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Investigating biological nitrogen fixation via single-cell transcriptomics. 通过单细胞转录组学研究生物固氮。
IF 5.6 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-11-20 DOI: 10.1093/jxb/erae454
Wendell J Pereira, Daniel Conde, Noé Perron, Henry W Schmidt, Christopher Dervinis, Rafael E Venado, Jean-Michel Ané, Matias Kirst

The extensive use of nitrogen fertilizers has detrimental environmental consequences, and it is fundamental for society to explore sustainable alternatives. One promising avenue is engineering root nodule symbiosis, a naturally occurring process in certain plant species within the nitrogen-fixing clade, into non-leguminous crops. Advancements in single-cell transcriptomics provide unprecedented opportunities to dissect the molecular mechanisms underlying root nodule symbiosis at the cellular level. This review summarizes key findings from single-cell studies in Medicago truncatula, Lotus japonicus, and Glycine max. We highlight how these studies address fundamental questions about the development of root nodule symbiosis, including the following findings: Single-cell transcriptomics has revealed a conserved transcriptional program in root hair and cortical cells during rhizobial infection, suggesting a common infection pathway across legume species. Characterization of determinate and indeterminate nodules using single-cell technologies supports the compartmentalization of nitrogen fixation, assimilation, and transport into distinct cell populations. Single-cell transcriptomics data has enabled the identification of novel root nodule symbiosis genes and provided new approaches for prioritizing candidate genes for functional characterization. Trajectory inference and RNA velocity analyses of single-cell transcriptomics data have allowed the reconstruction of cellular lineages and dynamic transcriptional states during root nodule symbiosis.

大量使用氮肥会对环境造成有害影响,因此社会必须探索可持续的替代方法。根瘤共生是固氮族中某些植物物种自然发生的过程,将根瘤共生工程化到非豆科作物中是一个很有前景的途径。单细胞转录组学的进步为在细胞水平剖析根瘤共生的分子机制提供了前所未有的机会。本综述总结了对Medicago truncatula、Lotus japonicus和Glycine max进行单细胞研究的主要发现。我们重点介绍了这些研究如何解决有关根瘤共生发展的基本问题,包括以下发现:单细胞转录组学揭示了根毛和皮层细胞在根瘤菌感染过程中的保守转录程序,表明豆科植物物种之间存在共同的感染途径。利用单细胞技术对确定性和非确定性结核进行表征,支持将固氮、同化和运输划分为不同的细胞群。单细胞转录组学数据帮助鉴定了新的根瘤共生基因,并为优先选择候选基因进行功能表征提供了新方法。通过对单细胞转录组学数据进行轨迹推断和 RNA 速度分析,可以重建根瘤共生过程中的细胞系和动态转录状态。
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引用次数: 0
Innovative modeling on the effects of low-temperature stress on rice yields. 低温胁迫对水稻产量影响的创新模型。
IF 5.6 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-11-18 DOI: 10.1093/jxb/erae452
Yanying Shi, Haoyu Ma, Tao Li, Erjing Guo, Tianyi Zhang, Xijuan Zhang, Xianli Yang, Lizhi Wang, Shukun Jiang, Yuhan Deng, Kaixin Guan, Mingzhe Li, Zhijuan Liu, Xiaoguang Yang

The increasing frequency and intensity of low-temperature events in temperate and cold rice production regions threaten rice yields under climate change. While process-based crop models can project climate impacts on rice yield, their accuracy under low-temperature conditions has not been well-evaluated. Our six-year chamber experiments revealed that low temperatures reduce spikelet fertility from panicle initiation to flowering, grain number per spike during panicle development, and grain weight during grain filling. We examined the algorithms of spikelet fertility response to temperature used in crop models. Results showed that simulation performance is poor for crop yields if the same function was used at different growth stages outside the booting stage. Indeed, we replaced a parameter spikelet fertility algorithm of the ORYZA model and developed the function of estimating grain number per spike and grain weight. After that, the improved equation algorithm was applied to 10 rice growth models. New functions considered the harmful effects of low temperatures on rice yield at different stages. In addition, the threshold temperatures of the cold tolerance were set for different rice varieties. The improved algorithm enhances the model's ability to simulate rice yields under climate change, providing a more reliable tool for adapting rice production to future climatic challenges.

