Systems Biology of Yield

The global demand for plant-derived products, such as feed and food, is increasing dramatically. It is hard to fathom, but in the coming decades two billion additional people will have to be fed while less arable land is available. Furthermore, crop productivity will be hampered by climate change. Drought in particular is expected to have major consequences for crop yield. Plants also have an important role in supplying a sustainable, CO2-neutral source for the ever-increasing energy needs. There is an obvious and urgent need to further increase crop productivity. As yield is the most important trait for breeding, a considerable amount of (eco)physiological research has been conducted on yield performance of crops. In contrast, knowledge on the molecular networks underpinning crop yield and plant organ size remains fragmented; partly because of its multifactorial nature in which many physiological processes, such as photosynthesis, water and mineral uptake and stress tolerance, determine the resources available to produce new cells, tissues and organs. Albeit plant growth and stress tolerance are obviously high-complex processes, novel approaches collectively called "systems biology" allows for a better understanding of this complexity. It is our ambition to decipher the molecular networks underpinning yield and organ growth, both under standard as well as mild drought stress conditions, in Arabidopsis and the C4 crop maize. Systems biology will ultimately provide a holistic view enabling the optimization of plant productivity, either by advanced plant breeding or genetic engineering.Our research involves a detailed analysis of genes and networks underlying organ growth of Arabidopsis and maize as well as a functional analysis of perturbation of these genes. Genes that are providing maize plants with enhanced growth characteristics are tested in field trials, both in Belgium and in the US. The yield lab has numerous academic collaborations across the world.

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Organ Size Regulation 

Molecular systems governing leaf growth: from genes to networks

Size control of multicellular organisms poses a longstanding biological question that has always fascinated scientists. Currently, the question is far from being resolved because of the complexity of and interconnection between cell division and cell expansion, two different events necessary to form a mature organ. Given the importance of plants for food and renewable energy sources, dissecting the genetic networks underlying plant growth and organ size is becoming a high priority in plant science worldwide. Our long term goal is therefore to unravel the molecular pathways that govern leaf size by using Arabidopsis and maize as a model plants.

To extend our knowledge of the genetic networks controlling leaf size, we aim at answering the following questions: What changes in growth phenotype can we observed? When during development are the changes occurring and which are the cellular processes that are affected? How do changes in molecular mechanisms drive these phenotypic changes? 
We therefore combine physiological (growth analysis on mutants or natural variants) and molecular analyses (e.g. transcript and metabolite profiling, protein-protein interactions, multiplex genome editing, single cell approaches) to study the mode of action of growth promoting genes and identify new potential growth regulators. We have, in the past, identified and studied several growth promoting genes and we are now further investigating their function as well as their targets and/or interacting proteins to expand the growth regulatory network. Whereas much research is done on single genes affecting leaf size, we study the connections existing between the different molecular players of the various processes driving leaf growth to build a more integrated growth regulatory network. To enhance the effectiveness of finding complex gene combinations that affect maize growth, the advanced ERC of Dirk Inzé aims to combine ‘classical’ breeding with multiplex genome editing of yield related genes, explaining the acronym, BREEDIT, a word fusion of breeding and editing.
As our understanding of the leaf growth processes in Arabidopsis and maize expands, it becomes increasingly clear that the regulation of the growth processes is to a great extent conserved between dicots and monocots. This comparison between the two major classes of flowering plants allows for the identification of specific and conserved growth regulatory mechanisms of which the potential to improve yield in a varieties of crops can be assessed. Besides an interest in how the growth processes compare between plant species, we are also fascinated by how the growth processes are coordinated in other plant organs that also contribute to plant yield, such as internodes and ears. We bring our research from the greenhouse to the field, to understand how we can translate the knowledge to agricultural applications.
Our final aim is to be able to model regulatory networks to understand organ growth and to evaluate their potential towards crop yield improvement.

