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Systematic identification of wheat spike developmental regulators by integrated multiomics, transcriptional network, GWAS, and genetic analyses

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Molecular Plant 2024年第3期17卷 438-459页

作者： Xuelei Lin Yongxin Xu Dongzhi Wang Yiman Yang Xiaoyu Zhang Xiaomin Bie Lixuan Gui Zhongxu Chen Yiliang Ding Long Mao Xueyong Zhang Fei Lu Xiansheng Zhang Cristobal Uauyo Xiangdong Fu Jun Xiao Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Nanjing Agricultural University NanjingJiangsu 210095China Key Laboratory of Crop Biology College of Life SciencesShandong Agricultural UniversityTaianShandong 271018China Department of Life Science Tcuni Inc.ChengduSichuan 610000China john innes centre Norwich Research ParkNorwich NR47UHUK Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China CAS-JIC centre of Excellence for Plant and Microbial Science(CEPAMS) Institute of Genetics and Developmental BiologyCASBeijing 100101China

The spike architecture of wheat plays a crucial role in determining grain number,making it a key trait for optimization in wheat breeding *** this study,we used a multi-omic approach to analyze the transcriptome and epigenome profiles of the young spike at eight developmental stages,revealing co-ordinated changes in chromatin accessibility and H3K27me3 abundance during the flowering *** constructed a core transcriptional regulatory network(TRN)that drives wheat spike formation and experimentally validated a multi-layer regulatorymodule involving TaSPL15,TaAGLG1,and *** integrating the TRN with genome-wide association studies,we identified 227 transcription factors,including 42 with known functions and 185 with unknown *** investigation of 61 novel transcription factors using multiple homozygous mutant lines revealed 36 transcription factors that regulate spike architecture or flowering time,such as TaMYC2-A1,TaMYB30-A1,and *** particular interest,TaMYB30-A1,downstream of and repressed by WFzP,was found to regulate fertile spikelet ***,the excellent haplotype of TaMYB30-A1,which contains a C allele at the WFzP binding site,was enriched during wheat breeding improvement in China,leading to improved agronomic ***,we constructed a free and open access Wheat Spike Multi-Omic Database(http://39.***.48.156:8800/#/).Our study identifies novel and high-confidence regulators and offers an effective strategy for dissecting the genetic basis of wheat spike development,with practical value forwheat breeding.

关键词： wheat spike development epigenome TRN TaMYB30-A1 breeding selection

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A reductionist approach to dissecting grain weight and yield in wheat

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Journal of Integrative Plant Biology 2019年第3期61卷 337-358页

作者： Jemima Brinton Cristobal Uauy john innes centre Norwich Research Park

Grain yield is a highly polygenic trait that is influenced by the environment and integrates events throughout the life cycle of a plant. In wheat, the major grain yield components often present compensatory effects among them, which alongside the polyploid nature of wheat,makes their genetic and physiological study challenging. We propose a reductionist and systematic approach as an initial step to understand the gene networks regulating each individual yield component. Here, we focus on grain weight and discuss the importance of examining individual subcomponents, not only to help in their genetic dissection, but also to inform our mechanistic understanding of how they interrelate. This knowledge should allow the development of novel combinations, across homoeologs and between complementary modes of action, thereby advancing towards a more integrated strategy for yield improvement. We argue that this will break barriers in terms of phenotypic variation,enhance our understanding of the physiology of yield, and potentially deliver improved on-farm yield.

关键词： Grain yield a highly polygenic integrates

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Genetic pathways controlling inflorescence architecture and development in wheat and barley

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Journal of Integrative Plant Biology 2019年第3期61卷 296-309页

作者： Adam Gauley Scott A.Boden Department of Crop Genetics John Innes Centre Norwich Research Park

Modifications of inflorescence architecture have been crucial for the successful domestication of wheat and barley, which are central members of the Triticeae tribe that provide essential grains for the human diet. Investigation of the genes and alleles that underpin domestication-related traits has provided valuable insights into the molecular regulation of inflorescence development of the Triticeae, and further investigation of modified forms of architecture are proving to be equally *** identified genes are involved in diverse biological processes, including transcriptional regulation, hormone biosynthesis and metabolism, post-transcriptional and post-translational regulation, which alter inflorescence architecture by modifying the development and fertility of lateral organs, called spikelets and florets. Recent advances in sequencing capabilities and the generation of mutant populations are accelerating the identification of genes that influence inflorescence development, which is important given that genetic variation for this trait promises to be a valuable resource for optimizing grain production. This review assesses recent advances in our understanding of the genes controlling inflorescence development in wheat and barley, with the aim of highlighting the importance of improvements in developmental biology for optimizing the agronomic performance of staple crop plants.