温带和寒带水稻产区低温事件的频率和强度不断增加,威胁着气候变化下的水稻产量。虽然基于过程的作物模型可以预测气候对水稻产量的影响,但其在低温条件下的准确性尚未得到很好的评估。我们为期六年的室内试验表明,低温会降低从圆锥花序开始到开花期间的小穗结实率、圆锥花序发育期间的每穗粒数以及籽粒灌浆期间的粒重。我们研究了作物模型中使用的小穗生育力对温度反应的算法。结果表明,如果在拔节期以外的不同生长阶段使用相同的函数,作物产量的模拟性能很差。因此,我们替换了 ORYZA 模型中的一个小穗生育力参数算法,并开发了估算每穗粒数和粒重的功能。之后,改进后的方程算法被应用于 10 个水稻生长模型。新函数考虑了不同阶段低温对水稻产量的有害影响。此外,还为不同的水稻品种设定了耐寒临界温度。改进后的算法提高了模型模拟气候变化下水稻产量的能力,为水稻生产适应未来气候挑战提供了更可靠的工具。
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引用次数: 0
Phytochrome-interacting factors PIF4 and PIF5 directly regulate autophagy during leaf senescence in Arabidopsis. 拟南芥叶片衰老过程中植物色素相互作用因子PIF4和PIF5直接调控自噬。
IF 5.6 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-11-16 DOI: 10.1093/jxb/erae469
Juhyeon Lee, Myeong Hoon Kang, Da-Min Choi, Anne Marmagne, Jeehye Park, Heeho Lee, Eunha Gwak, Jong Chan Lee, Jeong-Il Kim, Céline Masclaux-Daubresse, Pyung Ok Lim

During leaf senescence, autophagy plays a critical role by removing damaged cellular components and participating in nutrient remobilization to sink organs. However, how AUTOPHGAY (ATG) genes are regulated during natural leaf senescence remains largely unknown. In this study, we attempted to identify upstream transcriptional regulator(s) of ATGs and their molecular basis during leaf senescence in Arabidopsis through the combined analyses of promoter binding, autophagy flux, and genetic interactions. We found that PIF4 and PIF5 (PIF4/PIF5) directly bind to the promoters of the ATG5, ATG12a, ATG12b, ATG8a, ATG8e, ATG8f, and ATG8g, inducing their transcription. These target ATGs are downregulated in pif4, pif5, and pif4pif5 mutants, resulting in decreased autophagic activity and slower degradation of chloroplast proteins and chlorophyll. Conversely, overexpression of ATG8s accelerated protein degradation with early leaf senescence. Moreover, our data suggests partial suppression of the pif4pif5 phenotype by ATG8a overexpression. PIF4/PIF5 also influences senescence induced by nutrient starvation, another hallmark of the autophagy pathway. Furthermore, we observed that the PIF4/PIF5-ATG regulatory module may contribute to seed maturation. Our study not only unveils transcriptional regulators of autophagy in natural leaf senescence but also underscores the potential role of PIF4/PIF5 as functional regulators in leaf senescence and nutrient remobilization.

