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Demesa-Arevalo E, Narasimhan M, Simon R. Intercellular Communication in Shoot Meristems. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:319-344. [PMID: 38424066 DOI: 10.1146/annurev-arplant-070523-035342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
The shoot meristem of land plants maintains the capacity for organ generation throughout its lifespan due to a group of undifferentiated stem cells. Most meristems are shaped like a dome with a precise spatial arrangement of functional domains, and, within and between these domains, cells interact through a network of interconnected signaling pathways. Intercellular communication in meristems is mediated by mobile transcription factors, small RNAs, hormones, and secreted peptides that are perceived by membrane-localized receptors. In recent years, we have gained deeper insight into the underlying molecular processes of the shoot meristem, and we discuss here how plants integrate internal and external inputs to control shoot meristem activities.
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Affiliation(s)
- Edgar Demesa-Arevalo
- Institute for Developmental Genetics, Heinrich Heine University, Düsseldorf, Germany;
| | - Madhumitha Narasimhan
- Institute for Developmental Genetics, Heinrich Heine University, Düsseldorf, Germany;
| | - Rüdiger Simon
- Institute for Developmental Genetics, Heinrich Heine University, Düsseldorf, Germany;
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2
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Wang X, Lu J, Han M, Wang Z, Zhang H, Liu Y, Zhou P, Fu J, Xie Y. Genome-wide expression quantitative trait locus analysis reveals silk-preferential gene regulatory network in maize. PHYSIOLOGIA PLANTARUM 2024; 176:e14386. [PMID: 38887947 DOI: 10.1111/ppl.14386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/20/2024]
Abstract
Silk of maize (Zea mays L.) contains diverse metabolites with complicated structures and functions, making it a great challenge to explore the mechanisms of metabolic regulation. Genome-wide identification of silk-preferential genes and investigation of their expression regulation provide an opportunity to reveal the regulatory networks of metabolism. Here, we applied the expression quantitative trait locus (eQTL) mapping on a maize natural population to explore the regulation of gene expression in unpollinated silk of maize. We obtained 3,985 silk-preferential genes that were specifically or preferentially expressed in silk using our population. Silk-preferential genes showed more obvious expression variations compared with broadly expressed genes that were ubiquitously expressed in most tissues. We found that trans-eQTL regulation played a more important role for silk-preferential genes compared to the broadly expressed genes. The relationship between 38 transcription factors and 85 target genes, including silk-preferential genes, were detected. Finally, we constructed a transcriptional regulatory network around the silk-preferential gene Bx10, which was proposed to be associated with response to abiotic stress and biotic stress. Taken together, this study deepened our understanding of transcriptome variation in maize silk and the expression regulation of silk-preferential genes, enhancing the investigation of regulatory networks on metabolic pathways.
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Affiliation(s)
- Xiaoli Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiawen Lu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingfang Han
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zheyuan Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongwei Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunjun Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Peng Zhou
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junjie Fu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuxin Xie
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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3
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Anikiej-Wiczenbach P, Kaźmierczak M. Unraveling the link between family of origin and parental responsiveness toward own child. Front Psychiatry 2023; 14:1255490. [PMID: 37876622 PMCID: PMC10591072 DOI: 10.3389/fpsyt.2023.1255490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 09/18/2023] [Indexed: 10/26/2023] Open
Abstract
This study investigates the influence of family of origin on parental responsiveness toward own child, taking into account gender differences. A total of 110 triads of mothers, fathers, and their first child aged 6-10 months participated in the standardized Free Play procedure. Parental responsiveness was assessed through observational measures (using Ainsworth procedure) and self-reported scales (Parental Responsiveness Scale). Results revealed correlations between objectively assessed responsiveness and self-reported parental styles in the family of origin, separately for mothers and fathers. Among mothers having daughters, parental sensitivity (an important aspect of observationally measured responsiveness) was positively correlated with having had a liberal loving mother and a negative correlation with an autocratic mother. Cooperation (another aspect of observationally measured responsiveness) was correlated positively with having had a liberal loving mother. Meanwhile, having a liberal unloving mother predicted lover sensitivity and cooperation. Similar correlations were not observed for mothers having sons. Among fathers having daughters, both aspects of observed responsiveness were positively correlated with having had a democratic father and negatively with autocratic or liberal unloving parents. Moreover, having a liberal unloving father and autocratic mother predicted their lower responsiveness toward daughters. These findings highlight the role of family dynamics in shaping parental responsiveness and emphasize the importance of understanding these dynamics in promoting responsive parenting.
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Ningning Z, Binbin L, Fan Y, Jianzhong C, Yuqian Z, Yejian W, Wenjie Z, Xinghua Z, Shutu X, Jiquan X. Molecular mechanisms of drought resistance using genome-wide association mapping in maize (Zea mays L.). BMC PLANT BIOLOGY 2023; 23:468. [PMID: 37803273 PMCID: PMC10557160 DOI: 10.1186/s12870-023-04489-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 09/26/2023] [Indexed: 10/08/2023]
Abstract
BACKGROUND Drought is a critical abiotic stress that influences maize yield and reduces grain yield when it occurs at the flowering or filling stage. To dissect the genetic architecture of grain yield under drought stress (DS), a genome-wide association analysis was conducted in a maize population composed of diverse inbred lines from five locations under well-watered and DS conditions at flowering in 2019 and 2020. RESULTS Using a fixed and random model circulating probability unification model, a total of 147 loci associated with grain yield or the drought resistance index (DRI) were identified, of which 54 loci were associated with a DRI with an average phenotypic variation explanation of 4.03%. Further, 10 of these loci explained more than 10% of the phenotypic variation. By integrating two public transcriptome datasets, 22 differentially expressed genes were considered as candidate genes, including the cloned gene ZmNAC49, which responds to drought by regulating stomatal density. Enrichment and protein interaction network showed that signaling pathways responded to drought resistance, including jasmonic acid and salicylic acid, mitogen-activated protein kinase, and abscisic acid-activated. Additionally, several transcription factors involved in DS were identified, including basic leucine zipper (GRMZM2G370026), NAC (GRMZM2G347043), and ethylene-responsive element binding protein (GRMZM2G169654). CONCLUSIONS In this study, we nominated several genes as candidate genes for drought resistance by intergrating association maping and transcription analysis. These results provide valuable information for understanding the genetic basis of drought tolerance at the mature stage and for designing drought-tolerant maize breeding.
