干旱降低了ToptA和A25,这在很大程度上与变暖的程度有关。与干旱条件相比,增温和干旱联合处理导致暖湿区种源的ToptA和光合电子传递速率最适温度(ToptJ)升高,Q10降低,但对A25和R25没有影响。综上所述,在水分充足的条件下,马尾松幼苗光合作用和呼吸作用的热驯化受到限制。然而,相对于冷干种源,干旱增加了暖湿种源的热驯化能力,这表明来自暖湿地区的马尾松幼苗可能更好地应对未来的温暖和干燥环境。
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引用次数: 0
Multi-season analysis reveals hundreds of drought-responsive genes in sorghum 多季节分析揭示了高粱中数百个干旱响应基因。
IF 5.7 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2026-02-02 DOI: 10.1111/tpj.70657
Benjamin Cole, Wenxin Zhang, Junming Shi, Hao Wang, Christopher Baker, Nelle Varoquaux, Joy Hollingsworth, Robert Hutmacher, Jeffery Dahlberg, Grady Pierroz, Kerrie W. Barry, Vasanth Singan, Yuko Yoshinaga, Christopher Daum, Matthew Zane, Matthew Blow, Ronan O’Malley, Shengqiang Shu, Jerry W. Jenkins, John T. Lovell, Jeremy Schmutz, John W. Taylor, Devin Coleman-Derr, Axel Visel, Peggy G. Lemaux, Elizabeth Purdom, John P. Vogel

Persistent drought affects global crop production and is becoming more severe in many parts of the world in recent decades. Deciphering how plants respond to drought will facilitate the development of flexible mitigation strategies. Sorghum bicolor L. Moench (sorghum), a major cereal crop and an emerging bioenergy crop, exhibits remarkable resilience to drought. To better understand the molecular traits that underlie sorghum's remarkable drought tolerance, we undertook a large-scale sorghum gene expression profiling effort, totaling nearly 1500 transcriptome profiles, across a 3-year field study with replicated plots in California's Central Valley. This study included time-resolved gene expression data from roots and leaves of two sorghum genotypes, BTx642 and RTx430, with different pre-flowering and post-flowering drought-tolerance adaptations under control and drought conditions. Quantification of genotype-specific drought tolerance effects was enabled by de novo sequencing, assembly, and annotation of both BTx642 and RTx430 genomes. These reference-quality genomes were used to construct a pangene set for characterizing conserved and genotype-specific expression. By integrating time-resolved transcriptomic responses to drought in the field across three consecutive years, we identified a set of 726 drought-responsive genes that responded similarly in all 3 years of our field study. Functional enrichment analysis identified abiotic stress, secondary cell wall-related processes and metabolism as particularly affected under both types of drought stress. We also found that some glyoxylate cycle pathway genes, including malate synthase and isocitrate lyase, are differentially regulated particularly during post-flowering drought stress, implicating this pathway as potentially important for drought responsiveness. This expansive dataset represents a unique resource for sorghum and drought research communities and provides a methodological framework for the integration of multi-faceted time-resolved transcriptomic datasets.