在叶片衰老过程中,自噬通过清除受损的细胞成分和参与养分向下沉器官的再动员发挥着关键作用。然而,在自然叶片衰老过程中,AUTOPHGAY(ATG)基因是如何被调控的在很大程度上仍是未知数。在本研究中,我们试图通过启动子结合、自噬通量和遗传相互作用的综合分析,确定拟南芥叶片衰老过程中 ATG 的上游转录调控因子及其分子基础。我们发现,PIF4 和 PIF5(PIF4/PIF5)直接与 ATG5、ATG12a、ATG12b、ATG8a、ATG8e、ATG8f 和 ATG8g 的启动子结合,诱导其转录。在 pif4、pif5 和 pif4pif5 突变体中,这些目标 ATG 下调,导致自噬活性降低,叶绿体蛋白质和叶绿素降解速度减慢。相反,过表达 ATG8s 会加速蛋白质降解,导致叶片提前衰老。此外,我们的数据表明,ATG8a 的过表达部分抑制了 pif4pif5 的表型。PIF4/PIF5 还影响营养饥饿诱导的衰老,这是自噬途径的另一个标志。此外,我们还观察到 PIF4/PIF5-ATG 调控模块可能有助于种子成熟。我们的研究不仅揭示了自然叶片衰老过程中自噬的转录调控因子,还强调了 PIF4/PIF5 作为叶片衰老和养分再动员功能调控因子的潜在作用。
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引用次数: 0
Diverse roles of phytohormonal signaling in modulating plant-virus interaction. 植物激素信号在调节植物与病毒相互作用中的不同作用
IF 5.6 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-11-16 DOI: 10.1093/jxb/erae468
Shambhavi Sharma, Manoj Prasad

Virus infection brings about changes in the transcriptome, proteome and metabolome status of the infected plant wherein substantial alterations in the abundance of phytohormones and associated components involved in their signaling pathways have been observed. In the recent years, extensive research in the field of plant virology has showcased the undisputable significance of phytohormone signaling during plant-virus interactions. Apart from acting as growth regulators, phytohormones elicit robust immune response, which restricts the viral multiplication within the plant as well as its propagation by vector. Interestingly, these pathways have been shown to not only act as isolated mechanisms but as complex intertwined regulatory cascades where, the cross-talk among different phytohormones and with other antiviral pathways takes place during plant-virus interplay. Viruses cleverly disrupt phytohormone homeostasis via their multifunctional effectors that seems to be smart approach adopted by viruses to circumvent phytohormone-mediated plant immune responses. In this review, we summarize the current understanding of role of phytohormone signaling pathways during plant-virus interaction in activating antiviral immune responses of plant and also, how viruses exploit these signaling pathways favoring their pathogenesis.

病毒感染会导致受感染植物的转录组、蛋白质组和代谢组状态发生变化,其中植物激素及其信号通路中的相关成分的丰度发生了重大变化。近年来,植物病毒学领域的广泛研究表明,植物激素信号在植物与病毒相互作用过程中的重要性毋庸置疑。除了作为生长调节剂外,植物激素还能引起强大的免疫反应,从而限制病毒在植物体内的繁殖以及通过载体的传播。有趣的是,这些途径已被证明不仅是孤立的机制,而且是复杂交织的调节级联,在植物与病毒相互作用的过程中,不同植物激素之间以及与其他抗病毒途径之间会发生交叉对话。病毒通过其多功能效应器巧妙地破坏了植物激素的平衡,这似乎是病毒规避植物激素介导的植物免疫反应的聪明方法。在这篇综述中,我们总结了目前对植物与病毒相互作用过程中植物激素信号通路在激活植物抗病毒免疫反应中的作用的理解,以及病毒如何利用这些信号通路促进其致病。
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引用次数: 0
Accounting for the impact of genotype and environment on variation in leaf respiration of wheat in Mexico and Australia. 墨西哥和澳大利亚小麦的基因型和环境对叶片呼吸变化的影响。
IF 5.6 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-11-16 DOI: 10.1093/jxb/erae449
O Gaju, K J Bloomfield, A C A Negrini, A F Bowerman, D Cullerne, B C Posch, C Bryant, Y Fan, M Spence, B Stone, M Gilliham, R T Furbank, G Molero, B J Pogson, K Mathews, A H Millar, A L Pearson, M P Reynolds, E Stroeher, N L Taylor, M H Turnbull, O K Atkin

