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A k-mer-based pangenome approach for cataloging seed-storage-protein genes in wheat to facilitate genotype-to-phenotype prediction and improvement of end-use quality. 基于k-mer的pangenome方法,对小麦种子贮藏蛋白基因进行编目,以促进基因型到表型的预测和最终使用质量的改善。
IF 17.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-01 Epub Date: 2024-05-24 DOI: 10.1016/j.molp.2024.05.006
Zhaoheng Zhang, Dan Liu, Binyong Li, Wenxi Wang, Jize Zhang, Mingming Xin, Zhaorong Hu, Jie Liu, Jinkun Du, Huiru Peng, Chenyang Hao, Xueyong Zhang, Zhongfu Ni, Qixin Sun, Weilong Guo, Yingyin Yao

Wheat is a staple food for more than 35% of the world's population, with wheat flour used to make hundreds of baked goods. Superior end-use quality is a major breeding target; however, improving it is especially time-consuming and expensive. Furthermore, genes encoding seed-storage proteins (SSPs) form multi-gene families and are repetitive, with gaps commonplace in several genome assemblies. To overcome these barriers and efficiently identify superior wheat SSP alleles, we developed "PanSK" (Pan-SSP k-mer) for genotype-to-phenotype prediction based on an SSP-based pangenome resource. PanSK uses 29-mer sequences that represent each SSP gene at the pangenomic level to reveal untapped diversity across landraces and modern cultivars. Genome-wide association studies with k-mers identified 23 SSP genes associated with end-use quality that represent novel targets for improvement. We evaluated the effect of rye secalin genes on end-use quality and found that removal of ω-secalins from 1BL/1RS wheat translocation lines is associated with enhanced end-use quality. Finally, using machine-learning-based prediction inspired by PanSK, we predicted the quality phenotypes with high accuracy from genotypes alone. This study provides an effective approach for genome design based on SSP genes, enabling the breeding of wheat varieties with superior processing capabilities and improved end-use quality.

小麦(Triticum aestivum L.)是世界上 35% 以上人口的主食,其面粉用于制作数百种烘焙食品。卓越的最终使用品质是一个主要的育种目标,然而,提高最终使用品质尤其费时费力。此外,编码种子贮藏蛋白(SSP)的基因组成了多基因家族,并且具有重复性,在多个基因组组装中普遍存在空白。为了克服这些障碍并高效鉴定优良的小麦 SSP 等位基因,我们开发了 "PanSK"(Pan-SSP k-mer),用于基于 SSP 的泛基因组资源进行基因型到表型的预测。PanSK 使用在泛基因组水平上代表每个 SSP 基因的 29-mer 序列来揭示陆地品种和现代栽培品种之间尚未开发的多样性。利用 k-mer 进行的全基因组关联研究发现了 23 个与最终使用质量相关的 SSP 基因,这些基因代表了新的改良目标。我们评估了黑麦secalin基因对最终使用质量的影响,发现从1BL/SRS小麦易位系中移除ω-secalins与最终使用质量的提高有关。最后,受 PanSK 的启发,我们利用基于机器学习的预测方法,仅从基因型就能高精度地预测出品质表型。这项研究为基于 SSP 基因的基因组设计提供了一种有效的方法,从而能够培育出加工能力更强、最终使用品质更好的小麦品种。
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引用次数: 0
Progressive meristem and single-cell transcriptomes reveal the regulatory mechanisms underlying maize inflorescence development and sex differentiation. 渐进分生组织和单细胞转录组揭示了玉米花序发育和性别分化的调控机制。
IF 17.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-01 Epub Date: 2024-06-13 DOI: 10.1016/j.molp.2024.06.007
Yonghao Sun, Liang Dong, Lu Kang, Wanshun Zhong, David Jackson, Fang Yang