关键词： Genetic pathways Modifications architecture

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Juicy Stories on Female Reproductive Tissue Development: Coordinating the Hormone Flows

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Journal of Integrative Plant Biology 2013年第9期55卷 847-863页

作者： Veronica A.Grieneisen Athanasius F.M.Marée Lars φstergaard Computational and Systems Biology John Innes Centre Norwich Research ParkNorwich NR4 7UH UK Crop Genetics John Innes Centre Norwich Research ParkNorwich NR4 7UH UK

In the past 20-30 years, developmental biologists have made tremendous progress in identifying genes required for the specifica-tion of individual cell types of an organ and in describing how they interact in genetic networks. In comparison, very little is known about the mechanisms that regulate tissue polarity and overall organ patterning. Gynoecia and fruits from members of the Brassicaceae family of flowering plants provide excellent model systems to study organ patterning and tissue specification because they become partitioned into distinct domains whose formation is determined by polarity establishment both at a cellular and whole tissue level. Interactions among key regulators of Arabidopsis gynoecium and fruit development have revealed a network of upstream transcription factor activities required for such tissue differentiation. Regulation of the plant hormone auxin is emerging as both an immediate downstream output and input of these activities, and here we aim to provide an overview of the current knowledge regarding the link between auxin and female reproductive development in plants. In this review, we will also demonstrate how available data can be exploited in a mathematical modeling approach to reveal and understand the feedback regulatory circuits that underpin the polarity establishment, necessary to guide auxin flows.

关键词： Auxin dynamics brassicaceae cell and tissue polarity fruit gynoecium mathematical modelling organ patterning ROPs wavepinning

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Temperature Modulates Tissue-Specification Program to Control Fruit Dehiscence in Brassicaceae

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Molecular Plant 2018年第4期11卷 598-606页

作者： Xin-Ran Li Joyita Deb S. Vinod Kumar Lars Фstergaard john innes centre Norwich Research Park Norwich NR4 7UH UK

Plants respond to diurnal and seasonal changes in temperature by reprogramming vital developmental pathways. Understanding the molecular mechanisms that define environmental modulation of plant growth and reproduction is critical in the context of climate change that threatens crop yield worldwide. Here, we report that elevated temperature accelerates fruit dehiscence in members of the Brassicaceae family including the model plant Arabidopsis thaliana and important crop species. Arabidopsis fruit development is controlled by a network of interacting regulatory genes. Among them, the INDEHISCENT （IND） gene is a key regulator of the valve-margin tissue that mediates fruit opening, hence facilitating fruit dehiscence. We demonstrated that the valve-margin development is accelerated at higher temperature and that IND is tar- geted for thermosensory control. Our results reveal that IND upregulation is facilitated via temperature- induced chromatin dynamics leading to accelerated valve-margin specification and dispersal of the seed. Specifically, we show that temperature-induced changes in IND expression are associated with ther- mosensory H2A.Z nucleosome dynamics. These findings establish a molecular framework connecting tis- sue identity with thermal sensing and set out directions for the production of temperature-resilient crops.

关键词： Brassicaceae seed dispersal fruit dehiscence temperature response gene regulation nucleosomedynamics

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SWR1 Chromatin-Remodeling Complex Subunits and H2A.Z Have Non-overlapping Functions in Immunity and Gene Regulation in Arabidopsis

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Molecular Plant 2016年第7期9卷 1051-1065页

作者： Souha Berriri Sreeramaiah N Gangappa and S Vinod Kumar Cell and Developmental Biology Department John Innes Centre Norwich NR4 7UH UK

Incorporation of the histone variant H2A.Z into nucleosomes by the SWR1 chromatin remodeling complex is a critical step in eukaryotic gene regulation. In Arabidopsis, SWRlc and H2A.Z have been shown to con- trol gene expression underlying development and environmental responses. Although they have been implicated in defense, the specific roles of the complex subunits and H2A.Z in immunity are not well under- stood. In this study, we analyzed the roles of the SWRlc subunits, PHOTOPERIOD-INDEPENDENT EARLY FLOWERING1 （PIE1）, ACTIN-RELATED PROTEIN6 （ARP6）, and SWR1 COMPLEX 6 （SWC6）, as well as H2A.Z, in defense and gene regulation. We found that SWRlc components play different roles in resistance to different pathogens. Loss of PIE1 and SWC6 function as well as depletion of H2A.Z led to reduced basal resistance, while loss of ARP6 fucntion resulted in enhanced resistance. We found that mutations in PIE1 and SWC6 resulted in impaired effector-triggered immunity. Mutation in SWRlc components and H2A.Z also resulted in compromised jasmonic acid/ethylene-mediated immunity. Genome-wide expres- sion analyses similarly reveal distinct roles for H2A.Z and SWRlc components in gene regulation, and sug- gest a potential role for PIE1 in the regulation of the cross talk between defense signaling pathways. Our data show that although they are part of the same complex, Arabidopsis SWRlc components could have non-redundant functions in plant immunity and gene regulation.