An approach to improving radiation use efficiency (RUE) in wheat is to screen for variability in rates of leaf respiration in darkness (Rdark). We used a high-throughput system to quantify variation in Rdark among a diverse range of spring wheat genotypes (301 lines) grown in two countries (Mexico and Australia) and two seasons (2017 and 2018), and in doing so quantify the relative importance of genotype (G) and environment (E) in influencing variations in leaf Rdark. Through careful design, residual (unexplained) variation represented less than 10% of the total observed. Up to a third of the variation in Rdark (and related traits) was under genetic control. This suggests opportunities for breeders to use Rdark as a novel selection tool. In addition, E accounted for more than half of the total variation in area-based rates of Rdark. Here, the day of measurement was crucial, suggesting that day-to-day variations in the environment influence rates of Rdark measured at a common temperature. Overall, this study provides new insights into the role G and E play in determining variation in rates of leaf Rdark of one of the most important cereal crops, with implications for future improvements in carbon use efficiency and yield.

提高小麦辐射利用效率(RUE)的一种方法是筛选黑暗中叶片呼吸速率(Rdark)的变异。我们利用高通量系统量化了在两个国家(墨西哥和澳大利亚)和两个季节(2017 年和 2018 年)生长的各种春小麦基因型(301 个品系)之间 Rdark 的变异,并以此量化了基因型(G)和环境(E)在影响叶片 Rdark 变异方面的相对重要性。通过精心设计,残余(无法解释的)变异占观察到的总变异的比例不到 10%。高达三分之一的 Rdark(及相关性状)变异受遗传控制。这为育种者提供了将 Rdark 用作新型选育工具的机会。此外,在基于区域的 Rdark 变异率中,E 占了一半以上。在这里,测量日至关重要,这表明环境的日变化会影响在相同温度下测量的 Rdark 率。总之,这项研究为了解 G 和 E 在决定最重要的谷类作物之一的叶 Rdark 率变化中的作用提供了新的视角,对未来提高碳利用效率和产量具有重要意义。
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引用次数: 0
Passive stomatal closure under extreme drought in an angiosperm species. 一种被子植物在极端干旱条件下的被动气孔关闭。
IF 8.3 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-11-15 DOI: 10.1093/jxb/erad510
Scott A M McAdam, Anju Manandhar, Cade N Kane, Joel A Mercado-Reyes

The phytohormone abscisic acid (ABA) plays a major role in closing the stomata of angiosperms. However, recent reports of some angiosperm species having a peaking-type ABA dynamic, in which under extreme drought ABA levels decline to pre-stressed levels, raises the possibility that passive stomatal closure by leaf water status alone can occur in species from this lineage. To test this hypothesis, we conducted instantaneous rehydration experiments in the peaking-type species Umbellularia californica through a long-term drought, in which ABA levels declined to pre-stress levels, yet stomata remain closed. We found that when ABA levels were lowest during extreme drought, stomata reopen rapidly to maximum rates of gas exchange on instantaneous rehydration, suggesting that the stomata of U. californica were passively closed by leaf water status alone. This contrasts with leaves early in drought, in which ABA levels were highest and stomata did not reopen on instantaneous rehydration. The transition from ABA-driven stomatal closure to passively driven stomatal closure as drought progresses in this species occurs at very low water potentials facilitated by highly embolism-resistant xylem. These results have important implications for understanding stomatal control during drought in angiosperms.