持续干旱影响全球作物生产,近几十年来在世界许多地区变得越来越严重。破译植物对干旱的反应将有助于制定灵活的缓解战略。高粱是一种重要的谷类作物和新兴的生物能源作物,具有显著的抗旱能力。为了更好地了解高粱卓越耐旱性背后的分子特征,我们进行了一项大规模的高粱基因表达谱研究,总计近1500个转录组谱,在加州中央山谷进行了为期3年的实地研究。本研究收集了在对照和干旱条件下具有不同花前和花后抗旱适应性的2种高粱基因型BTx642和RTx430的根和叶的时间分辨基因表达数据。通过对BTx642和RTx430基因组的从头测序、组装和注释,可以量化基因型特异性耐旱性效应。这些参考质量的基因组被用来构建一个泛基因集,用于表征保守的和基因型特异性的表达。通过整合连续三年对干旱的时间分辨转录组反应,我们确定了一组726个干旱反应基因,这些基因在我们所有三年的实地研究中都有相似的反应。功能富集分析发现,在这两种干旱胁迫下,非生物胁迫、次级细胞壁相关过程和代谢受到了特别的影响。我们还发现一些乙醛酸循环途径基因,包括苹果酸合成酶和异柠檬酸裂解酶,在开花后干旱胁迫下受到差异调节,这表明该途径对干旱响应可能很重要。这个庞大的数据集为高粱和干旱研究界提供了一个独特的资源,并为整合多方面的时间分辨率转录组数据集提供了一个方法框架。
{"title":"Multi-season analysis reveals hundreds of drought-responsive genes in sorghum","authors":"Benjamin Cole,&nbsp;Wenxin Zhang,&nbsp;Junming Shi,&nbsp;Hao Wang,&nbsp;Christopher Baker,&nbsp;Nelle Varoquaux,&nbsp;Joy Hollingsworth,&nbsp;Robert Hutmacher,&nbsp;Jeffery Dahlberg,&nbsp;Grady Pierroz,&nbsp;Kerrie W. Barry,&nbsp;Vasanth Singan,&nbsp;Yuko Yoshinaga,&nbsp;Christopher Daum,&nbsp;Matthew Zane,&nbsp;Matthew Blow,&nbsp;Ronan O’Malley,&nbsp;Shengqiang Shu,&nbsp;Jerry W. Jenkins,&nbsp;John T. Lovell,&nbsp;Jeremy Schmutz,&nbsp;John W. Taylor,&nbsp;Devin Coleman-Derr,&nbsp;Axel Visel,&nbsp;Peggy G. Lemaux,&nbsp;Elizabeth Purdom,&nbsp;John P. Vogel","doi":"10.1111/tpj.70657","DOIUrl":"10.1111/tpj.70657","url":null,"abstract":"<p>Persistent drought affects global crop production and is becoming more severe in many parts of the world in recent decades. Deciphering how plants respond to drought will facilitate the development of flexible mitigation strategies. <i>Sorghum bicolor</i> L. Moench (sorghum), a major cereal crop and an emerging bioenergy crop, exhibits remarkable resilience to drought. To better understand the molecular traits that underlie sorghum's remarkable drought tolerance, we undertook a large-scale sorghum gene expression profiling effort, totaling nearly 1500 transcriptome profiles, across a 3-year field study with replicated plots in California's Central Valley. This study included time-resolved gene expression data from roots and leaves of two sorghum genotypes, BTx642 and RTx430, with different pre-flowering and post-flowering drought-tolerance adaptations under control and drought conditions. Quantification of genotype-specific drought tolerance effects was enabled by <i>de novo</i> sequencing, assembly, and annotation of both BTx642 and RTx430 genomes. These reference-quality genomes were used to construct a pangene set for characterizing conserved and genotype-specific expression. By integrating time-resolved transcriptomic responses to drought in the field across three consecutive years, we identified a set of 726 drought-responsive genes that responded similarly in all 3 years of our field study. Functional enrichment analysis identified abiotic stress, secondary cell wall-related processes and metabolism as particularly affected under both types of drought stress. We also found that some glyoxylate cycle pathway genes, including malate synthase and isocitrate lyase, are differentially regulated particularly during post-flowering drought stress, implicating this pathway as potentially important for drought responsiveness. This expansive dataset represents a unique resource for sorghum and drought research communities and provides a methodological framework for the integration of multi-faceted time-resolved transcriptomic datasets.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"125 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2026-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12863931/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146103309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Nuclear DNA of plastid origin (NUPTs), neglected driver of genome variation and evolutionary innovation 质体起源核DNA (NUPTs):基因组变异和进化创新中被忽视的驱动力。
IF 5.7 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2026-02-02 DOI: 10.1111/tpj.70685
Lorenzo Carretero-Paulet, Juan Pablo Marczuk-Rojas, Aaron Gálvez-Salido

Plant nuclear genomes contain a variable, though typically minor, fraction of DNA sequences of plastid origin known as NUPTs. Unlike the massive transfer of DNA and genes from the proto-organelle genome to the nucleus that occurred during the endosymbiotic event that gave rise to plastids, the formation of NUPTs is an ongoing process that does not imply concomitant DNA loss. Although NUPTs are generally considered to be potentially deleterious insertions that are continuously generated and rapidly eliminated at near-constant turnover rates, accumulating evidence reveals alternative evolutionary trajectories. In this review, we discuss recent findings that highlight the episodic formation of NUPTs, their subsequent proliferation, and their eventual long-term fixation within the nuclear genome. We also explore their non-random spatial association with specific genomic elements. NUPTs show preferential overlap with specific superfamilies of transposable elements, which may facilitate their proliferation and dispersal throughout the nuclear genome. Regarding protein-coding genes, the contribution of NUPTs varies among species. In contrast, NUPTs are found to be consistently enriched among certain classes of non-coding RNA genes, notably rRNA, tRNA, and specific regulatory RNA families, suggesting that they are involved in the evolution of gene regulation and translational machinery. Overall, these findings underscore the unexpected complexity of the mechanisms underlying NUPT formation and support the idea that they are a significant source of genome variation and evolutionary innovation. Further research is necessary to fully elucidate the mechanisms underlying NUPT formation, as well as to determine their potential adaptive significance in plant genome evolution.