关键词： arabidopsis SWR1 chromatin remodeling H2A.Z immunity gene regulation

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Signaling at the Root Surface： The Role of Cutin Monomers in Mycorrhization

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Molecular Plant 2013年第5期6卷 1381-1383页

作者： Jeremy D. Murray Donna R. Cousins Kirsty J. Jackson Chengwu Liu Cell and Developmental Biology John Innes Centre Norwich NR4 7UH UK

Most vascular plants interact with arbuscular mycorrhizal fungi （AMF） and are thereby provided significant advantages in nutrient acquisition, especially phosphate. The widespread retention of this symbiosis in vascular plants is testament to its importance and ancient origins. This highlight focuses on the reports of two of the first genes identified through for- ward genetic screens for AMF symbiotic mutants： Required for Abuscular Mycorrhization 1 （RAM1） and RAM2, which respectively encode a GRAS transcription factor and a glyc- erol-3-phosphate acyl-transferase （GPAT） that are required for the formation of fungal entry structures （hyphopodia） on the root surface.

关键词： arbuscular mycorrhizal irst genes identified genetic screens

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Arabidopsis Mutants and the Network of M icrotu bu le-Associated Functions

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Molecular Plant 2008年第6期1卷 888-898页

作者： Henrik Buschmann Clive W. Lloyd Department of Cell and Developmental Biology John Innes Centre 1 Colney Lane Norwich NR4 7UH UK

In early eukaryotes, the microtubule system was engaged in mitosis, intracellular transport, and flagellumbased motility. In the plant lineage, the evolution of a multicellular body involved the conservation of some core functions, the loss of others, and the elaboration of new microtubule functions associated with the multicellular plant habit. This diversification is reflected by the presence of both conserved （animal/fungi-like） and novel （plant-like） sequences encoding microtubule-related functions in the Arabidopsis genome. The collection of microtubule mutants has grown rapidly over recent years. These mutants present a wide range of phenotypes, consistent with the hypothesis of a functional diversification of the microtubule system. In this review, we focus on mutant analysis and, in particular, discuss double mutant analysis as a valuable tool for pinpointing pathways of gene function. A future challenge will be to define the complete network of genetic and physical interactions of microtubule function in plants. In addition to reviewing recent progress in the functional analysis of the ＇MAPome＇, we present an online database of Arabidopsis mutants impaired in microtubule functions.

关键词： cell division cell morphogenesis cytoskeleton genetics development Arabidopsis.

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Systems Biology Approach Pinpoints Minimum Requirements for Auxin Distribution during Fruit Opening

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Molecular Plant 2019年第6期12卷 863-878页

作者： Xin-Ran Li Renske M.A.Vroomans Samantha Fox Veronica A.Grieneisen Lars Φstergaard Athanasius F.M.Maree Crop Genetics John Innes Centre Norwich NR4 7UH UK Computational and Systems Biology John Innes Centre Norwich NR4 7UH UK centre of Excellence in Computational and Experimental Developmental Biology Institute of Biotechnology University of Helsinki 00014 Helsinki Finland Cell and Developmental Biology John Innes Centre Norwich NR4 7UH UK School of Biosciences Cardiff University Cardiff CF10 3AX Wales UK

The phytohormone auxin is implied in steering various developmental decisions during plant morphogenesis in a concentration-dependent *** maxima have been shown to maintain meristematic activity,for example,of the root apical meristem,and position new sites of outgrowth,such as during lateral root initiation and *** recently,it has been demonstrated that sites of auxin minima also provide positional *** the developingArabidopsis fruit,auxin minima are required for correct differentiation of the valve *** remains unclear,however,how this auxin minimum is generated and ***,we employ a systems biology approach to model auxin transport based on experimental *** allows us to determine the minimal requirements for its *** simulations reveal that two alternative processes-which we coin "flux-barrier" and "flux-passage"-are both able to generate an auxin minimum,but under different parameter *** models are in principle able to yield similar auxin profiles but present qualitatively distinct patterns of auxin *** models were tested by tissue-specific inducible ablation,revealing that the auxin minimum in the fruit is most likely generated by a flux-passage *** predictions were further supported through 3D PIN localization imaging and implementing experimentally observed transporter *** such an experimental-modeling cycle,we predict how the auxin minimum gradually matures during fruit development to ensure timely fruit opening and seed dispersal.

关键词： auxin mathematical modeling polar auxin transport fruit development systems biology of patterning

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Hot n＇ Cold： Molecular Signatures of Domestication Bring Fresh Insights into Environmental Adaptation

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Molecular Plant 2015年第10期8卷 1439-1441页

作者： Catherine Gardener S. Vinod Kumar Cell and Developmental Biology Department John Innes Centre Norwich NR4 7UH UK

Recent investigations of divergent rice genotypes have identified previously unknown molecular adaptations conferring heat and chilling tolerance in their corresponding local environments （Figure 1）. These studies s... 详细信息

关键词： domestication environmental adaptation

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