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Refining polyploid breeding in sweet potato through allele dosage enhancement 通过增加等位基因剂量来改进甘薯多倍体育种
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-12-12 DOI: 10.1038/s41477-024-01873-y
Xiangbo Zhang, Chaochen Tang, Bingzhi Jiang, Rong Zhang, Ming Li, Yaoyao Wu, Zhufang Yao, Lifei Huang, Zhongxia Luo, Hongda Zou, Yiling Yang, Minyi Wu, Ao Chen, Shan Wu, Xingliang Hou, Xu Liu, Zhangjun Fei, Junjie Fu, Zhangying Wang
Allele dosage plays a key role in the phenotypic variation of polyploids. Here we present a genome-wide variation map of hexaploid sweet potato that captures allele dosage information, constructed from deep sequencing of 294 hexaploid accessions. Genome-wide association studies identified quantitative trait loci with dosage effects on 23 agronomic traits. Our analyses reveal that sweet potato breeding has progressively increased the dosage of favourable alleles to enhance trait performance. Notably, the Mesoamerican gene pool has evolved towards higher dosages of favourable alleles at multiple loci, which have been increasingly introgressed into modern Chinese cultivars. We substantiated the breeding-driven dosage accumulation through transgenic validation of IbEXPA4, an expansin gene influencing tuberous root weight. In addition, we explored causative sequence variations that alter the expression of the Orange gene, which regulates flesh colour. Our findings illuminate the breeding history of sweet potato and establish a foundation for leveraging allele dosages in polyploid breeding practices. Deep genome sequencing and comprehensive phenotyping of 294 hexaploid sweet potato accessions reveal the effect of allele dosage on phenotypic variation, offering valuable insights into the breeding history of sweet potato.
等位基因剂量在多倍体表型变异中起关键作用。本文通过对294份六倍体甘薯的深度测序,绘制了一份包含等位基因剂量信息的六倍体甘薯全基因组变异图谱。全基因组关联研究确定了23个农艺性状的剂量效应数量性状位点。我们的分析表明,甘薯育种逐渐增加有利等位基因的剂量,以提高性状性能。值得注意的是,中美洲的基因库已经在多个位点上向更高剂量的有利等位基因进化,这些等位基因越来越多地渗入现代中国品种。我们通过对影响块根重量的扩张蛋白基因IbEXPA4的转基因验证,证实了育种驱动的剂量积累。此外,我们探索了改变橙色基因表达的致病序列变异,该基因调节肉色。我们的发现阐明了甘薯的育种历史,并为多倍体育种实践中利用等位基因剂量奠定了基础。
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引用次数: 0
Evolution of a SHOOTMERISTEMLESS transcription factor binding site promotes fruit shape determination SHOOTMERISTEMLESS转录因子结合位点的进化促进了果实形状的决定
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-12-12 DOI: 10.1038/s41477-024-01854-1
Zhi-Cheng Hu, Mateusz Majda, Hao-Ran Sun, Yao Zhang, Yi-Ning Ding, Quan Yuan, Tong-Bing Su, Tian-Feng Lü, Feng Gao, Gui-Xia Xu, Richard S. Smith, Lars Østergaard, Yang Dong
In animals and plants, organ shape is primarily determined during primordium development by carefully coordinated growth and cell division1–3. Rare examples of post-primordial change in morphology (reshaping) exist that offer tractable systems for the study of mechanisms required for organ shape determination and diversification. One such example is morphogenesis in Capsella fruits whose heart-shaped appearance emerges by reshaping of the ovate spheroid gynoecium upon fertilization4. Here we use whole-organ live-cell imaging and single-cell RNA sequencing (scRNA-seq) analysis to show that Capsella fruit shape determination is based on dynamic changes in cell growth and cell division coupled with local maintenance of meristematic identity. At the molecular level, we reveal an auxin-induced mechanism that is required for morphological alteration and ultimately determined by a single cis-regulatory element. This element resides in the promoter of the Capsella rubella SHOOTMERISTEMLESS5 (CrSTM) gene. The CrSTM meristem identity factor positively regulates its own expression through binding to this element, thereby providing a feed-forward loop at the position and time of protrusion emergence to form the heart. Independent evolution of the STM-binding element in STM promoters across Brassicaceae species correlates with those undergoing a gynoecium-to-fruit shape change. Accordingly, genetic and phenotypic studies show that the STM-binding element is required to facilitate the shape transition and suggest a conserved molecular mechanism for organ morphogenesis. This study identifies a molecular mechanism promoting fruit shape variation. Local meristem identity is maintained through autoregulatory activation of the STM gene to allow post-fertilization changes in fruit morphology.