植物核基因组包含一个可变的,虽然通常很少,DNA序列的质体起源称为nupt的部分。与产生质体的内共生过程中DNA和基因从原细胞器基因组向细胞核的大量转移不同,nupt的形成是一个持续的过程,并不意味着伴随着DNA的丢失。尽管nupt通常被认为是潜在的有害插入,不断产生并以接近恒定的周转率迅速消除,但越来越多的证据揭示了另一种进化轨迹。在这篇综述中,我们讨论了最近的发现,强调了nupt的偶发性形成,它们随后的增殖,以及它们最终在核基因组中的长期固定。我们还探讨了它们与特定基因组元素的非随机空间关联。nupt与转座因子的特定超家族表现出优先重叠,这可能促进它们在核基因组中的增殖和扩散。关于蛋白质编码基因,nupt的贡献因物种而异。相反,nupt在某些非编码RNA基因中持续富集,特别是rRNA、tRNA和特定调控RNA家族,这表明它们参与了基因调控和翻译机制的进化。总的来说,这些发现强调了NUPT形成机制的意想不到的复杂性,并支持了它们是基因组变异和进化创新的重要来源的观点。需要进一步的研究来充分阐明NUPT形成的机制,并确定它们在植物基因组进化中的潜在适应意义。
{"title":"Nuclear DNA of plastid origin (NUPTs), neglected driver of genome variation and evolutionary innovation","authors":"Lorenzo Carretero-Paulet,&nbsp;Juan Pablo Marczuk-Rojas,&nbsp;Aaron Gálvez-Salido","doi":"10.1111/tpj.70685","DOIUrl":"10.1111/tpj.70685","url":null,"abstract":"<p>Plant nuclear genomes contain a variable, though typically minor, fraction of DNA sequences of plastid origin known as NUPTs. Unlike the massive transfer of DNA and genes from the proto-organelle genome to the nucleus that occurred during the endosymbiotic event that gave rise to plastids, the formation of NUPTs is an ongoing process that does not imply concomitant DNA loss. Although NUPTs are generally considered to be potentially deleterious insertions that are continuously generated and rapidly eliminated at near-constant turnover rates, accumulating evidence reveals alternative evolutionary trajectories. In this review, we discuss recent findings that highlight the episodic formation of NUPTs, their subsequent proliferation, and their eventual long-term fixation within the nuclear genome. We also explore their non-random spatial association with specific genomic elements. NUPTs show preferential overlap with specific superfamilies of transposable elements, which may facilitate their proliferation and dispersal throughout the nuclear genome. Regarding protein-coding genes, the contribution of NUPTs varies among species. In contrast, NUPTs are found to be consistently enriched among certain classes of non-coding RNA genes, notably rRNA, tRNA, and specific regulatory RNA families, suggesting that they are involved in the evolution of gene regulation and translational machinery. Overall, these findings underscore the unexpected complexity of the mechanisms underlying NUPT formation and support the idea that they are a significant source of genome variation and evolutionary innovation. Further research is necessary to fully elucidate the mechanisms underlying NUPT formation, as well as to determine their potential adaptive significance in plant genome evolution.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"125 3","pages":""},"PeriodicalIF":5.7,"publicationDate":"2026-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12863932/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146103260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
SlTIP2;3 mediates H2O2 transport to activate GA signaling and maintain stomatal conductance under high vapor pressure deficit. SlTIP2;3介导H2O2运输,激活GA信号,维持高蒸汽压赤字下气孔导度。
IF 5.7 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2026-02-01 DOI: 10.1111/tpj.70705
Bo Li, Xiaofan Zhao, Jialei Geng, Shuhui Zhang, Jianming Li