Drought Tolerance

Systems biology of drought tolerance in Arabidopsis and maize

With the rapidly growing world population and the increasing demand for food, the importance to stabilize plant yield even under adverse environmental conditions is evident.
One of the most destructive factors for worldwide agriculture is drought stress. As illustrated in Europe by the drought period of summer of 2018, drought stress in moderate climates becomes more severe and has a clear negative impact on plant growth and yield. Even when the water availability is only slightly decreased, mechanisms are rapidly induced to repress plant growth. Understanding the drought-induced growth inhibition at molecular level forms a first major step towards future engineering of plants with reduced yield penalties under drought. We examine distinct aspects of drought stress ranging from the early signalling upon drought perception, adaptive growth responses as well as molecular and cellular adjustments upon re-watering. We routinely test  lines for growth enhancement under drought conditions and assess the drought tolerance of modulation of genes identified in the drought transcriptomic studies.

To facilitate the different watering regimes required for drought studies and to increase the resolution and sensitivity of phenotyping, we invested in the development of automated watering and imaging plant phenotyping platforms. The phenotyping platforms are tailored depending on the research question and the species. For Arabidopsis and maize seedlings, we use the Weighing, Imaging and Watering Machine (WIWAM) to establish an appropriate setup enabling the capture of early drought responses in actively growing leaves, by tracking leaf growth over time and measuring expression changes with a high time-resolution. Growth and transcriptional responses to in soil drought are extremely complex, with the time of day as a crucial factor influencing the extent, the specificity and sometimes also the direction of the expression changes.  

The PHENOVISION platform was developed to monitor the drought responses throughout maize development. Three camera systems are available on the PHENOVISION platforms. The first one consists of RGB cameras in a multi-view imaging setup for the three-dimensional reconstruction of plants and the measurement of growth-related phenotypic traits. Plant physiology-related traits are measured or approximated by exploring a larger stretch of the electromagnetic spectrum. A thermal infrared camera captures energy emitted at 8-13 µm and the corresponding contextual plant and leaf temperature is used as a proxy for plant water use behaviour. A state-of-the-art hyperspectral imaging system, consisting of a visible to near-infrared camera (VNIR, 400-1000 nm) and a short-wave infrared camera (SWIR, 1000-2500 nm), constitutes a novel tool for close-range sensing of plant physiological traits based on reflectance spectra captured on whole-plant and individual leaf level. The irrigation stations offer the possibility to apply water and up to three different solutions so that distinct soil water or nutrient deficit conditions can be imposed throughout the development of the plants.
Our final aim is to be able to understand the molecular re-wiring upon drought perception and to develop crops with increased yield stability in a changing climate.

Collaborations

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Collaborator Topic Institute
Gerrit Beemmster Modeling University Antwerp Belgium
Enrico Pè Maize Genetics Scuola Superiore Sant'Anna Pisa, Italy
Isabel Roldan-Ruiz Biomass ILVO Belgium
Vasileios Fotopoulos Stress Tolerance Cyprus University of Technology Cyprus
Adriana S. Hemerly The Anaphase-Promoting compex Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Brazil
Michael Muszynski Maize Leaf Development University of Hawa ii at Monoa, Tropical plant ans soil sciences USA
Paul Verslues Drought Academica Sinica Taiwan
Felix Fritschi Field trails University of Missouri USA
Nelson Saibo C4 metabolism Institute if Chemical and Biological Technology (ITQB) Portugal
Jianbing Yan maize GWAS Huazhong Agricultural University China
Mike Bevan Modeling University Antwerp Belgium
Yunhai Li DA1 pathway State Key Laboratory of Plants Cell and Chromosome Engineering China
Clinton Whipple Maize inflorescence

The yield lab also actively participates in the European Infrastructure for Plant Phenotyping (EMPHASIS), European Plant Phenotyping Network (EPPN2020), Belgian Plant Phenotyping Network (BPPN) and the European Consortium for Open Field Experimentation (ECOFE). ECOFE joins existing field stations across Europe with the aim to further develop them in a coordinated and highly standardized way. This will provide European scientists with the unique opportunity to systematically tackle fundamental problems like the mitigation of climate change effects and the biological limits to crop productivity across a wide range of environments, stretching from Scandinavia to the Mediterranean, and from Ireland to the eastern border of the EU.