Crop systems biology

The Crop systems biology theme deals with complex phenotypic traits expressed at crop level by using information from “omics”, underlying biochemical and molecular-physiological understanding, and linking that information in a coherent and logical way to yield and quality-determining processes. Crop systems biology also helps to bridge the genotype-phenotype gap and to realize model-based, marker-assisted breeding.

Responsible innovation in the potato sector

Description:

The Dutch start-up company Solynta has developed a diploid potato capable of hybrid breeding which may resolve serious limitations of conventional potato-breeding and allow the rapid development of new potato varieties attuned to specific local or regional needs. However, this innovation will require new seed tuber production and cropping systems, involving a radical socio-technical transition which may have disruptive and controversial impacts on the sector. CSA is involved in a research programme aimed to guide this transition in a societally responsible way by involving relevant stakeholders from the sector, civil society, government and knowledge institutions in a dialogue focusing on various options for valorisation. The main research question of this programme is: How to create optimal conditions for a responsible development of hybrid potato breeding in ways that benefit the productivity, sustainability and diversity of the current potato production system. Historically, the development of hybrid breeding has been part of a comprehensive socio-technical transition of agriculture that can be characterized as the global emergence of agro-industrial production chains. This development has led to a strongly polarized debate about the merits and impacts of industrialized agricultural production. In the context of this debate, the new hybrid breeding technology raises important questions about its implications for the potato production system in the Netherlands and on a global level.

Types of research:

Within this programme there is room for participation of MSc students in field experiments in which different types of material will be evaluated (either in the Netherlands or abroad) but also for participation in analyses of the potato value chain and in analyses of impact of technology development as well as for involvement in research questions regarding responsible innovation.

Location:

The Netherlands or abroad

Contact:

For detailed information on potential thesis subjects contact Paul Struik (paul.struik@wur.nl)

Making cereals more nutritious: zinc translocation and allocation in major cereals

Description:

There is a world-wide effort to enhance micro-nutrient density in staple crops in order to improve the nutritional quality of foodstuffs eaten by the poorer majority of the world population. Zinc is among the target micro-nutrients for this effort. A theme the Centre for Crop Systems Analysis, the Soil Quality Group and Human Nutrition and Epidemiology from Wageningen University all work on, partly in joint research efforts.

Studies carried out within this framework have established methods to grow zinc deprived rice, wheat and cowpea and have shown differences between these species that support the need for more studies of these inter specific differences next to cultivar (intra specific) differences. Recently the interaction between crop nitrogen nutrition and Zn allocation has been shown to be of importance. This might also explain why under enhanced CO2 predicted for 2050 both protein and Zn levels are decreased, showing a looming aggravation of so-called hidden-hunger.

There are a number of major research question for this work.

  • What is the relative role of re-allocation and direct uptake during grain formation as source of zinc in cereal or legume grains in dependency of plant mineral and nitrogen nutrition, genotype and their interactions.
  • Where and how is Zn stored in cereal or legume grains in relation to the role in human nutrition and the role in plants and as a function of plant mineral nutrition, genotype and their interactions.
  • Can we model mineral allocation and re-allocation within plants to provide a tool for a more targeted breeding.
  • Can we use models to link the vast body of subcellular level understanding of transport and sequestration processes to whole plant  crop level and allocation under field conditions.
  • This may vary between purely experimental to purely modelling, to relevant combinations of these.
  • .... you may obviously formulate other research questions a try to convince me about their scientific relevance ....

Location:

Wageningen or in collaboration with partners like IRRI in the Philippines.

Period:

Experiments in Wageningen need to be carried out at decent light levels so between April and September.

Contact:

Tjeerd Jan Stomph (tjeerdjan.stomph@wur.nl)

Root anatomy in response to nutrient stress

Description:

Root anatomical traits have important roles in soil resource capture, especially in environments with suboptimal water and nutrient availability. The maize root system consists of three major root classes: seminal axial (or seed-borne) and nodal axial (shoot-borne) roots which all produce lateral (root-borne) roots of the first and second order. Lateral roots typically constitute the major portion of root systems, accounting for approximately 90% of the total root length.

Phenotypic plasticity is the ability of an organism to alter its phenotype in response to the environment and may involve changes in physiology, anatomy, or development. Plasticity has been observed for a number of root anatomical traits and is important for adaptation to environments with drought or suboptimal nutrient availability. Lateral root growth and behavior has been shown to be plastic in response to the microenvironment that the root is experiencing. Lateral roots can proliferate and even branch further when the roots encounter resources, such as water or nutrients, that a plant needs to grow. However, little is understood about anatomical trait plasticity of lateral roots in response to nutrient stress. The expression of anatomical traits in lateral roots presumably has a direct influence on plant growth and nutrient acquisition and therefore plant performance.