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Affiliation(s)
- Zhang Ningning
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Liu Binbin
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ye Fan
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chang Jianzhong
- Agricultural University of Shanxi, Taiyuan, Shanxi, 030600, China
| | - Zhou Yuqian
- Crop Institute of Gansu Academy of Agricultural Sciences, Lanzhou, Gansu, 730000, China
| | - Wang Yejian
- Institute of Grain Crops, Academy of Agricultural Sciences of Xinjiang, Urumqi, Xinjiang, 830000, China
| | - Zhang Wenjie
- Crop Institute of Ningxia Academy of Agricultural Sciences, Yinchuan, Ningxia, 750000, China
| | - Zhang Xinghua
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xu Shutu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Xue Jiquan
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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Tanaka W, Yamauchi T, Tsuda K. Genetic basis controlling rice plant architecture and its modification for breeding. BREEDING SCIENCE 2023; 73:3-45. [PMID: 37168811 PMCID: PMC10165344 DOI: 10.1270/jsbbs.22088] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/25/2022] [Indexed: 05/13/2023]
Abstract
The shoot and root system architectures are fundamental for crop productivity. During the history of artificial selection of domestication and post-domestication breeding, the architecture of rice has significantly changed from its wild ancestor to fulfil requirements in agriculture. We review the recent studies on developmental biology in rice by focusing on components determining rice plant architecture; shoot meristems, leaves, tillers, stems, inflorescences and roots. We also highlight natural variations that affected these structures and were utilized in cultivars. Importantly, many core regulators identified from developmental mutants have been utilized in breeding as weak alleles moderately affecting these architectures. Given a surge of functional genomics and genome editing, the genetic mechanisms underlying the rice plant architecture discussed here will provide a theoretical basis to push breeding further forward not only in rice but also in other crops and their wild relatives.
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Affiliation(s)
- Wakana Tanaka
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Takaki Yamauchi
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Katsutoshi Tsuda
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Corresponding author (e-mail: )
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6
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Julca I, Tan QW, Mutwil M. Toward kingdom-wide analyses of gene expression. TRENDS IN PLANT SCIENCE 2023; 28:235-249. [PMID: 36344371 DOI: 10.1016/j.tplants.2022.09.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/22/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Gene expression data for Archaeplastida are accumulating exponentially, with more than 300 000 RNA-sequencing (RNA-seq) experiments available for hundreds of species. The gene expression data stem from thousands of experiments that capture gene expression in various organs, tissues, cell types, (a)biotic perturbations, and genotypes. Advances in software tools make it possible to process all these data in a matter of weeks on modern office computers, giving us the possibility to study gene expression in a kingdom-wide manner for the first time. We discuss how the expression data can be accessed and processed and outline analyses that take advantage of cross-species analyses, allowing us to generate powerful and robust hypotheses about gene function and evolution.
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Affiliation(s)
- Irene Julca
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Qiao Wen Tan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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7
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Xu X, Jackson D. Single-cell analysis opens a goldmine for plant functional studies. Curr Opin Biotechnol 2023; 79:102858. [PMID: 36493588 DOI: 10.1016/j.copbio.2022.102858] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022]
Abstract
Functional studies in biology require the identification of genes, regulatory elements, and networks, followed by a deep understanding of how they orchestrate to specify cell types, mediate signaling, and respond to internal and external cues over evolutionary timescales. Advances in single-cell analysis have enabled biologists to tackle these questions at the resolution of the individual cell. Here, we highlight recent studies in plants that have embraced single-cell analyses to facilitate functional studies. This review will provide guidance and perspectives for incorporating these advanced approaches in plant research for the coming decades.
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Affiliation(s)
- Xiaosa Xu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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Kitagawa M, Xu X, Jackson D. Trafficking and localization of KNOTTED1 related mRNAs in shoot meristems. Commun Integr Biol 2022; 15:158-163. [PMID: 35832536 PMCID: PMC9272838 DOI: 10.1080/19420889.2022.2095125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Multicellular organisms use transcripts and proteins as signaling molecules for cell-to-cell communication. Maize KNOTTED1 (KN1) was the first homeodomain transcription factor identified in plants, and functions in maintaining shoot stem cells. KN1 acts non-cell autonomously, and both its messenger RNA (mRNA) and protein traffic between cells through intercellular nanochannels called plasmodesmata. KN1 protein and mRNA trafficking are regulated by a chaperonin subunit and a catalytic subunit of the RNA exosome, respectively. These studies suggest that the function of KN1 in stem cell regulation requires the cell-to-cell transport of both its protein and mRNA. However, in situ hybridization experiments published 25 years ago suggested that KN1 mRNA was missing from the epidermal (L1) layer of shoot meristems, suggesting that only the KN1 protein could traffic. Here, we show evidence that KN1 mRNA is present at a low level in L1 cells of maize meristems, supporting an idea that both KN1 protein and mRNA traffic to the L1 layer. We also summarize mRNA expression patterns of KN1 homologs in diverse angiosperm species, and discuss KN1 trafficking mechanisms.
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Affiliation(s)
| | - Xiaosa Xu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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Xiao Y, Guo J, Dong Z, Richardson A, Patterson E, Mangrum S, Bybee S, Bertolini E, Bartlett M, Chuck G, Eveland AL, Scanlon MJ, Whipple C. Boundary domain genes were recruited to suppress bract growth and promote branching in maize. SCIENCE ADVANCES 2022; 8:eabm6835. [PMID: 35704576 PMCID: PMC9200273 DOI: 10.1126/sciadv.abm6835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Grass inflorescence development is diverse and complex and involves sophisticated but poorly understood interactions of genes regulating branch determinacy and leaf growth. Here, we use a combination of transcript profiling and genetic and phylogenetic analyses to investigate tasselsheath1 (tsh1) and tsh4, two maize genes that simultaneously suppress inflorescence leaf growth and promote branching. We identify a regulatory network of inflorescence leaf suppression that involves the phase change gene tsh4 upstream of tsh1 and the ligule identity gene liguleless2 (lg2). We also find that a series of duplications in the tsh1 gene lineage facilitated its shift from boundary domain in nongrasses to suppressed inflorescence leaves of grasses. Collectively, these results suggest that the boundary domain genes tsh1 and lg2 were recruited to inflorescence leaves where they suppress growth and regulate a nonautonomous signaling center that promotes inflorescence branching, an important component of yield in cereal grasses.
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Affiliation(s)
- Yuguo Xiao
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT 84602, USA
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Jinyan Guo
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT 84602, USA
| | - Zhaobin Dong
- Plant Gene Expression Center, Albany, CA 94710, USA
| | - Annis Richardson
- Plant Gene Expression Center, Albany, CA 94710, USA
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, Scotland, UK
| | - Erin Patterson
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Sidney Mangrum
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT 84602, USA
| | - Seth Bybee
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT 84602, USA
| | | | - Madelaine Bartlett
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - George Chuck
- Plant Gene Expression Center, Albany, CA 94710, USA
| | | | - Michael J. Scanlon
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Clinton Whipple
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT 84602, USA
- Corresponding author.
