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2. Predicting yield of individual field-grown rapeseed plants from rosette-stage leaf gene expression.

Author

De Meyer, Sam, Cruz, Daniel Felipe, De Swaef, Tom, Lootens, Peter, De Block, Jolien, Bird, Kevin, Sprenger, Heike, Van de Voorde, Michael, Hawinkel, Stijn, Van Hautegem, Tom, Inzé, Dirk, Nelissen, Hilde, Roldán-Ruiz, Isabel, and Maere, Steven

Subjects
Brassica napus, Plant Leaves, Gene Expression, Phenotype, Genetics, Mathematical Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Abstract

In the plant sciences, results of laboratory studies often do not translate well to the field. To help close this lab-field gap, we developed a strategy for studying the wiring of plant traits directly in the field, based on molecular profiling and phenotyping of individual plants. Here, we use this single-plant omics strategy on winter-type Brassica napus (rapeseed). We investigate to what extent early and late phenotypes of field-grown rapeseed plants can be predicted from their autumnal leaf gene expression, and find that autumnal leaf gene expression not only has substantial predictive power for autumnal leaf phenotypes but also for final yield phenotypes in spring. Many of the top predictor genes are linked to developmental processes known to occur in autumn in winter-type B. napus accessions, such as the juvenile-to-adult and vegetative-to-reproductive phase transitions, indicating that the yield potential of winter-type B. napus is influenced by autumnal development. Our results show that single-plant omics can be used to identify genes and processes influencing crop yield in the field.

Published
2023

6. Analysis of Plant Stress Response Using Hyperspectral Imaging and Kernel Ridge Regression

Author

Asaari, Mohd Shahrimie Mohd, Mertens, Stien, Dhondt, Stijn, Inzé, Dirk, Scheunders, Paul, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Rüdiger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Hirche, Sandra, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Li, Yong, Series Editor, Liang, Qilian, Series Editor, Martín, Ferran, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Möller, Sebastian, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Speidel, Joachim, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zamboni, Walter, Series Editor, Zhang, Junjie James, Series Editor, Mahyuddin, Nor Muzlifah, editor, Mat Noor, Nor Rizuan, editor, and Mat Sakim, Harsa Amylia, editor

Published
2022
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10. Maize mutant screens: from classical methods to new CRISPR‐based approaches.

Author

Lorenzo, Christian Damian, Blasco‐Escámez, David, Beauchet, Arthur, Wytynck, Pieter, Sanches, Matilde, Garcia del Campo, Jose Rodrigo, Inzé, Dirk, and Nelissen, Hilde

Subjects
CRISPRS, REVERSE genetics, GENETIC models, GENOME editing, TRANSPOSONS, CORN
Abstract

Summary: Mutations play a pivotal role in shaping the trajectory and outcomes of a species evolution and domestication. Maize (Zea mays) has been a major staple crop and model for genetic research for more than 100 yr. With the arrival of site‐directed mutagenesis and genome editing (GE) driven by the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), maize mutational research is once again in the spotlight. If we combine the powerful physiological and genetic characteristics of maize with the already available and ever increasing toolbox of CRISPR‐Cas, prospects for its future trait engineering are very promising. This review aimed to give an overview of the progression and learnings of maize screening studies analyzing forward genetics, natural variation and reverse genetics to focus on recent GE approaches. We will highlight how each strategy and resource has contributed to our understanding of maize natural and induced trait variability and how this information could be used to design the next generation of mutational screenings. [ABSTRACT FROM AUTHOR]

Published
2024
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18. The transcriptional repressor complex FRS7-FRS12 regulates flowering time and growth in Arabidopsis

Author

Ritter, Andrés, Iñigo, Sabrina, Fernández-Calvo, Patricia, Heyndrickx, Ken S, Dhondt, Stijn, Shi, Hua, De Milde, Liesbeth, Vanden Bossche, Robin, De Clercq, Rebecca, Eeckhout, Dominique, Ron, Mily, Somers, David E, Inzé, Dirk, Gevaert, Kris, De Jaeger, Geert, Vandepoele, Klaas, Pauwels, Laurens, and Goossens, Alain

Subjects
Plant Biology, Biochemistry and Cell Biology, Biological Sciences, Genetics, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Aldehyde Oxidoreductases, Arabidopsis, Arabidopsis Proteins, Base Sequence, Basic Helix-Loop-Helix Transcription Factors, Circadian Rhythm, Flowers, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Hypocotyl, Isoenzymes, Light, Photoperiod, Signal Transduction, Transcription, Genetic
Abstract

Most living organisms developed systems to efficiently time environmental changes. The plant-clock acts in coordination with external signals to generate output responses determining seasonal growth and flowering time. Here, we show that two Arabidopsis thaliana transcription factors, FAR1 RELATED SEQUENCE 7 (FRS7) and FRS12, act as negative regulators of these processes. These proteins accumulate particularly in short-day conditions and interact to form a complex. Loss-of-function of FRS7 and FRS12 results in early flowering plants with overly elongated hypocotyls mainly in short days. We demonstrate by molecular analysis that FRS7 and FRS12 affect these developmental processes in part by binding to the promoters and repressing the expression of GIGANTEA and PHYTOCHROME INTERACTING FACTOR 4 as well as several of their downstream signalling targets. Our data reveal a molecular machinery that controls the photoperiodic regulation of flowering and growth and offer insight into how plants adapt to seasonal changes.