植物激素脱落酸(ABA)在被子植物气孔关闭过程中起着重要作用。然而,最近有报道称,一些被子植物物种具有峰值型 ABA 动态,在极端干旱情况下,ABA 水平会下降到受压前的水平。为了验证这一假设,我们在峰值型物种加州脐橙(Umbellularia californica)中进行了瞬时补水实验,在长期干旱的情况下,ABA 水平会下降到应激前的水平,但气孔仍然关闭。我们发现,在极端干旱期间,当 ABA 水平最低时,加州脐橙的气孔仅受叶片水分状况的影响而被动关闭,而在瞬时补水时,气孔会迅速重新开放,达到最大气体交换速率。这与干旱初期的叶片形成鲜明对比,干旱初期叶片的 ABA 水平最高,气孔不会在瞬间补水时重新打开。该物种在干旱过程中从 ABA 驱动的气孔关闭过渡到被动驱动的气孔关闭,是在极低的水势下发生的,高度抗栓塞的木质部起到了促进作用。这些结果对于理解被子植物干旱期间的气孔控制具有重要意义。
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引用次数: 0
High water use efficiency due to maintenance of photosynthetic capacity in sorghum under water stress. 高粱在水分胁迫下保持光合能力,从而提高了水分利用效率。
IF 5.6 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-11-15 DOI: 10.1093/jxb/erae418
Yazen Al-Salman, Francisco Javier Cano, Emma Mace, David Jordan, Michael Groszmann, Oula Ghannoum

Environmental change requires more crop production per water use to meet the rising global food demands. However, improving crop intrinsic water use efficiency (iWUE) usually comes at the expense of carbon assimilation. Sorghum is a key crop in many vulnerable agricultural systems with higher tolerance to water stress (WS) than most widely planted crops. To investigate physiological controls on iWUE and its inheritance in sorghum, we screened 89 genotypes selected based on inherited haplotypes from an elite line or five exotics lines, containing a mix of geographical origins and dry versus milder climates, which included different aquaporin (AQP) alleles. We found significant variation among key highly heritable gas exchange and hydraulic traits, with some being significantly affected by variation in haplotypes among parental lines. Plants with a higher proportion of the non-stomatal component of iWUE still maintained iWUE under WS by maintaining photosynthetic capacity, independently of reduction in leaf hydraulic conductance. Haplotypes associated with two AQPs (SbPIP1.1 and SbTIP3.2) influenced iWUE and related traits. These findings expand the range of traits that bridge the trade-off between iWUE and productivity in C4 crops, and provide possible genetic regions that can be targeted for breeding.

环境变化要求提高作物的单位用水产量,以满足不断增长的全球粮食需求。然而,提高作物内在水分利用效率(iWUE)通常以牺牲碳同化为代价。高粱是许多脆弱农业系统中的主要作物,它对水胁迫(WS)的耐受性高于大多数广泛种植的作物。为了研究高粱对 iWUE 的生理调控及其遗传性,我们筛选了 89 个基因型,这些基因型是根据一个精英品系或五个外来品系的遗传单倍型选出的,其中包括不同的地理起源、干旱气候与温和气候,以及不同的水汽素(AQP)等位基因。我们发现主要的高遗传性气体交换和水力性状之间存在显著差异,其中一些受亲本品系单倍型差异的影响较大。在 WS 条件下,iWUE 非气孔成分比例较高的植株仍能通过保持光合能力来维持 iWUE,而与叶片水力传导的降低无关。与两个AQPs(SbPIP1.1和SbTIP3.2)相关的单倍型影响了iWUE和相关性状。这些发现扩大了 C4 作物中 iWUE 与生产力之间权衡的性状范围,并提供了可作为育种目标的遗传区域。
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引用次数: 0
Machine learning-enabled computer vision for plant phenotyping: a primer on AI/ML and a case study on stomatal patterning. 用于植物表型的机器学习计算机视觉:AI/ML 入门和气孔形态案例研究。
IF 5.6 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-11-15 DOI: 10.1093/jxb/erae395
Grace D Tan, Ushasi Chaudhuri, Sebastian Varela, Narendra Ahuja, Andrew D B Leakey