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Matthes MS, Darnell Z, Best NB, Guthrie K, Robil JM, Amstutz J, Durbak A, McSteen P. Defects in meristem maintenance, cell division, and cytokinin signaling are early responses in the boron deficient maize mutant tassel-less1. PHYSIOLOGIA PLANTARUM 2022; 174:e13670. [PMID: 35292977 DOI: 10.1111/ppl.13670] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/28/2022] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Meristems house the stem cells needed for the developmental plasticity observed in adverse environmental conditions and are crucial for determining plant architecture. Meristem development is particularly sensitive to deficiencies of the micronutrient boron, yet how boron integrates into meristem development pathways is unknown. We addressed this question using the boron-deficient maize mutant, tassel-less1 (tls1). Reduced boron uptake in tls1 leads to a progressive impairment of meristem development that manifests in vegetative and reproductive defects. We show, that the tls1 tassel phenotype (male reproductive structure) was partially suppressed by mutations in the CLAVATA1 (CLV1)-ortholog, thick tassel dwarf1 (td1), but not by other mutants in the well characterized CLV-WUSCHEL pathway, which controls meristem size. The suppression of tls1 by td1 correlates with altered signaling of the phytohormone cytokinin. In contrast, mutations in the meristem maintenance gene knotted1 (kn1) enhanced both vegetative and reproductive defects in tls1. In addition, reduced transcript levels of kn1 and cell cycle genes are early defects in tls1 tassel meristems. Our results show that specific meristem maintenance and hormone pathways are affected in tls1, and suggest that reduced boron levels induced by tls1 are the underlying cause of the observed defects. We, therefore, provide new insights into the molecular mechanisms affected by boron deficiency in maize, leading to a better understanding of how genetic and environmental factors integrate during shoot meristem development.
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Affiliation(s)
- Michaela S Matthes
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, Missouri, USA
| | - Zoe Darnell
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, Missouri, USA
| | - Norman B Best
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, Missouri, USA
| | - Katy Guthrie
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, Missouri, USA
| | - Janlo M Robil
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, Missouri, USA
| | - Jen Amstutz
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, Missouri, USA
| | - Amanda Durbak
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
| | - Paula McSteen
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, Missouri, USA
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Laureyns R, Joossens J, Herwegh D, Pevernagie J, Pavie B, Demuynck K, Debray K, Coussens G, Pauwels L, Van Hautegem T, Bontinck M, Strable J, Nelissen H. An in situ sequencing approach maps PLASTOCHRON1 at the boundary between indeterminate and determinate cells. PLANT PHYSIOLOGY 2022; 188:782-794. [PMID: 34791481 PMCID: PMC8825424 DOI: 10.1093/plphys/kiab533] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/28/2021] [Indexed: 05/03/2023]
Abstract
The plant shoot apex houses the shoot apical meristem, a highly organized and active stem-cell tissue where molecular signaling in discrete cells determines when and where leaves are initiated. We optimized a spatial transcriptomics approach, in situ sequencing (ISS), to colocalize the transcripts of 90 genes simultaneously on the same section of tissue from the maize (Zea mays) shoot apex. The RNA ISS technology reported expression profiles that were highly comparable with those obtained by in situ hybridizations (ISHs) and allowed the discrimination between tissue domains. Furthermore, the application of spatial transcriptomics to the shoot apex, which inherently comprised phytomers that are in gradual developmental stages, provided a spatiotemporal sequence of transcriptional events. We illustrate the power of the technology through PLASTOCHRON1 (PLA1), which was specifically expressed at the boundary between indeterminate and determinate cells and partially overlapped with ROUGH SHEATH1 and OUTER CELL LAYER4 transcripts. Also, in the inflorescence, PLA1 transcripts localized in cells subtending the lateral primordia or bordering the newly established meristematic region, suggesting a more general role of PLA1 in signaling between indeterminate and determinate cells during the formation of lateral organs. Spatial transcriptomics builds on RNA ISH, which assays relatively few transcripts at a time and provides a powerful complement to single-cell transcriptomics that inherently removes cells from their native spatial context. Further improvements in resolution and sensitivity will greatly advance research in plant developmental biology.
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Affiliation(s)
- Reinout Laureyns
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Jessica Joossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Denia Herwegh
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Julie Pevernagie
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Benjamin Pavie
- VIB Center for Brain & Disease Research, Leuven 3000, Belgium
- Department of Neurosciences, KU Leuven, Leuven Brain Institute, Leuven 3000, Belgium
- VIB Bio Imaging Core, Gent 9052, Belgium
| | - Kirin Demuynck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Kevin Debray
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Griet Coussens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Laurens Pauwels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Tom Van Hautegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | | | - Josh Strable
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
- Author for communication:
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12
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Swift J, Greenham K, Ecker JR, Coruzzi GM, McClung CR. The biology of time: dynamic responses of cell types to developmental, circadian and environmental cues. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:764-778. [PMID: 34797944 PMCID: PMC9215356 DOI: 10.1111/tpj.15589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 05/26/2023]
Abstract
As sessile organisms, plants are finely tuned to respond dynamically to developmental, circadian and environmental cues. Genome-wide studies investigating these types of cues have uncovered the intrinsically different ways they can impact gene expression over time. Recent advances in single-cell sequencing and time-based bioinformatic algorithms are now beginning to reveal the dynamics of these time-based responses within individual cells and plant tissues. Here, we review what these techniques have revealed about the spatiotemporal nature of gene regulation, paying particular attention to the three distinct ways in which plant tissues are time sensitive. (i) First, we discuss how studying plant cell identity can reveal developmental trajectories hidden in pseudotime. (ii) Next, we present evidence that indicates that plant cell types keep their own local time through tissue-specific regulation of the circadian clock. (iii) Finally, we review what determines the speed of environmental signaling responses, and how they can be contingent on developmental and circadian time. By these means, this review sheds light on how these different scales of time-based responses can act with tissue and cell-type specificity to elicit changes in whole plant systems.
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Affiliation(s)
- Joseph Swift
- Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Kathleen Greenham
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN 55108, USA
| | - Joseph R. Ecker
- Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Gloria M. Coruzzi
- Department of Biology, Center for Genomics and Systems Biology, New York University, NY, USA
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13
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Denyer T, Timmermans MCP. Crafting a blueprint for single-cell RNA sequencing. TRENDS IN PLANT SCIENCE 2022; 27:92-103. [PMID: 34580023 DOI: 10.1016/j.tplants.2021.08.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/23/2021] [Accepted: 08/31/2021] [Indexed: 05/05/2023]
Abstract
Droplet-based single-cell RNA sequencing (scRNA-Seq) has moved rapidly from a technology with great potential to a method applied to ever-broader questions. The detailed information that scRNA-Seq offers has proven incredibly powerful in resolving cell responses to developmental and environmental cues. However, to maximize the potential of this technology, a panoply of upstream, practical points require consideration. Principal among these are the optimization of cell-isolation procedures, accommodating biotic/abiotic stress responses, and discerning the number of cells and sequencing reads needed. To complement excellent reviews outlining applications and data analysis tools for scRNA-Seq, we here discuss these considerations and provide practical tips to tailor experimental design and ensure the best possible outcome.
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Affiliation(s)
- Tom Denyer
- Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Marja C P Timmermans
- Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany.