在动物和植物中,器官形状主要是在原基发育过程中通过精心协调的生长和细胞分裂决定的。存在一些罕见的后原始形态变化(重塑)的例子,为研究器官形状确定和多样化所需的机制提供了可处理的系统。一个这样的例子是小油菜果实的形态发生,其心形外观是在受精后卵形球形雌蕊的重塑中形成的。在这里,我们使用全器官活细胞成像和单细胞RNA测序(scRNA-seq)分析表明,甘蓝果实形状的决定是基于细胞生长和细胞分裂的动态变化,以及局部分生组织特性的维持。在分子水平上,我们揭示了生长素诱导的机制,这是形态学改变所必需的,最终由单个顺式调节元件决定。该元件位于风疹shoomeristemless5 (CrSTM)基因的启动子中。CrSTM分生组织身份因子通过与该元件结合正向调节自身表达,从而在突起出现的位置和时间提供前馈回路形成心脏。十字花科植物STM启动子中STM结合元件的独立进化与那些经历雌蕊到果实形状变化的物种有关。因此,遗传和表型研究表明,stm结合元件是促进形状转变所必需的,并提示器官形态发生的保守分子机制。
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引用次数: 0
Patterns of forest disturbance 森林扰动模式
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-12-10 DOI: 10.1038/s41477-024-01885-8
Catherine Walker
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引用次数: 0
Yoda screams again 尤达又尖叫起来
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-12-09 DOI: 10.1038/s41477-024-01886-7
Guillaume Tena
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引用次数: 0
Exploring the function of plant root diffusion barriers in sealing and shielding for environmental adaptation 探讨植物根系扩散屏障在封闭和屏蔽环境适应中的作用
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-12-05 DOI: 10.1038/s41477-024-01842-5
Yi-Qun Gao, Yu Su, Dai-Yin Chao
Plant roots serve as the primary interface between the plant and the soil, encountering numerous challenges ranging from water balance to nutrient uptake. One of the central mechanisms enabling plants to thrive in diverse ecosystems is the building of apoplastic diffusion barriers. These barriers control the flow of solutes into and out of the roots, maintaining water and nutrient homeostasis. In this Review, we summarize recent advances in understanding the establishment, function and ecological significance of root apoplastic diffusion barriers. We highlight the plasticity of apoplastic diffusion barriers under various abiotic stresses such as drought, salinity and nutrient deficiency. We also propose new frontiers by discussing the current bottlenecks in the study of plant apoplastic diffusion barriers. This Review summarizes recent progress in the understanding of plant apoplastic diffusion barriers, their formation and their function in an environmental context. Open questions and promising research directions in this field are addressed.