Published
2017

19. ETHYLENE RESPONSE FACTOR6, A Central Regulator of Plant Growth in Response to Stress.

Author

Li, Ting, Peng, Zhen, Kangxi, Du, Inzé, Dirk, and Dubois, Marieke

Abstract

ETHYLENE RESPONSE FACTOR6 (ERF6) has emerged as a central player in stress‐induced plant growth inhibition. It orchestrates complex pathways that enable plants to acclimate and thrive in challenging environments. In response to various abiotic and biotic stresses, ERF6 is promptly activated through both ethylene‐dependent and ‐independent pathways, and contributes to enhanced stress tolerance mechanisms by activating a broad spectrum of genes at various developmental stages. Despite the crucial role of ERF6, there is currently a lack of published comprehensive insights into its function in plant growth and stress response. In this respect, based on the tight connection between ethylene and ERF6, we review the latest research findings on how ethylene regulates stress responses and the mechanisms involved. In addition, we summarize the trends and advances in ERF6‐mediated plant performance under optimal and stressful conditions. Finally, we also highlight key questions and suggest potential paths to unravel the ERF6 regulon in future research. Summary statement: The ETHYLENE RESPONSE FACTOR 6 (ERF6) is a central regulator of plant growth and stress response in Arabidopsis thaliana. In this work, we review the recent advances in our common understanding of the role of ethylene in growth and stress responses, and the contribution of ERF6 therein. [ABSTRACT FROM AUTHOR]

Published
2025
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24. Corrigendum: Proximal hyperspectral imaging detects diurnal and drought-induced changes in maize physiology

Author

Mertens, Stien, primary, Verbraeken, Lennart, additional, Sprenger, Heike, additional, Demuynck, Kirin, additional, Maleux, Katrien, additional, Cannoot, Bernard, additional, De Block, Jolien, additional, Maere, Steven, additional, Nelissen, Hilde, additional, Bonaventure, Gustavo, additional, Crafts-Brandner, Steven J., additional, Vogel, Jonathan T., additional, Bruce, Wesley, additional, Inzé, Dirk, additional, and Wuyts, Nathalie, additional

Published
2024
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26. RALFL34 regulates formative cell divisions in Arabidopsis pericycle during lateral root initiation

Author

Murphy, Evan, Vu, Lam Dai, Van den Broeck, Lisa, Lin, Zhefeng, Ramakrishna, Priya, van de Cotte, Brigitte, Gaudinier, Allison, Goh, Tatsuaki, Slane, Daniel, Beeckman, Tom, Inzé, Dirk, Brady, Siobhan M, Fukaki, Hidehiro, and De Smet, Ive

Subjects
Biochemistry and Cell Biology, Biological Sciences, Arabidopsis, Arabidopsis Proteins, Cell Division, Gene Expression Regulation, Plant, Peptide Hormones, Plant Roots, Transcription Factors, Arabidopsis thaliana, ERF, GATA23, lateral root initiation, RAPID ALKALINIZATION FACTOR, RAPID ALKALINIZATION FACTOR (RALF)., Genetics, Plant Biology, Crop and Pasture Production, Plant Biology & Botany, Crop and pasture production, Biochemistry and cell biology, Plant biology
Abstract

In plants, many signalling molecules, such as phytohormones, miRNAs, transcription factors, and small signalling peptides, drive growth and development. However, very few small signalling peptides have been shown to be necessary for lateral root development. Here, we describe the role of the peptide RALFL34 during early events in lateral root development, and demonstrate its specific importance in orchestrating formative cell divisions in the pericycle. Our results further suggest that this small signalling peptide acts on the transcriptional cascade leading to a new lateral root upstream of GATA23, an important player in lateral root formation. In addition, we describe a role for ETHYLENE RESPONSE FACTORs (ERFs) in regulating RALFL34 expression. Taken together, we put forward RALFL34 as a new, important player in lateral root initiation.

Published
2016

28. Histone 2B monoubiquitination complex integrates transcript elongation with RNA processing at circadian clock and flowering regulators

Author

Woloszynska, Magdalena, Le Gall, Sabine, Neyt, Pia, Boccardi, Tommaso M., Grasser, Marion, Längst, Gernot, Aesaert, Stijn, Coussens, Griet, Dhondt, Stijn, Van De Slijke, Eveline, Bruno, Leonardo, Fung-Uceda, Jorge, Mas, Paloma, Van Montagu, Marc, Inzé, Dirk, Himanen, Kristiina, De Jaeger, Geert, Grasser, Klaus D., and Van Lijsebettens, Mieke

Published
2019

34. GS yellow , a Multifaceted Tag for Functional Protein Analysis in Monocot and Dicot Plants

Author

Besbrugge, Nienke, Van Leene, Jelle, Eeckhout, Dominique, Cannoot, Bernard, Kulkarni, Shubhada R., De Winne, Nancy, Persiau, Geert, Van De Slijke, Eveline, Bontinck, Michiel, Aesaert, Stijn, Impens, Francis, Gevaert, Kris, Van Damme, Daniel, Van Lijsebettens, Mieke, Inzé, Dirk, Vandepoele, Klaas, Nelissen, Hilde, and De Jaegera, Geert

Published
2018

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