Maize develops separate ear and tassel inflorescences with initially similar morphology but ultimately different architecture and sexuality. The detailed regulatory mechanisms underlying these changes still remain largely unclear. In this study, through analyzing the time-course meristem transcriptomes and floret single-cell transcriptomes of ear and tassel, we revealed the regulatory dynamics and pathways underlying inflorescence development and sex differentiation. We identified 16 diverse gene clusters with differential spatiotemporal expression patterns and revealed biased regulation of redox, programmed cell death, and hormone signals during meristem differentiation between ear and tassel. Notably, based on their dynamic expression patterns, we revealed the roles of two RNA-binding proteins in regulating inflorescence meristem activity and axillary meristem formation. Moreover, using the transcriptional profiles of 53 910 single cells, we uncovered the cellular heterogeneity between ear and tassel florets. We found that multiple signals associated with either enhanced cell death or reduced growth are responsible for tassel pistil suppression, while part of the gibberellic acid signal may act non-cell-autonomously to regulate ear stamen arrest during sex differentiation. We further showed that the pistil-protection gene SILKLESS 1 (SK1) functions antagonistically to the known pistil-suppression genes through regulating common molecular pathways, and constructed a regulatory network for pistil-fate determination. Collectively, our study provides a deep understanding of the regulatory mechanisms underlying inflorescence development and sex differentiation in maize, laying the foundation for identifying new regulators and pathways for maize hybrid breeding and improvement.

玉米的穗花序和抽穗花序最初形态相似,但最后结构和性状却不同。这些变化背后的详细调控机制在很大程度上仍不清楚。本研究通过分析穗和缨的分生组织转录组和小花单细胞转录组,揭示了花序发育和性别分化的调控动态和途径。我们发现了16个具有不同时空表达模式的基因簇,并揭示了氧化还原、程序性细胞死亡和激素信号对穗和缨之间分生组织分化的偏向调控。特别是,根据它们的动态模式,我们揭示了两种 RNA 结合蛋白在调控花序分生组织活性和腋生分生组织形成中的作用。此外,利用 53,910 个单细胞的转录图谱,我们发现了穗小花和缨小花之间的细胞异质性。我们发现,与细胞死亡增强或生长减弱相关的多种信号是造成穗状花序雌蕊抑制的原因,而部分 GA 信号可能在性分化过程中以非细胞自主的方式调节穗状花序雄蕊的停滞。我们进一步发现,雌蕊保护基因SILKLESS 1(SK1)通过调控共同的分子通路与已知的雌蕊抑制基因起拮抗作用,并构建了雌蕊命运决定的调控模型。总之,我们的研究加深了对玉米花序发育和性别分化调控机制的理解,为确定玉米杂交育种和改良的新调控因子和途径奠定了基础。
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引用次数: 0
Plant triterpenoid saponins function as susceptibility factors to promote the pathogenicity of Botrytis cinerea. 植物三萜皂苷作为易感因子可促进灰霉病菌的致病性。
IF 17.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-01 Epub Date: 2024-05-27 DOI: 10.1016/j.molp.2024.05.008
Francisco J Escaray, Amelia Felipo-Benavent, Cristian J Antonelli, Begoña Balaguer, Maria Pilar Lopez-Gresa, Pablo Vera

The gray mold fungus Botrytis cinerea is a necrotrophic pathogen that causes diseases in hundreds of plant species, including high-value crops. Its polyxenous nature and pathogenic success are due to its ability to perceive host signals in its favor. In this study, we found that laticifer cells of Euphorbia lathyris are a source of susceptibility factors required by B. cinerea to cause disease. Consequently, poor-in-latex (pil) mutants, which lack laticifer cells, show full resistance to this pathogen, whereas lot-of-latex mutants, which produce more laticifer cells, are hypersusceptible. These S factors are triterpenoid saponins, which are widely distributed natural products of vast structural diversity. The downregulation of laticifer-specific oxydosqualene cyclase genes, which encode the first committed step enzymes for triterpene and, therefore, saponin biosynthesis, conferred disease resistance to B. cinerea. Likewise, the Medicago truncatula lha-1 mutant, compromised in triterpenoid saponin biosynthesis, showed enhanced resistance. Interestingly, the application of different purified triterpenoid saponins pharmacologically complemented the disease-resistant phenotype of pil and hla-1 mutants and enhanced disease susceptibility in different plant species. We found that triterpenoid saponins function as plant cues that signal transcriptional reprogramming in B. cinerea, leading to a change in its growth habit and infection strategy, culminating in the abundant formation of infection cushions, the multicellular appressoria apparatus dedicated to plant penetration and biomass destruction in B. cinerea. Taken together, these results provide an explanation for how plant triterpenoid saponins function as disease susceptibility factors to promote B. cinerea pathogenicity.