Artificial intelligence and machine learning (AI/ML) can be used to automatically analyze large image datasets. One valuable application of this approach is estimation of plant trait data contained within images. Here we review 39 papers that describe the development and/or application of such models for estimation of stomatal traits from epidermal micrographs. In doing so, we hope to provide plant biologists with a foundational understanding of AI/ML and summarize the current capabilities and limitations of published tools. While most models show human-level performance for stomatal density (SD) quantification at superhuman speed, they are often likely to be limited in how broadly they can be applied across phenotypic diversity associated with genetic, environmental, or developmental variation. Other models can make predictions across greater phenotypic diversity and/or additional stomatal/epidermal traits, but require significantly greater time investment to generate ground-truth data. We discuss the challenges and opportunities presented by AI/ML-enabled computer vision analysis, and make recommendations for future work to advance accelerated stomatal phenotyping.

人工智能和机器学习(AI/ML)可用于自动分析大型图像数据集。这种方法的一个重要应用就是估算图像中包含的植物性状数据。在此,我们综述了 39 篇论文,这些论文介绍了从表皮显微照片估算气孔性状的此类模型的开发和/或应用。在此过程中,我们希望能为植物生物学家提供对人工智能/人工智能的基本认识,并总结目前已发表工具的能力和局限性。虽然大多数模型在气孔密度(SD)量化方面都能以超人的速度表现出人类水平的性能,但它们在广泛应用于与遗传、环境或发育变异相关的表型多样性方面往往会受到限制。其他模型可以对更大的表型多样性和/或更多的气孔/表皮性状进行预测,但需要投入更多的时间来生成地面实况数据。我们讨论了人工智能/人工智能支持的计算机视觉分析所带来的挑战和机遇,并对未来推进加速气孔表型分析的工作提出了建议。
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引用次数: 0
Ethylene-mediated stomatal responses to dehydration and rehydration in seed plants. 乙烯介导的气孔对种子植物脱水和复水的反应
IF 8.3 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-11-15 DOI: 10.1093/jxb/erae060
Md Mahadi Hasan, Xu-Dong Liu, Guang-Qian Yao, Jianquan Liu, Xiang-Wen Fang

Ethylene, a plant hormone that significantly influences both plant growth and response to stress, plays a well-established role in stress signaling. However, its impact on stomatal opening and closure during dehydration and rehydration remains relatively unexplored and is still debated. Exogenous ethylene has been proven to induce stomatal closure through a series of signaling pathways, including the accumulation of reactive oxygen species, subsequent synthesis of nitric oxide and hydrogen sulfide, and SLOW ANION CHANNEL-ASSOCIATED 1 activation. Thus, it has been suggested that ethylene might function to induce stomatal closure synergistically with abscisic acid (ABA). Furthermore, it has also been shown that increased ethylene can inhibit ABA- and jasmonic acid-induced stomatal closure, thus hindering drought-induced closure during dehydration. Simultaneously, other stresses, such as chilling, ozone pollution, and K+ deficiency, inhibit drought- and ABA-induced stomatal closure in an ethylene synthesis-dependent manner. However, ethylene has been shown to take on an opposing role during rehydration, preventing stomatal opening in the absence of ABA through its own signaling pathway. These findings offer novel insights into the function of ethylene in stomatal regulation during dehydration and rehydration, giving a better understanding of the mechanisms underlying ethylene-induced stomatal movement in seed plants.