植物根系作为植物和土壤之间的主要界面,面临着从水分平衡到养分吸收的许多挑战。使植物在不同生态系统中茁壮成长的核心机制之一是外质体扩散屏障的建立。这些屏障控制溶质进出根部的流动,维持水分和养分的平衡。本文就根外质扩散屏障的建立、功能及其生态意义等方面的研究进展作一综述。我们强调了在干旱、盐度和营养缺乏等各种非生物胁迫下外胞体扩散屏障的可塑性。我们还讨论了目前植物外胞体扩散障碍研究的瓶颈,提出了新的研究领域。
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引用次数: 0
A micropeptide decelerator 微肽减速剂
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-12-04 DOI: 10.1038/s41477-024-01881-y
Jun Lyu
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引用次数: 0
Plant microbiota feedbacks through dose-responsive expression of general non-self response genes 植物微生物群通过一般非自应答基因的剂量响应性表达进行反馈
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-12-03 DOI: 10.1038/s41477-024-01856-z
Andreas Keppler, Michelle Roulier, Sebastian Pfeilmeier, Gabriella C. Petti, Anna Sintsova, Benjamin A. Maier, Miriam Bortfeld-Miller, Shinichi Sunagawa, Cyril Zipfel, Julia A. Vorholt
The ability of plants to perceive and react to biotic and abiotic stresses is critical for their health. We recently identified a core set of genes consistently induced by members of the leaf microbiota, termed general non-self response (GNSR) genes. Here we show that GNSR components conversely impact leaf microbiota composition. Specific strains that benefited from this altered assembly triggered strong plant responses, suggesting that the GNSR is a dynamic system that modulates colonization by certain strains. Examination of the GNSR to live and inactivated bacteria revealed that bacterial abundance, cellular composition and exposure time collectively determine the extent of the host response. We link the GNSR to pattern-triggered immunity, as diverse microbe- or danger-associated molecular patterns cause dynamic GNSR gene expression. Our findings suggest that the GNSR is the result of a dose-responsive perception and signalling system that feeds back to the leaf microbiota and contributes to the intricate balance of plant–microbiome interactions. The plant general non-self response system is triggered by leaf microbiota members and, in turn, impacts their colonization.
植物感知和应对生物和非生物胁迫的能力对它们的健康至关重要。我们最近发现了一组核心基因,这些基因一直由叶片微生物群成员诱导,称为一般非自我反应(GNSR)基因。在这里,我们表明GNSR成分反过来影响叶片微生物群组成。受益于这种改变组合的特定菌株引发了强烈的植物反应,这表明GNSR是一个动态系统,可以调节某些菌株的定植。对活菌和灭活菌的GNSR检测表明,细菌丰度、细胞组成和暴露时间共同决定了宿主反应的程度。我们将GNSR与模式触发免疫联系起来,因为多种微生物或危险相关的分子模式导致动态GNSR基因表达。我们的研究结果表明,GNSR是剂量响应感知和信号系统的结果,该系统反馈给叶片微生物群,并有助于植物-微生物群相互作用的复杂平衡。
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引用次数: 0
The near-complete genome assembly of hexaploid wild oat reveals its genome evolution and divergence with cultivated oats 六倍体野生燕麦基因组的近完整组装揭示了其与栽培燕麦基因组的进化和分化
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-12-03 DOI: 10.1038/s41477-024-01866-x
Qiang He, Wei Li, Yuqing Miao, Yu Wang, Ningkun Liu, Jianan Liu, Tao Li, Yao Xiao, Hongyu Zhang, Yaru Wang, Hanfei Liang, Yange Yun, Shuhui Wang, Qingbin Sun, Hongru Wang, Zhizhong Gong, Huilong Du
Avena sterilis, the ancestral species of cultivated oats, is a valuable genetic resource for oat improvement. Here we generated a near-complete 10.99 Gb A. sterilis genome and a high-quality 10.89 Gb cultivated oat genome. Genome evolution analysis revealed the centromeres dynamic and structural variations landscape associated with domestication between wild and cultivated oats. Population genetic analysis of 117 wild and cultivated oat accessions worldwide detected many candidate genes associated with important agronomic traits for oat domestication and improvement. Remarkably, a large fragment duplication from chromosomes 4A to 4D harbouring many agronomically important genes was detected during oat domestication and was fixed in almost all cultivated oats from around the world. The genes in the duplication region from 4A showed significantly higher expression levels and lower methylation levels than the orthologous genes located on 4D in A. sterilis. This study provides valuable resources for evolutionary and functional genomics and genetic improvement of oat. The near-complete genome of hexaploid wild oat, along with 117 global wild and cultivated accessions, reveals genome divergence between wild and cultivated oats and a large fragment duplication event from chromosomes 4A to 4D during oat domestication.