灰霉病菌(Botrytis cinerea)是一种坏死性病原体,可导致数百种植物(包括高价值作物)发病。这种多腺性和致病性的成功是由于它能够感知寄主对其有利的信号。我们发现,Euphorbia lathyris 的小叶细胞是 B. cinerea 致病所需的易感因子(S)的来源。因此,缺乏鳞叶细胞的poor-in-latex(pil)突变体对这种病原体表现出完全的抗性,而产生更多鳞叶细胞的lot-of-latex(lol)突变体则易感。这些 S因子是三萜类皂苷,是分布广泛、结构多样的天然产物。下调拉蒂西弗特异性氧代喹啉环化酶(OSCs)基因(OSCs 编码三萜类生物合成的第一步酶,因此也是皂苷生物合成的第一步酶)可增强对 B. cinerea 的抗病性。同样,Medicago truncatula lha-1 突变体的三萜类皂苷生物合成受到影响,但其抗病性有所增强。有趣的是,不同纯化三萜类皂苷的药理应用补充了 pil 和 hla-1 突变体的抗病表型,并增强了不同植物物种对疾病的敏感性。我们发现,三萜类皂苷作为植物线索,可发出信号,对银环孢菌进行转录重编程,从而改变其生长习性和感染策略,最终大量形成感染垫(IC),这是银环孢菌专门用于植物穿透和生物量破坏的多细胞附生器。我们的研究结果解释了植物三萜类皂苷如何作为疾病易感性因子(S)促进 B. cinerea 的致病性。
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引用次数: 0
Nuclear transport receptors underpin plastidial retrograde signaling. 核转运受体支撑着质体逆行信号转导
IF 17.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-01 Epub Date: 2024-06-07 DOI: 10.1016/j.molp.2024.06.003
Min Jia, Yangnan Gu
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引用次数: 0
Non-transcriptional regulatory activity of SMAX1 and SMXL2 mediates karrikin-regulated seedling response to red light in Arabidopsis. SMAX1和SMXL2的非转录调控活性介导拟南芥幼苗对红光的反应。
IF 17.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-01 Epub Date: 2024-05-27 DOI: 10.1016/j.molp.2024.05.007
Wenwen Chang, Qiao Qiao, Qingtian Li, Xin Li, Yanyan Li, Xiahe Huang, Yingchun Wang, Jiayang Li, Bing Wang, Lei Wang

Karrikins and strigolactones govern plant development and environmental responses through closely related signaling pathways. The transcriptional repressor proteins SUPPRESSOR OF MAX2 1 (SMAX1), SMAX1-like2 (SMXL2), and D53-like SMXLs mediate karrikin and strigolactone signaling by directly binding downstream genes or by inhibiting the activities of transcription factors. In this study, we characterized the non-transcriptional regulatory activities of SMXL proteins in Arabidopsis. We discovered that SMAX1 and SMXL2 with mutations in their ethylene-response factor-associated amphiphilic repression (EAR) motif had undetectable or weak transcriptional repression activities but still partially rescued the hypocotyl elongation defects and fully reversed the cotyledon epinasty defects of the smax1 smxl2 mutant. SMAX1 and SMXL2 directly interact with PHYTOCHROME INTERACTION FACTOR 4 (PIF4) and PIF5 to enhance their protein stability by interacting with phytochrome B (phyB) and suppressing the association of phyB with PIF4 and PIF5. The karrikin-responsive genes were then identified by treatment with GR24ent-5DS, a GR24 analog showing karrikin activity. Interestingly, INDOLE-3-ACETIC ACID INDUCIBLE 29 (IAA29) expression was repressed by GR24ent-5DS treatment in a PIF4- and PIF5-dependent and EAR-independent manner, whereas KARRIKIN UPREGULATED F-BOX 1 (KUF1) expression was induced in a PIF4- and PIF5-independent and EAR-dependent manner. Furthermore, the non-transcriptional regulatory activity of SMAX1, which is independent of the EAR motif, had a global effect on gene expression. Taken together, these results indicate that non-transcriptional regulatory activities of SMAX1 and SMXL2 mediate karrikin-regulated seedling response to red light.