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14
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Du Y, Wu B, Xing Y, Zhang Z. Conservation and divergence: Regulatory networks underlying reproductive branching in rice and maize. J Adv Res 2022; 41:179-190. [PMID: 36328747 PMCID: PMC9637487 DOI: 10.1016/j.jare.2022.01.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/27/2021] [Accepted: 01/26/2022] [Indexed: 12/31/2022] Open
Abstract
Branching pattern in maize and rice determines the inflorescence architecture and thus the final grain yield. The branching pattern is determined by meristem size, bud initiation and outgrowth, and controlled by endogenous and external factors. Genetic control of inflorescence branching including CLV-WUS feedback loop, Auxin-cytokinin crosstalk and miR156/SPL/miR172 in maize and rice is summarized. The comprehensive genetic networks associated with crop branching, will promote the transformation of molecular designs breeding based on regulatory networks via genome editing, then produce optimized inflorescence architecture.
Background Cereal crops are a major source of raw food and nutrition for humans worldwide. Inflorescence of cereal crops is their reproductive organ, which also contributes to crop productivity. The branching pattern in flowering plant species not only determines inflorescence architecture but also determines the grain yield. There are good reviews describing the grass inflorescence architecture contributing to the final grain yield. However, very few discuss the aspects of inflorescence branching. Aim of review This review aimed at systematically and comprehensively summarizing the latest progress in the field of conservation and divergence of genetic regulatory network that controls inflorescence branching in maize and rice, provide strategies to efficiently utilize the achievements in reproductive branching for crop yield improvement, and suggest a potential regulatory network underlying the inflorescence branching and vegetative branching system. Key scientific concepts of review Inflorescence branching is the consequence of a series of developmental events including the initiation, outgrowth, determinacy, and identity of reproductive axillary meristems, and it is controlled by a complex functional hierarchy of genetic networks. Initially, we compared the inflorescence architecture of maize and rice; then, we reviewed the genetic regulatory pathways controlling the inflorescence meristem size, bud initiation, and outgrowth, and the key transition steps that shape the inflorescence branching in maize and rice; additionally, we summarized strategies to effectively apply the recent advances in inflorescence branching for crop yield improvement. Finally, we discussed how the newly discovered hormones coordinate the regulation of inflorescence branching and yield traits. Furthermore, we discussed the possible reason behind distinct regulatory pathways for vegetative and inflorescence branching.
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15
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Pernisová M, Vernoux T. Auxin Does the SAMba: Auxin Signaling in the Shoot Apical Meristem. Cold Spring Harb Perspect Biol 2021; 13:a039925. [PMID: 33903154 PMCID: PMC8634999 DOI: 10.1101/cshperspect.a039925] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Plants, in contrast to animals, are unique in their capacity to postembryonically develop new organs due to the activity of stem cell populations, located in specialized tissues called meristems. Above ground, the shoot apical meristem generates aerial organs and tissues throughout plant life. It is well established that auxin plays a central role in the functioning of the shoot apical meristem. Auxin distribution in the meristem is not uniform and depends on the interplay between biosynthesis, transport, and degradation. Auxin maxima and minima are created, and result in transcriptional outputs that drive the development of new organs and contribute to meristem maintenance. To uncover and understand complex signaling networks such as the one regulating auxin responses in the shoot apical meristem remains a challenge. Here, we will discuss our current understanding and point to important research directions for the future.
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Affiliation(s)
- Markéta Pernisová
- Laboratoire Reproduction et Développement des Plantes, University at Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France
- Functional Genomics and Proteomics, National Centre for Biomolecula Research, Faculty of Science, Masaryk University and CEITEC MU, 62500 Brno, Czech Republic
| | - Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, University at Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France
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16
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Systematic Characterization of TCP Gene Family in Four Cotton Species Revealed That GhTCP62 Regulates Branching in Arabidopsis. BIOLOGY 2021; 10:biology10111104. [PMID: 34827097 PMCID: PMC8614845 DOI: 10.3390/biology10111104] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/21/2021] [Accepted: 10/25/2021] [Indexed: 01/14/2023]
Abstract
TEOSINTE-BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors play an essential role in regulating various physiological and biochemical functions during plant growth. However, the function of TCP transcription factors in G. hirsutum has not yet been studied. In this study, we performed genome-wide identification and correlation analysis of the TCP transcription factor family in G. hirsutum. We identified 72 non-redundant GhTCP genes and divided them into seven subfamilies, based on phylogenetic analysis. Most GhTCP genes in the same subfamily displayed similar exon and intron structures and featured highly conserved motif structures in their subfamily. Additionally, the pattern of chromosomal distribution demonstrated that GhTCP genes were unevenly distributed on 24 out of 26 chromosomes, and that fragment replication was the main replication event of GhTCP genes. In TB1 sub-family genes, GhTCP62 was highly expressed in the axillary buds, suggesting that GhTCP62 significantly affected cotton branching. Additionally, subcellular localization results indicated that GhTCP62 is located in the nucleus and possesses typical transcription factor characteristics. The overexpression of GhTCP62 in Arabidopsis resulted in fewer rosette-leaf branches and cauline-leaf branches. Furthermore, the increased expression of HB21 and HB40 genes in Arabidopsis plants overexpressing GhTCP62 suggests that GhTCP62 may regulate branching by positively regulating HB21 and HB40.
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17
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Strable J, Nelissen H. The dynamics of maize leaf development: Patterned to grow while growing a pattern. CURRENT OPINION IN PLANT BIOLOGY 2021; 63:102038. [PMID: 33940553 DOI: 10.1016/j.pbi.2021.102038] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 05/12/2023]
Abstract
Leaves are a significant component of the shoot system in grasses, functioning in light capture and photosynthesis. Leaf width, length, and angle are expressions of development that collectively define canopy architecture. Thus, the distinctive morphology of grass leaves is an interdependent readout of developmental patterning and growth along the proximal-distal, medial-lateral, and adaxial-abaxial axes. Here, we review the chronology of patterning and growth, namely along the proximal-distal axis, during maize leaf development. We underscore that patterning and growth occur simultaneously, making use of shared developmental gradients and molecular pathways.
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Affiliation(s)
- Josh Strable
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA 27695.
| | - Hilde Nelissen
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, 9052, Ghent, Belgium.
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18
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Gene duplication at the Fascicled ear1 locus controls the fate of inflorescence meristem cells in maize. Proc Natl Acad Sci U S A 2021; 118:2019218118. [PMID: 33579824 PMCID: PMC7896288 DOI: 10.1073/pnas.2019218118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The maize ear is unbranched and terminates in a single point. The ear and tassel inflorescences of Fascicled ear mutants fail to grow as a single point and instead are branched. This phenotype results from the misexpression of duplicated transcription factors, ZMM8 and DRL2. We hypothesize that these gene rearrangements create regulatory sequences that cause misexpression in early inflorescence meristems, thus activating a laminar program, ablating the meristem, and producing branches. This work demonstrates that zmm8 and drl2 must be restricted from the inflorescence meristem to maintain its terminal point, and conversely, a mechanism by which branching may be imposed. Manipulation of these genes can be used to alter plant architecture, potentially to improve agronomic traits. Plant meristems are self-renewing groups of pluripotent stem cells that produce lateral organs in a stereotypical pattern. Of interest is how the radially symmetrical meristem produces laminar lateral organs. Both the male and female inflorescence meristems of the dominant Fascicled ear (Fas1) mutant fail to grow as a single point and instead show deep branching. Positional cloning of two independent Fas1 alleles identified an ∼160 kb region containing two floral genes, the MADS-box gene, zmm8, and the YABBY gene, drooping leaf2 (drl2). Both genes are duplicated within the Fas1 locus and spatiotemporally misexpressed in the mutant inflorescence meristems. Increased zmm8 expression alone does not affect inflorescence development; however, combined misexpression of zmm8, drl2, and their syntenic paralogs zmm14 and drl1, perturbs meristem organization. We hypothesize that misexpression of the floral genes in the inflorescence and their potential interaction cause ectopic activation of a laminar program, thereby disrupting signaling necessary for maintenance of radially symmetrical inflorescence meristems. Consistent with this hypothesis, RNA sequencing and in situ analysis reveal altered expression patterns of genes that define distinct zones of the meristem and developing leaf. Our findings highlight the importance of strict spatiotemporal patterns of expression for both zmm8 and drl2 and provide an example of phenotypes arising from tandem gene duplications.