无菌燕麦是栽培燕麦的祖先种,是燕麦改良的宝贵遗传资源。在这里,我们获得了一个近乎完整的10.99 Gb的a . sterilis基因组和一个高质量的10.89 Gb的栽培燕麦基因组。基因组进化分析揭示了野生燕麦和栽培燕麦在驯化过程中着丝粒的动态和结构变化。对全球117个野生和栽培燕麦材料的群体遗传分析发现了许多与燕麦驯化和改良重要农艺性状相关的候选基因。值得注意的是,在燕麦驯化过程中,从染色体4A到4D中发现了一个包含许多重要农学基因的大片段重复,并且在世界上几乎所有栽培燕麦中都被固定下来。与位于4D的同源基因相比,4A重复区基因的表达水平显著提高,甲基化水平显著降低。该研究为燕麦进化和功能基因组学以及遗传改良提供了宝贵的资源。
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引用次数: 0
Regulation and function of a polarly localized lignin barrier in the exodermis 外表皮极性定位木质素屏障的调控与功能
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-12-02 DOI: 10.1038/s41477-024-01864-z
Concepcion Manzano, Kevin W. Morimoto, Lidor Shaar-Moshe, G. Alex Mason, Alex Cantó-Pastor, Mona Gouran, Damien De Bellis, Robertas Ursache, Kaisa Kajala, Neelima Sinha, Julia Bailey-Serres, Niko Geldner, J. Carlos del Pozo, Siobhan M. Brady
Multicellular organisms control environmental interactions through specialized barriers in specific cell types. A conserved barrier in plant roots is the endodermal Casparian strip (CS), a ring-like structure made of polymerized lignin that seals the endodermal apoplastic space. Most angiosperms have another root cell type, the exodermis, that is reported to form a barrier. Our understanding of exodermal developmental and molecular regulation and function is limited as this cell type is absent from Arabidopsis thaliana. We demonstrate that in tomato (Solanum lycopersicum), the exodermis does not form a CS. Instead, it forms a polar lignin cap (PLC) with equivalent barrier function to the endodermal CS but distinct genetic control. Repression of the exodermal PLC in inner cortical layers is conferred by the SlSCZ and SlEXO1 transcription factors, and these two factors genetically interact to control its polar deposition. Several target genes that act downstream of SlSCZ and SlEXO1 in the exodermis are identified. Although the exodermis and endodermis produce barriers that restrict mineral ion uptake, the exodermal PLC is unable to fully compensate for the lack of a CS. The presence of distinct lignin structures acting as apoplastic barriers has exciting implications for a root’s response to abiotic and biotic stimuli. In tomato roots, the exodermis forms a genetically distinct polar lignin cap (PLC) barrier from the Casparian strip. SlSCZ and SlEXO1 repress PLC deposition in inner layers. The PLC cannot fully compensate for the CS as a mineral ion barrier.
多细胞生物通过特定细胞类型的特殊屏障来控制环境相互作用。植物根中的一个保守屏障是内胚层卡斯帕里斯带(CS),这是一种由聚合木质素组成的环状结构,可封闭内胚层外胞体空间。大多数被子植物有另一种根细胞类型——外表皮,据报道,外表皮可以形成屏障。由于拟南芥中不存在这种细胞类型,我们对外表皮发育和分子调控功能的了解有限。我们证明在番茄(Solanum lycopersicum),外表皮不形成CS。相反,它形成一个极性木质素帽(PLC),具有与内胚层CS相当的屏障功能,但遗传控制不同。外皮层内皮层PLC的抑制是由SlSCZ和SlEXO1转录因子赋予的,这两个因子在遗传上相互作用以控制其极性沉积。外表皮中几个作用于SlSCZ和SlEXO1下游的靶基因被鉴定出来。尽管外表皮和内皮层产生屏障来限制矿物质离子的摄取,但外表皮PLC不能完全补偿CS的缺乏。不同木质素结构的存在作为胞外屏障,对根对非生物和生物刺激的反应具有令人兴奋的意义。
{"title":"Regulation and function of a polarly localized lignin barrier in the exodermis","authors":"Concepcion Manzano, Kevin W. Morimoto, Lidor Shaar-Moshe, G. Alex Mason, Alex Cantó-Pastor, Mona Gouran, Damien De Bellis, Robertas Ursache, Kaisa Kajala, Neelima Sinha, Julia Bailey-Serres, Niko Geldner, J. Carlos del Pozo, Siobhan M. Brady","doi":"10.1038/s41477-024-01864-z","DOIUrl":"10.1038/s41477-024-01864-z","url":null,"abstract":"Multicellular organisms control environmental interactions through specialized barriers in specific cell types. A conserved barrier in plant roots is the endodermal Casparian strip (CS), a ring-like structure made of polymerized lignin that seals the endodermal apoplastic space. Most angiosperms have another root cell type, the