卡里金和绞股蓝内酯通过密切相关的信号通路控制植物发育和环境响应。转录抑制蛋白 SUPPRESSOR OF MAX2 1(SMAX1)、SMAX1-like2(SMXL2)和 D53-like SMXLs 通过直接结合下游基因或抑制转录因子的活性来介导卡里金和赤霉内酯的信号转导。在这项研究中,我们研究了拟南芥中 SMXL 蛋白的非转录调控活动。我们发现,SMAX1和SMXL2的乙烯反应因子相关两亲抑制(EAR)基因座突变后,其转录抑制活性未被发现或很弱,但仍能部分挽救smax1 smxl2突变体的下胚轴伸长缺陷,并完全逆转子叶外倾缺陷。SMAX1和SMXL2与植物色素互作因子4(PIF4)和PIF5直接互作,并通过与植物色素B(phyB)互作和抑制phyB与PIF4和PIF5的结合来提高PIF4和PIF5的蛋白稳定性。用具有卡里金活性的 GR24 类似物 GR24ent-5DS 处理后,进一步确定了卡里金反应基因。有趣的是,INDOLE-3-ACETIC ACID INDUCIBLE 29(IAA29)的表达在 GR24ent-5DS 处理后以 PIF4 和 PIF5 依赖和 EAR 不依赖的方式受到抑制,而 KARRIKIN UPREGULATED F-BOX 1(KUF1)的表达则以 PIF4 和 PIF5 依赖和 EAR 不依赖的方式被诱导。此外,SMAX1 的非转录调控活性独立于 EAR 基序,对基因表达有全面影响。综上所述,这些结果揭示了 SMAX1 和 SMXL2 的非转录调控活性介导了卡里金调控的幼苗对红光的反应。
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引用次数: 0
Embracing substrate multispecificity in plant ABC transporters. 植物 ABC 转运体的底物多特异性。
IF 17.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-01 Epub Date: 2024-05-29 DOI: 10.1016/j.molp.2024.05.009
Markus M Geisler
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引用次数: 0
Dynamic modulation of nodulation factor receptor levels by phosphorylation-mediated functional switch of a RING-type E3 ligase during legume nodulation. 在豆科植物拔节过程中,通过磷酸化介导的 RING 型 E3 连接酶的功能转换,对拔节因子受体水平进行动态调节。
IF 17.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-01 Epub Date: 2024-05-31 DOI: 10.1016/j.molp.2024.05.010
Hao Li, Yajuan Ou, Jidan Zhang, Kui Huang, Ping Wu, Xiaoli Guo, Hui Zhu, Yangrong Cao

The precise control of receptor levels is crucial for initiating cellular signaling transduction in response to specific ligands; however, such mechanisms regulating nodulation factor (NF) receptor (NFR)-mediated perception of NFs to establish symbiosis remain unclear. In this study, we unveil the pivotal role of the NFR-interacting RING-type E3 ligase 1 (NIRE1) in regulating NFR1/NFR5 homeostasis to optimize rhizobial infection and nodule development in Lotus japonicus. We demonstrated that NIRE1 has a dual function in this regulatory process. It associates with both NFR1 and NFR5, facilitating their degradation through K48-linked polyubiquitination before rhizobial inoculation. However, following rhizobial inoculation, NFR1 phosphorylates NIRE1 at a conserved residue, Tyr-109, inducing a functional switch in NIRE1, which enables NIRE1 to mediate K63-linked polyubiquitination, thereby stabilizing NFR1/NFR5 in infected root cells. The introduction of phospho-dead NIRE1Y109F leads to delayed nodule development, underscoring the significance of phosphorylation at Tyr-109 in orchestrating symbiotic processes. Conversely, expression of the phospho-mimic NIRE1Y109E results in the formation of spontaneous nodules in L. japonicus, further emphasizing the critical role of the phosphorylation-dependent functional switch in NIRE1. In summary, these findings uncover a fine-tuned symbiotic mechanism that a single E3 ligase could undergo a phosphorylation-dependent functional switch to dynamically and precisely regulate NF receptor protein levels.