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19
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Jayakodi M, Schreiber M, Stein N, Mascher M. Building pan-genome infrastructures for crop plants and their use in association genetics. DNA Res 2021; 28:6117190. [PMID: 33484244 PMCID: PMC7934568 DOI: 10.1093/dnares/dsaa030] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Indexed: 12/20/2022] Open
Abstract
Pan-genomic studies aim at representing the entire sequence diversity within a species to provide useful resources for evolutionary studies, functional genomics and breeding of cultivated plants. Cost reductions in high-throughput sequencing and advances in sequence assembly algorithms have made it possible to create multiple reference genomes along with a catalogue of all forms of genetic variations in plant species with large and complex or polyploid genomes. In this review, we summarize the current approaches to building pan-genomes as an in silico representation of plant sequence diversity and outline relevant methods for their effective utilization in linking structural with phenotypic variation. We propose as future research avenues (i) transcriptomic and epigenomic studies across multiple reference genomes and (ii) the development of user-friendly and feature-rich pan-genome browsers.
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Affiliation(s)
- Murukarthick Jayakodi
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Mona Schreiber
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Nils Stein
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.,Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, Göttingen, Germany
| | - Martin Mascher
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Saxony, Germany
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20
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Tripathi RK, Wilkins O. Single cell gene regulatory networks in plants: Opportunities for enhancing climate change stress resilience. PLANT, CELL & ENVIRONMENT 2021; 44:2006-2017. [PMID: 33522607 PMCID: PMC8359182 DOI: 10.1111/pce.14012] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 05/05/2023]
Abstract
Global warming poses major challenges for plant survival and agricultural productivity. Thus, efforts to enhance stress resilience in plants are key strategies for protecting food security. Gene regulatory networks (GRNs) are a critical mechanism conferring stress resilience. Until recently, predicting GRNs of the individual cells that make up plants and other multicellular organisms was impeded by aggregate population scale measurements of transcriptome and other genome-scale features. With the advancement of high-throughput single cell RNA-seq and other single cell assays, learning GRNs for individual cells is now possible, in principle. In this article, we report on recent advances in experimental and analytical methodologies for single cell sequencing assays especially as they have been applied to the study of plants. We highlight recent advances and ongoing challenges for scGRN prediction, and finally, we highlight the opportunity to use scGRN discovery for studying and ultimately enhancing abiotic stress resilience in plants.
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Affiliation(s)
- Rajiv K. Tripathi
- Department of Biological SciencesUniversity of ManitobaWinnipegManitobaCanada
| | - Olivia Wilkins
- Department of Biological SciencesUniversity of ManitobaWinnipegManitobaCanada
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21
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Chen Z, Li W, Gaines C, Buck A, Galli M, Gallavotti A. Structural variation at the maize WUSCHEL1 locus alters stem cell organization in inflorescences. Nat Commun 2021; 12:2378. [PMID: 33888716 PMCID: PMC8062686 DOI: 10.1038/s41467-021-22699-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 03/23/2021] [Indexed: 01/28/2023] Open
Abstract
Structural variation in plant genomes is a significant driver of phenotypic variability in traits important for the domestication and productivity of crop species. Among these are traits that depend on functional meristems, populations of stem cells maintained by the CLAVATA-WUSCHEL (CLV-WUS) negative feedback-loop that controls the expression of the WUS homeobox transcription factor. WUS function and impact on maize development and yield remain largely unexplored. Here we show that the maize dominant Barren inflorescence3 (Bif3) mutant harbors a tandem duplicated copy of the ZmWUS1 gene, ZmWUS1-B, whose novel promoter enhances transcription in a ring-like pattern. Overexpression of ZmWUS1-B is due to multimerized binding sites for type-B RESPONSE REGULATORs (RRs), key transcription factors in cytokinin signaling. Hypersensitivity to cytokinin causes stem cell overproliferation and major rearrangements of Bif3 inflorescence meristems, leading to the formation of ball-shaped ears and severely affecting productivity. These findings establish ZmWUS1 as an essential meristem size regulator in maize and highlight the striking effect of cis-regulatory variation on a key developmental program. The WUSCHEL transcription factor promotes plant stem cell proliferation. Here the authors show that the maize Bif3 mutant contains a duplication of the ZmWUS1 locus leading to cytokinin hypersensitivity and overproliferation at the shoot meristem demonstrating the role of WUSCHEL in maize and how structural variation can impact plant morphology.
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Affiliation(s)
- Zongliang Chen
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Wei Li
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Craig Gaines
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - Amy Buck
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA.,Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - Mary Galli
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA. .,Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA.
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22
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Ma X, Denyer T, Javelle M, Feller A, Timmermans MCP. Genome-wide analysis of plant miRNA action clarifies levels of regulatory dynamics across developmental contexts. Genome Res 2021; 31:811-822. [PMID: 33863807 PMCID: PMC8092011 DOI: 10.1101/gr.270918.120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 03/04/2021] [Indexed: 01/12/2023]
Abstract
Development of complex organisms requires the delicate and dynamic spatiotemporal regulation of gene expression. Central to this are microRNAs (miRNAs). These mobile small RNAs offer specificity in conveying positional information and versatility in patterning the outcomes of gene expression. However, the parameters that shape miRNA output during development are still to be clarified. Here, we address this question on a genome-wide scale, using the maize shoot apex as a model. We show that patterns and levels of miRNA accumulation are largely determined at the transcriptional level, but are finessed post-transcriptionally in a tissue-dependent manner. The stem cell environments of the shoot apical meristem and vasculature appear particularly liable to this. Tissue-specific effects are also apparent at the level of target repression, with target cleavage products in the vasculature exceeding those of other tissues. Our results argue against a clearance mode of regulation purely at the level of transcript cleavage, leading us to propose that transcript cleavage provides a baseline level of target repression, onto which miRNA-driven translational repression can act to toggle the mode of target regulation between clearance and rheostat. Our data show how the inherent complexities of miRNA pathways allow the accumulation and activity of these small RNAs to be tailored in space and time to bring about the gene expression versatility needed during development.