exodermis, that is reported to form a barrier. Our understanding of exodermal developmental and molecular regulation and function is limited as this cell type is absent from Arabidopsis thaliana. We demonstrate that in tomato (Solanum lycopersicum), the exodermis does not form a CS. Instead, it forms a polar lignin cap (PLC) with equivalent barrier function to the endodermal CS but distinct genetic control. Repression of the exodermal PLC in inner cortical layers is conferred by the SlSCZ and SlEXO1 transcription factors, and these two factors genetically interact to control its polar deposition. Several target genes that act downstream of SlSCZ and SlEXO1 in the exodermis are identified. Although the exodermis and endodermis produce barriers that restrict mineral ion uptake, the exodermal PLC is unable to fully compensate for the lack of a CS. The presence of distinct lignin structures acting as apoplastic barriers has exciting implications for a root’s response to abiotic and biotic stimuli. In tomato roots, the exodermis forms a genetically distinct polar lignin cap (PLC) barrier from the Casparian strip. SlSCZ and SlEXO1 repress PLC deposition in inner layers. The PLC cannot fully compensate for the CS as a mineral ion barrier.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 1","pages":"118-130"},"PeriodicalIF":15.8,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41477-024-01864-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142758278","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
The vision for adapted crops and soils: how to prioritize investments to achieve sustainable nutrition for all 适应作物和土壤的愿景:如何优先投资以实现人人享有可持续营养
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-11-29 DOI: 10.1038/s41477-024-01867-w
Jeffrey E. Herrick, Cary Fowler, Lindiwe Majele Sibanda, Rattan Lal, Anna M. Nelson
The Vision for Adapted Crops and Soils (VACS) is a global movement, launched in 2023, to improve human nutrition in the face of a changing climate and degraded lands. VACS emphasizes an integrated approach to investments in crops and soils, concentrating on the potential of traditional and indigenous ‘opportunity crops’. VACS also addresses priorities, including climate change and drought, biodiversity, soil fertility, gender equality and women’s empowerment, water, sanitation and health.
适应性作物和土壤愿景(VACS)是一项全球运动,于2023年启动,旨在面对气候变化和土地退化,改善人类营养。VACS强调对作物和土壤进行综合投资,重点关注传统和本土“机会作物”的潜力。VACS还处理优先事项,包括气候变化和干旱、生物多样性、土壤肥力、性别平等和增强妇女权能、水、卫生和健康。
{"title":"The vision for adapted crops and soils: how to prioritize investments to achieve sustainable nutrition for all","authors":"Jeffrey E. Herrick, Cary Fowler, Lindiwe Majele Sibanda, Rattan Lal, Anna M. Nelson","doi":"10.1038/s41477-024-01867-w","DOIUrl":"10.1038/s41477-024-01867-w","url":null,"abstract":"The Vision for Adapted Crops and Soils (VACS) is a global movement, launched in 2023, to improve human nutrition in the face of a changing climate and degraded lands. VACS emphasizes an integrated approach to investments in crops and soils, concentrating on the potential of traditional and indigenous ‘opportunity crops’. VACS also addresses priorities, including climate change and drought, biodiversity, soil fertility, gender equality and women’s empowerment, water, sanitation and health.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"10 12","pages":"1840-1846"},"PeriodicalIF":15.8,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142753752","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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