受体水平的精确控制对于启动细胞信号传导以响应特定配体至关重要,然而,在感知 NF 以建立共生关系的过程中,调节结核因子(NF)受体(NFR1/NFR5)的这种机制仍不清楚。本研究揭示了NFR-Interacting RING型E3连接酶1(NIRE1)在调节NFR1/NFR5平衡以优化日本莲的根瘤菌感染和结核发育中的关键作用。NIRE1 在这一调控过程中具有双重功能。NIRE1 同时与 NFR1/NFR5 结合,在接种根瘤菌之前通过与 K48 链接的多泛素化促进它们的降解。接种根瘤菌后,NFR1 在一个保守残基 Tyr-109 上磷酸化 NIRE1,从而诱导 NIRE1 的功能转换。这种转换使 NIRE1 能够介导 K63 链接的多泛素化,从而稳定受感染根细胞中的 NFR1/NFR5。引入磷酸化死亡的 NIRE1Y109F 会导致结核发育延迟,这突出了 Tyr-109 处的磷酸化在协调共生过程中的重要性。相反,表达磷酸化模拟 NIRE1Y109E 会导致日本莴苣自发形成结核,这进一步强调了 NIRE1 中磷酸化依赖性功能开关的关键作用。总之,这些发现提供了单个 E3 连接酶进行磷酸化依赖性功能转换、动态和精确调节 NF 受体蛋白水平的首例证据。
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引用次数: 0
Guardian of the rice: Unveiling OsSSP1 for broad-spectrum disease resistance. 水稻卫士:揭示 OsSSP1 的广谱抗病性。
IF 17.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-01 Epub Date: 2024-06-06 DOI: 10.1016/j.molp.2024.06.002
You-Jin Lim, Yong-Hwan Lee
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引用次数: 0
Polycomb and trithorax: Their yin-yang dynamics in plants. 多角体和三喙体:它们在植物中的阴阳动态。
IF 17.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-03 Epub Date: 2024-05-23 DOI: 10.1016/j.molp.2024.05.005
Fan Xu, Daolei Zhang, Liang Le, Li Pu
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引用次数: 0
Histological and single-nucleus transcriptome analyses reveal the specialized functions of ligular sclerenchyma cells and key regulators of leaf angle in maize. 组织学和单核转录组分析揭示了玉米叶状细纹细胞的特殊功能和叶角的关键调控因子
IF 27.5 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2024-06-03 Epub Date: 2024-05-07 DOI: 10.1016/j.molp.2024.05.001
Qibin Wang, Qiuyue Guo, Qingbiao Shi, Hengjia Yang, Meiling Liu, Yani Niu, Shuxuan Quan, Di Xu, Xiaofeng Chen, Laiyi Li, Wenchang Xu, Fanying Kong, Haisen Zhang, Pinghua Li, Bosheng Li, Gang Li

Leaf angle (LA) is a crucial factor that affects planting density and yield in maize. However, the regulatory mechanisms underlying LA formation remain largely unknown. In this study, we performed a comparative histological analysis of the ligular region across various maize inbred lines and revealed that LA is significantly influenced by a two-step regulatory process involving initial cell elongation followed by subsequent lignification in the ligular adaxial sclerenchyma cells (SCs). Subsequently, we performed both bulk and single-nucleus RNA sequencing, generated a comprehensive transcriptomic atlas of the ligular region, and identified numerous genes enriched in the hypodermal cells that may influence their specialization into SCs. Furthermore, we functionally characterized two genes encoding atypical basic-helix-loop-helix (bHLH) transcription factors, bHLH30 and its homolog bHLH155, which are highly expressed in the elongated adaxial cells. Genetic analyses revealed that bHLH30 and bHLH155 positively regulate LA expansion, and molecular experiments demonstrated their ability to activate the transcription of genes involved in cell elongation and lignification of SCs. These findings highlight the specialized functions of ligular adaxial SCs in LA regulation by restricting further extension of ligular cells and enhancing mechanical strength. The transcriptomic atlas of the ligular region at single-nucleus resolution not only deepens our understanding of LA regulation but also enables identification of numerous potential targets for optimizing plant architecture in modern maize breeding.

叶角(LA)是影响玉米种植密度和产量的关键因素。然而,LA 形成的调控机制在很大程度上仍不为人所知。在这项研究中,我们对不同玉米近交系的叶舌区进行了组织学比较分析,结果表明,LA 的大小受两步调控过程的显著影响,其中包括最初的细胞伸长,随后是叶舌正面基部细胞(SC)的木质化。我们进行了大量 RNA 测序和单核 RNA 测序,生成了韧皮部区域的综合转录组图谱,并确定了下胚层细胞中富集的许多基因,这些基因可能会影响它们向 SC 的特化。此外,我们还从功能上鉴定了两个编码非典型碱性螺旋-环-螺旋(bHLH)转录因子的基因,分别是 bHLH30 及其同源物 bHLH155,它们在伸长的正面细胞中高度表达。遗传分析表明,bHLH30 和 bHLH155 能正向调节 LA 的扩展,分子实验证明它们能激活参与 SC 细胞伸长和木质化的基因转录。这些发现凸显了韧皮部正面SC在LA调控中的特殊功能,即限制韧皮部细胞的进一步延伸并增强机械强度。单核分辨率的韧带区域转录组图谱不仅加深了我们对LA调控的理解,还为现代玉米育种中优化植物结构确定了许多潜在靶标。
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引用次数: 0
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Molecular Plant
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