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Affiliation(s)
- Xiaoli Ma
- Center for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Tom Denyer
- Center for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany
| | | | - Antje Feller
- Center for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Marja C P Timmermans
- Center for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany
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23
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Miya M, Yoshikawa T, Sato Y, Itoh JI. Genome-wide analysis of spatiotemporal expression patterns during rice leaf development. BMC Genomics 2021; 22:169. [PMID: 33750294 PMCID: PMC7941727 DOI: 10.1186/s12864-021-07494-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rice leaves consist of three distinct regions along a proximal-distal axis, namely the leaf blade, sheath, and blade-sheath boundary region. Each region has a unique morphology and function, but the genetic programs underlying the development of each region are poorly understood. To fully elucidate rice leaf development and discover genes with unique functions in rice and grasses, it is crucial to explore genome-wide transcriptional profiles during the development of the three regions. RESULTS In this study, we performed microarray analysis to profile the spatial and temporal patterns of gene expression in the rice leaf using dissected parts of leaves sampled in broad developmental stages. The dynamics in each region revealed that the transcriptomes changed dramatically throughout the progress of tissue differentiation, and those of the leaf blade and sheath differed greatly at the mature stage. Cluster analysis of expression patterns among leaf parts revealed groups of genes that may be involved in specific biological processes related to rice leaf development. Moreover, we found novel genes potentially involved in rice leaf development using a combination of transcriptome data and in situ hybridization, and analyzed their spatial expression patterns at high resolution. We successfully identified multiple genes that exhibit localized expression in tissues characteristic of rice or grass leaves. CONCLUSIONS Although the genetic mechanisms of leaf development have been elucidated in several eudicots, direct application of that information to rice and grasses is not appropriate due to the morphological and developmental differences between them. Our analysis provides not only insights into the development of rice leaves but also expression profiles that serve as a valuable resource for gene discovery. The genes and gene clusters identified in this study may facilitate future research on the unique developmental mechanisms of rice leaves.
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Affiliation(s)
- Masayuki Miya
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, 113-8657, Japan
| | - Takanori Yoshikawa
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Yutaka Sato
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, 305-8518, Japan
| | - Jun-Ichi Itoh
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, 113-8657, Japan.
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24
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Strable J. Developmental genetics of maize vegetative shoot architecture. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:19. [PMID: 37309417 PMCID: PMC10236122 DOI: 10.1007/s11032-021-01208-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/25/2021] [Indexed: 06/13/2023]
Abstract
More than 1.1 billion tonnes of maize grain were harvested across 197 million hectares in 2019 (FAOSTAT 2020). The vast global productivity of maize is largely driven by denser planting practices, higher yield potential per area of land, and increased yield potential per plant. Shoot architecture, the three-dimensional structural arrangement of the above-ground plant body, is critical to maize grain yield and biomass. Structure of the shoot is integral to all aspects of modern agronomic practices. Here, the developmental genetics of the maize vegetative shoot is reviewed. Plant architecture is ultimately determined by meristem activity, developmental patterning, and growth. The following topics are discussed: shoot apical meristem, leaf architecture, axillary meristem and shoot branching, and intercalary meristem and stem activity. Where possible, classical and current studies in maize developmental genetics, as well as recent advances leveraged by "-omics" analyses, are highlighted within these sections. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01208-1.
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Affiliation(s)
- Josh Strable
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
- Present Address: Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695 USA
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25
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Chen Z, Gallavotti A. Improving architectural traits of maize inflorescences. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:21. [PMID: 37309422 PMCID: PMC10236070 DOI: 10.1007/s11032-021-01212-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/02/2021] [Indexed: 06/13/2023]
Abstract
The domestication and improvement of maize resulted in radical changes in shoot architecture relative to its wild progenitor teosinte. In particular, critical modifications involved a reduction of branching and an increase in inflorescence size to meet the needs for human consumption and modern agricultural practices. Maize is a major contributor to global agricultural production by providing large and inexpensive quantities of food, animal feed, and ethanol. Maize is also a classic system for studying the genetic regulation of inflorescence formation and its enlarged female inflorescences directly influence seed production and yield. Studies on the molecular and genetic networks regulating meristem proliferation and maintenance, including receptor-ligand interactions, transcription factor regulation, and hormonal control, provide important insights into maize inflorescence development and reveal potential avenues for the targeted modification of specific architectural traits. In this review, we summarize recent findings on the molecular mechanisms controlling inflorescence formation and discuss how this knowledge can be applied to improve maize productivity in the face of present and future environmental challenges.
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Affiliation(s)
- Zongliang Chen
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854-8020 USA
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854-8020 USA
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901 USA
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26
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Rivera HE, Aichelman HE, Fifer JE, Kriefall NG, Wuitchik DM, Wuitchik SJS, Davies SW. A framework for understanding gene expression plasticity and its influence on stress tolerance. Mol Ecol 2021; 30:1381-1397. [PMID: 33503298 DOI: 10.1111/mec.15820] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/10/2020] [Accepted: 01/20/2021] [Indexed: 12/18/2022]
Abstract
Phenotypic plasticity can serve as a stepping stone towards adaptation. Recently, studies have shown that gene expression contributes to emergent stress responses such as thermal tolerance, with tolerant and susceptible populations showing distinct transcriptional profiles. However, given the dynamic nature of gene expression, interpreting transcriptomic results in a way that elucidates the functional connection between gene expression and the observed stress response is challenging. Here, we present a conceptual framework to guide interpretation of gene expression reaction norms in the context of stress tolerance. We consider the evolutionary and adaptive potential of gene expression reaction norms and discuss the influence of sampling timing, transcriptomic resilience, as well as complexities related to life history when interpreting gene expression dynamics and how these patterns relate to host tolerance. We highlight corals as a case study to demonstrate the value of this framework for non-model systems. As species face rapidly changing environmental conditions, modulating gene expression can serve as a mechanistic link from genetic and cellular processes to the physiological responses that allow organisms to thrive under novel conditions. Interpreting how or whether a species can employ gene expression plasticity to ensure short-term survival will be critical for understanding the global impacts of climate change across diverse taxa.
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Affiliation(s)
- Hanny E Rivera
- Department of Biology, Boston University, Boston, MA, USA
| | | | - James E Fifer
- Department of Biology, Boston University, Boston, MA, USA
| | | | | | - Sara J S Wuitchik
- Department of Biology, Boston University, Boston, MA, USA.,FAS Informatics, Harvard University, Cambridge, MA, USA
| | - Sarah W Davies
- Department of Biology, Boston University, Boston, MA, USA
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27
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Xu X, Crow M, Rice BR, Li F, Harris B, Liu L, Demesa-Arevalo E, Lu Z, Wang L, Fox N, Wang X, Drenkow J, Luo A, Char SN, Yang B, Sylvester AW, Gingeras TR, Schmitz RJ, Ware D, Lipka AE, Gillis J, Jackson D. Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery. Dev Cell 2021; 56:557-568.e6. [PMID: 33400914 DOI: 10.1016/j.devcel.2020.12.015] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/31/2020] [Accepted: 12/15/2020] [Indexed: 12/30/2022]
Abstract
Crop productivity depends on activity of meristems that produce optimized plant architectures, including that of the maize ear. A comprehensive understanding of development requires insight into the full diversity of cell types and developmental domains and the gene networks required to specify them. Until now, these were identified primarily by morphology and insights from classical genetics, which are limited by genetic redundancy and pleiotropy. Here, we investigated the transcriptional profiles of 12,525 single cells from developing maize ears. The resulting developmental atlas provides a single-cell RNA sequencing (scRNA-seq) map of an inflorescence. We validated our results by mRNA in situ hybridization and by fluorescence-activated cell sorting (FACS) RNA-seq, and we show how these data may facilitate genetic studies by predicting genetic redundancy, integrating transcriptional networks, and identifying candidate genes associated with crop yield traits.