As global climate change intensifies, the resultant increase in atmospheric vapor pressure deficit (VPD) significantly affects plant growth and distribution. Under high VPD (HVPD) conditions, plants face a contradiction between increased water evaporation and carbon fixation. A reduction in stomatal conductance (gs) can lead to carbon starvation, causing cellular damage or even death. Aquaporins, which are pivotal in water transport, play a crucial role in modulating plant water balance and gs under HVPD conditions; however, the underlying mechanisms remain inadequately understood. Tomato (Solanum lycopersicum L.) is an important economic crop. This study found that SlTIP2;3 is a key hub for tomato's response to HVPD and regulation of whole-plant hydraulic conductance (Kplant) and gs. The overexpression of SlTIP2;3 was observed to increase Kplant and gs under HVPD, enhancing water transport and mitigating the decline in gs. Additionally, the overexpression of SlTIP2;3 improved root and stem morphology, optimizing water absorption and distribution. In this context, SlTIP2;3, as a hydrogen peroxide (H2O2) transporter, facilitates H2O2 diffusion into cells, regulating gibberellin (GA) synthesis and signaling, thus enhancing both Kplant and gs. This study presents novel evidence indicating that SlTIP2;3 plays a mediating role in the H2O2-GA signaling pathway, which co-regulates plant adaptation to HVPD environments and contributes to maintaining high Kplant and gs. These findings provide valuable molecular insights into plant responses to climate change-induced water stress and support the genetic enhancement of drought-resistant crops.

{"title":"SlTIP2;3 mediates H<sub>2</sub>O<sub>2</sub> transport to activate GA signaling and maintain stomatal conductance under high vapor pressure deficit.","authors":"Bo Li, Xiaofan Zhao, Jialei Geng, Shuhui Zhang, Jianming Li","doi":"10.1111/tpj.70705","DOIUrl":"https://doi.org/10.1111/tpj.70705","url":null,"abstract":"<p><p>As global climate change intensifies, the resultant increase in atmospheric vapor pressure deficit (VPD) significantly affects plant growth and distribution. Under high VPD (HVPD) conditions, plants face a contradiction between increased water evaporation and carbon fixation. A reduction in stomatal conductance (g<sub>s</sub>) can lead to carbon starvation, causing cellular damage or even death. Aquaporins, which are pivotal in water transport, play a crucial role in modulating plant water balance and g<sub>s</sub> under HVPD conditions; however, the underlying mechanisms remain inadequately understood. Tomato (Solanum lycopersicum L.) is an important economic crop. This study found that SlTIP2;3 is a key hub for tomato's response to HVPD and regulation of whole-plant hydraulic conductance (K<sub>plant</sub>) and g<sub>s</sub>. The overexpression of SlTIP2;3 was observed to increase K<sub>plant</sub> and g<sub>s</sub> under HVPD, enhancing water transport and mitigating the decline in g<sub>s</sub>. Additionally, the overexpression of SlTIP2;3 improved root and stem morphology, optimizing water absorption and distribution. In this context, SlTIP2;3, as a hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) transporter, facilitates H<sub>2</sub>O<sub>2</sub> diffusion into cells, regulating gibberellin (GA) synthesis and signaling, thus enhancing both K<sub>plant</sub> and g<sub>s</sub>. This study presents novel evidence indicating that SlTIP2;3 plays a mediating role in the H<sub>2</sub>O<sub>2</sub>-GA signaling pathway, which co-regulates plant adaptation to HVPD environments and contributes to maintaining high K<sub>plant</sub> and g<sub>s</sub>. These findings provide valuable molecular insights into plant responses to climate change-induced water stress and support the genetic enhancement of drought-resistant crops.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"125 3","pages":"e70705"},"PeriodicalIF":5.7,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146123169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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The Plant Journal
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