乙烯是一种植物激素,对植物生长和对胁迫的反应都有显著影响,在胁迫信号传导中发挥着公认的作用。然而,乙烯在脱水和补水过程中对气孔开闭的影响仍相对缺乏研究,目前仍存在争议。事实证明,外源乙烯可通过一系列信号通路诱导气孔关闭,包括活性氧(ROS)的积累、一氧化氮(NO)和硫化氢(H2S)的后续合成以及 SLOW ANION CHANNEL-ASSOCIATED 1(SLAC1)的激活。因此,有人认为乙烯可能与脱落酸(ABA)协同诱导气孔关闭。此外,研究还表明,乙烯增加可抑制脱落酸(ABA)和茉莉酸(JA)诱导的气孔关闭,从而阻碍干旱诱导的脱水过程中的气孔关闭。同时,其他胁迫,如寒冷、臭氧污染和 K+ 缺乏,也会通过依赖乙烯合成的方式抑制干旱和 ABA 诱导的气孔关闭。然而,乙烯在补水过程中发挥了相反的作用,在没有 ABA 的情况下通过自身的信号途径阻止气孔开放。这些发现为乙烯在脱水和复水过程中调节气孔的功能提供了新的见解,使人们对乙烯诱导种子植物气孔运动的机制有了更好的了解。
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引用次数: 0
The H3K27me3 histone mark correlates with repression of colour and aroma development post-harvest in strawberry fruit. H3K27me3 组蛋白标记与草莓果实采后色泽和香气发育的抑制相关。
IF 5.6 2区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-11-15 DOI: 10.1093/jxb/erae464
Ashley Baldwin, Tamara Lechon, Angela Marchbank, Simon Scofield, Kerstin Lieu, Charlotte L Wilson, Richard A Ludlow, Robert J Herbert, Hans-Wilhelm Nützmann, Hilary J Rogers

Strawberry ripening is non-climacteric, and post-harvest fruit enter senescence and deteriorate rapidly. Chilled storage induces transcriptome wide changes in gene expression, including the down-regulation of aroma related genes. Histone marks are associated with transcriptional activation or repression; the H3K27me3 mark is mainly associated with repression of gene expression. Here genes associated with H3K27me3 were identified through ChIP-seq in ripe red strawberry fruit at harvest and after 5 days of chilled storage in the dark. The number of ChIP peaks increased with storage time, indicating an increased role for this mark in regulation of gene expression following chilled dark storage. Comparing ChIP-seq data to RNA-seq data from the same material identified 440 genes whose expression correlates with H3K27me3 repression. Abiotic stress genes, especially cold stress response genes, were down-regulated during storage. Increased association with the H3K27me3 mark indicates that they may be repressed via this epigenetic mark. Other functional groups included cell wall and carbohydrate metabolism. The association with the H3K27me3 mark of two transcription factors (FaHY5 and FaTRAB1) and FaADH, involved in ester biosynthesis, was validated by ChIP-PCR. These three genes are all down-regulated during storage and indicate a network of H3K27me3 gene repression affecting both anthocyanin and ester biosynthesis.

草莓的成熟期为非周期性,采收后果实进入衰老期并迅速变质。冷藏会诱导基因表达发生广泛的转录组变化,包括香气相关基因的下调。组蛋白标记与转录激活或抑制有关;H3K27me3 标记主要与基因表达抑制有关。在此,我们通过 ChIP-seq 对收获时和在黑暗中冷藏 5 天后的成熟红草莓果实中与 H3K27me3 相关的基因进行了鉴定。ChIP 峰的数量随着贮藏时间的延长而增加,表明在冷藏黑暗贮藏后,该标记在基因表达调控中的作用增强。将 ChIP-seq 数据与来自相同材料的 RNA-seq 数据进行比较,发现有 440 个基因的表达与 H3K27me3 抑制相关。非生物胁迫基因,尤其是冷胁迫反应基因,在贮藏期间下调。这些基因与 H3K27me3 标记的关联性增加,表明它们可能通过这种表观遗传标记受到抑制。其他功能组包括细胞壁和碳水化合物代谢。ChIP-PCR 验证了两个转录因子(FaHY5 和 FaTRAB1)和参与酯类生物合成的 FaADH 与 H3K27me3 标记的关联。这三个基因在贮藏过程中均出现下调,表明 H3K27me3 基因抑制网络影响了花青素和酯的生物合成。
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引用次数: 0
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