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Affiliation(s)
- Xiaosa Xu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Megan Crow
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Brian R Rice
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Forrest Li
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Benjamin Harris
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Lei Liu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Zefu Lu
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Liya Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Nathan Fox
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Xiaofei Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jorg Drenkow
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Anding Luo
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Si Nian Char
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Anne W Sylvester
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | | | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; USDA-ARS, Robert W. Holley Center, Ithaca, NY 14853, USA
| | - Alexander E Lipka
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jesse Gillis
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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Satterlee JW, Strable J, Scanlon MJ. Plant stem-cell organization and differentiation at single-cell resolution. Proc Natl Acad Sci U S A 2020; 117:33689-33699. [PMID: 33318187 DOI: 10.1101/2020.08.25.267427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023] Open
Abstract
Plants maintain populations of pluripotent stem cells in shoot apical meristems (SAMs), which continuously produce new aboveground organs. We used single-cell RNA sequencing (scRNA-seq) to achieve an unbiased characterization of the transcriptional landscape of the maize shoot stem-cell niche and its differentiating cellular descendants. Stem cells housed in the SAM tip are engaged in genome integrity maintenance and exhibit a low rate of cell division, consistent with their contributions to germline and somatic cell fates. Surprisingly, we find no evidence for a canonical stem-cell organizing center subtending these cells. In addition, trajectory inference was used to trace the gene expression changes that accompany cell differentiation, revealing that ectopic expression of KNOTTED1 (KN1) accelerates cell differentiation and promotes development of the sheathing maize leaf base. These single-cell transcriptomic analyses of the shoot apex yield insight into the processes of stem-cell function and cell-fate acquisition in the maize seedling and provide a valuable scaffold on which to better dissect the genetic control of plant shoot morphogenesis at the cellular level.
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Affiliation(s)
- James W Satterlee
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Josh Strable
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Michael J Scanlon
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
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29
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Abstract
Plants possess the remarkable ability to grow and produce new organs throughout their lifespan, owing to the activities of persistent populations of pluripotent stem cells within their meristematic tips. Here we isolated individual cells from the microscopic shoot apical meristem (SAM) of maize and provide single-cell transcriptomic analysis of a plant shoot meristem. This study enabled an unbiased analysis of the developmental genetic organization of the maize shoot apex and uncovered evolutionarily divergent and conserved signatures of SAM homeostasis. The fine-scale resolution of single-cell analysis was used to reconstruct the process of shoot cell differentiation, whereby stem cells acquire diverse and distinct cell fates over developmental time in wild-type and mutant maize seedlings. Plants maintain populations of pluripotent stem cells in shoot apical meristems (SAMs), which continuously produce new aboveground organs. We used single-cell RNA sequencing (scRNA-seq) to achieve an unbiased characterization of the transcriptional landscape of the maize shoot stem-cell niche and its differentiating cellular descendants. Stem cells housed in the SAM tip are engaged in genome integrity maintenance and exhibit a low rate of cell division, consistent with their contributions to germline and somatic cell fates. Surprisingly, we find no evidence for a canonical stem-cell organizing center subtending these cells. In addition, trajectory inference was used to trace the gene expression changes that accompany cell differentiation, revealing that ectopic expression of KNOTTED1 (KN1) accelerates cell differentiation and promotes development of the sheathing maize leaf base. These single-cell transcriptomic analyses of the shoot apex yield insight into the processes of stem-cell function and cell-fate acquisition in the maize seedling and provide a valuable scaffold on which to better dissect the genetic control of plant shoot morphogenesis at the cellular level.
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30
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Yu X, Leiboff S, Li X, Guo T, Ronning N, Zhang X, Muehlbauer GJ, Timmermans MC, Schnable PS, Scanlon MJ, Yu J. Genomic prediction of maize microphenotypes provides insights for optimizing selection and mining diversity. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:2456-2465. [PMID: 32452105 PMCID: PMC7680549 DOI: 10.1111/pbi.13420] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 05/05/2020] [Accepted: 05/13/2020] [Indexed: 05/25/2023]
Abstract
Effective evaluation of millions of crop genetic stocks is an essential component of exploiting genetic diversity to achieve global food security. By leveraging genomics and data analytics, genomic prediction is a promising strategy to efficiently explore the potential of these gene banks by starting with phenotyping a small designed subset. Reliable genomic predictions have enhanced selection of many macroscopic phenotypes in plants and animals. However, the use of genomicprediction strategies for analysis of microscopic phenotypes is limited. Here, we exploited the power of genomic prediction for eight maize traits related to the shoot apical meristem (SAM), the microscopic stem cell niche that generates all the above-ground organs of the plant. With 435 713 genomewide single-nucleotide polymorphisms (SNPs), we predicted SAM morphology traits for 2687 diverse maize inbreds based on a model trained from 369 inbreds. An empirical validation experiment with 488 inbreds obtained a prediction accuracy of 0.37-0.57 across eight traits. In addition, we show that a significantly higher prediction accuracy was achieved by leveraging the U value (upper bound for reliability) that quantifies the genomic relationships of the validation set with the training set. Our findings suggest that double selection considering both prediction and reliability can be implemented in choosing selection candidates for phenotyping when exploring new diversity is desired. In this case, individuals with less extreme predicted values and moderate reliability values can be considered. Our study expands the turbocharging gene banks via genomic prediction from the macrophenotypes into the microphenotypic space.
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Affiliation(s)
- Xiaoqing Yu
- Department of AgronomyIowa State UniversityAmesIAUSA
| | - Samuel Leiboff
- Plant Biology SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
| | - Xianran Li
- Department of AgronomyIowa State UniversityAmesIAUSA
| | - Tingting Guo
- Department of AgronomyIowa State UniversityAmesIAUSA
| | - Natalie Ronning
- Plant Biology SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
| | - Xiaoyu Zhang
- Department of Plant BiologyUniversity of GeorgiaAthensGAUSA
| | - Gary J. Muehlbauer
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
| | | | | | - Michael J. Scanlon
- Plant Biology SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
| | - Jianming Yu
- Department of AgronomyIowa State UniversityAmesIAUSA
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31
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Fouracre JP, Poethig RS. Lonely at the top? Regulation of shoot apical meristem activity by intrinsic and extrinsic factors. CURRENT OPINION IN PLANT BIOLOGY 2020; 58:17-24. [PMID: 33099210 PMCID: PMC7752823 DOI: 10.1016/j.pbi.2020.08.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/22/2020] [Accepted: 08/28/2020] [Indexed: 05/22/2023]
Abstract
All the above-ground organs of a plant are derived from stem cells that reside in shoot apical meristems (SAM). Over the past 25 years, the genetic pathways that control the proliferation of stem cells within the SAM, and the differentiation of their progenitors into lateral organs, have been described in great detail. However, longstanding questions regarding the importance of communication between cells within the SAM and lateral organs have, until recently, remained unanswered. In this review, we describe recent investigations into the extent, nature and significance of signaling both to and from the SAM.
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Affiliation(s)
- Jim P Fouracre
- Biology Department, University of Pennsylvania, 433 S. University Ave, Philadelphia, PA, 19104, USA
| | - Richard Scott Poethig
- Biology Department, University of Pennsylvania, 433 S. University Ave, Philadelphia, PA, 19104, USA.
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32
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Plewiński P, Ćwiek-Kupczyńska H, Rudy E, Bielski W, Rychel-Bielska S, Stawiński S, Barzyk P, Krajewski P, Naganowska B, Wolko B, Książkiewicz M. Innovative transcriptome-based genotyping highlights environmentally responsive genes for phenology, growth and yield in a non-model grain legume. PLANT, CELL & ENVIRONMENT 2020; 43:2680-2698. [PMID: 32885839 DOI: 10.1111/pce.13880] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/21/2020] [Accepted: 08/22/2020] [Indexed: 06/11/2023]
Abstract
The narrow-leafed lupin, Lupinus angustifolius L., is a grain legume crop, cultivated both as a green manure and as a source of protein for animal feed and human food production. During its domestication process, numerous agronomic traits were improved, however, only two trait-related genes were identified hitherto, both by linkage mapping. Genome-wide association studies (GWAS), exploiting genomic sequencing, did not select any novel candidate gene. In the present study, an innovative method of 3'-end reduced representation transcriptomic profiling, a massive analysis of cDNA ends, has been used for genotyping of 126 L. angustifolius lines surveyed by field phenotyping. Significant genotype × environment interactions were identified for all phenology and yield traits analysed. Principal component analysis of population structure evidenced European domestication bottlenecks, visualized by clustering of breeding materials and cultivars. GWAS provided contribution towards deciphering vernalization pathway in legumes, and, apart from highlighting known domestication loci (Ku/Julius and mol), designated novel candidate genes for L. angustifolius traits. Early phenology was associated with genes from vernalization, cold-responsiveness and phosphatidylinositol signalling pathways whereas high yield with genes controlling photosynthesis performance and abiotic stress (drought or heat) tolerance. PCR-based toolbox was developed and validated to enable tracking desired alleles in marker-assisted selection. Narrow-leafed lupin was genotyped with an innovative method of transcriptome profiling and phenotyped for phenology, growth and yield traits in field. Early phenology was found associated with genes from cold-response, vernalization and phosphatidylinositol signalling pathways, whereas high yield with genes running photosystem II and drought or heat stress response. Key loci were supplied with PCR-based toolbox for marker-assisted selection.
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Affiliation(s)
- Piotr Plewiński
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Hanna Ćwiek-Kupczyńska
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Elżbieta Rudy
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Wojciech Bielski
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Sandra Rychel-Bielska
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Stanisław Stawiński
- Department in Przebędowo, Plant Breeding Smolice Ltd., Murowana Goślina, Poland
| | - Paweł Barzyk
- Department in Wiatrowo, Poznań Plant Breeding Ltd., Wiatrowo, Poland
| | - Paweł Krajewski
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Barbara Naganowska
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Bogdan Wolko
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Michał Książkiewicz
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
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33
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Conklin PA, Johnston R, Conlon BR, Shimizu R, Scanlon MJ. Plant homeodomain proteins provide a mechanism for how leaves grow wide. Development 2020; 147:dev.193623. [PMID: 32994171 PMCID: PMC7595687 DOI: 10.1242/dev.193623] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/13/2020] [Indexed: 01/24/2023]
Abstract
The mechanisms whereby leaf anlagen undergo proliferative growth and expansion to form wide, flat leaves are unclear. The maize gene NARROWSHEATH1 (NS1) is a WUSCHEL-related homeobox3 (WOX3) homolog expressed at the margins of leaf primordia, and is required for mediolateral outgrowth. To investigate the mechanisms of NS1 function, we used chromatin immunoprecipitation and laser-microdissection RNA-seq of leaf primordial margins to identify gene targets bound and modulated by NS1. Microscopic analyses of cell division and gene expression in expanding leaves, and reverse genetic analyses of homologous NS1 target genes in Arabidopsis, reveal that NS1 controls mediolateral outgrowth by repression of a growth inhibitor and promotion of cell division at primordial leaf margins. Intriguingly, homologous WOX gene products are expressed in stem cell-organizing centers and traffic to adjoining cells to activate stem-cell identity non-autonomously. In contrast, WOX3/NS1 does not traffic, and stimulates cell divisions in the same cells in which it is transcribed. Highlighted Article: The NS1 homeodomain transcription factor regulates lateral organ outgrowth from shoot meristems and leaf primordial margins by repressing the expression of negative growth regulators.
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Affiliation(s)
- Phillip A Conklin
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Robyn Johnston
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.,The Elshire Group Limited, Palmerston North 4472, New Zealand
| | - Brianne R Conlon
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Rena Shimizu
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Michael J Scanlon
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
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34
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Cammarata J, Scanlon MJ. A functionally informed evolutionary framework for the study of LRR-RLKs during stem cell maintenance. JOURNAL OF PLANT RESEARCH 2020; 133:331-342. [PMID: 32333315 DOI: 10.1007/s10265-020-01197-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/15/2020] [Indexed: 05/27/2023]
Abstract
Plants maintain populations of stem cells to generate new organs throughout the course of their lives. The pathways that regulate plant stem cell maintenance have garnered great interest over the past decades, as variation in these pathways contributes plant morphological diversity and can be harnessed for crop improvement. In order to facilitate cross-species comparisons of gene function and better understand how these stem cell regulatory pathways evolved, we undertook a functionally informed phylogenetic analysis of leucine-rich receptor-like kinases (LRR-RLK) and related proteins across diverse land plant model systems. Based on our phylogenetic analysis and on functional data, we propose a naming scheme for these stem cell signaling genes. We discovered evidence for frequent loss of protein domains in angiosperms but not in bryophytes. In addition, several clades of stem cell signaling genes are closely related to genes that function in immunity, although these distinct developmental and immune functions likely separated or after the divergence of lycophytes and angiosperms. Overall, the phylogenetic framework and evolutionary hypotheses we provide here will empower future research on cross-species comparisons of stem cell signaling pathways.
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Affiliation(s)
- Joseph Cammarata
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Michael J Scanlon
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, USA.
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