Types of work:

You will conduct a series of experiments in the growth chamber using a set of diverse genotypes. Plants will be grown under various nutrient regimes and lateral root responses to nutrient stress will be assessed. Anatomical phenotypes of lateral roots in different environments will be mapped based on root order and position on the axial root. Projects will involve microscopy, image analysis, and development of a conceptual framework for root adaptation to nutrient stress.

Location:

Wageningen (WUR Crop Systems Analysis)

Contact:

Dr Hannah Schneider (hannah.schneider@wur.nl)

Uncover the genetic architecture of root traits using bioinformatics

Description:

Root traits are important for soil resource capture and plant stress tolerance. A root anatomical trait called Multiseriate Cortical Sclerenchyma (MCS) has recently been shown to have an important role in compaction stress tolerance. It is speculated that this trait is also important for drought, cold temperature, and nutrient stress tolerance. However, little is known about its genetic architecture or association with geographical origin of cultivars.

Recent phenotyping and genotyping efforts have made data available that enables bioinformatic analysis to dissect the genetic architecture of MCS. This will provide insight on the loci and overarching mechanisms contributing to MCS phenotypic variation and provide insights into its adaptive value for a wide range of abiotic stress tolerance.

Types of work:

This study will involve bioinformatics work mining publicly available root phenotypic, genotypic, and tissue-specific expression data to find links between root anatomy, genes, geographical origin of cultivars, and adaptation to abiotic stress. Methods including genome-wide association mapping, co-expression networks, and predicted consequences of minor allele variants will be used.

Location:

Wageningen (WUR Crop Systems Analysis)

Contact:

Dr Hannah Schneider (hannah.schneider@wur.nl)

The effects of climate change extremes on the physiology of potato

Background:

Potato is one of the most important food crops in the world. Climate change will likely have a large impact on potato productivity, quality and production practices. It is therefore essential that the effects of climate change on potato production are researched. The effects of gradual climate change (higher average temperatures and changing annual rainfall) on potato yield and quality have been researched elaborately and can be modelled rather accurately. The effect of climate extremes (e.g. heat waves, excessive and irregular rainfall, extreme droughts), however, is still poorly understood. Therefore, a PhD project with both CSA and PPS aims to investigate the effect of climate extremes on potato. The thesis student will work at CSA.

Research:

We are looking for an enthusiastic MSc student who would like to work on this topic. From May until September there will be a climate chamber experiment with a Dutch potato cultivar. The goal of this experiment is to investigate the effects of climate extremes on the physiology of the potato plant. This will be done through altering certain input variables such as temperature, CO2, light, irrigation and fertilization in the climate chamber. Depending on the research interest and background of the student, the thesis can focus on topics such as:

  • The effect of climate extremes on plant and tuber development
  • The relation between crucial stages of crop development and the timing of climate extremes
  • The effect of heat waves on quality of the potato (e.g. dry matter, secondary growth)
  • The combined effect of CO2 and climate extremes on the photosynthetic response

The thesis will involve practical work in the climate chamber, data collection and data analysis. There will also be room for your own ideas and input!

The student could start from May onwards (depending on preference of the student; e.g. more interest in data analysis then one could start later). In summary: you will be part of practical research, with a focus on climate change and potato physiology. If you are interested or have any questions, don’t hesitate to contact me!

Requirements:

Research Methods in Crop Science (CSA30806), CSA-30306 Advanced Crop Physiology and/or Modelling functional diversity in crop production (CSA32806)

Contact:

Suzanne Brouwer (suzanne.brouwer@wur.nl)

Assessment of physiological age of seed potatoes and the subsequent crop performance

Background

The current potato (Solanum tuberosum L.) production system relies mainly on vegetative propagation through seed tubers. The physiological age (the physiological state of the seed tuber which influences its productive capacity) is crucial for the growth vigour of seed tubers and subsequent crop development and yield. In practice, planting physiologically older seed tubers results in earlier canopy growth with a shorter growing period, and planting younger seed tubers results in slower canopy development with a longer growing period. However, due to its high complexity and variability across years, there is a lack of clarity and adequate information on the physiological age. This hinders producers making a good planning of storage and planting, and contributed to recent problems of poor crop establishment and yield, both in the Netherlands and abroad.

Challenge

To develop a reliable tool to assess physiological age and to predict crop performance

Methods

In this research, we use potato cultivars of contrasting maturity types and different rates of physiological ageing of seed tubers and store them at different temperatures. Specifically, we will exploit plant metabolomics to analyse changes in the metabolite profiles of cultivars in response to storage temperatures, and to look for potential biochemical indicators of physiological age. Data collected will be applied in modelling the development of physiological age during storage accounting for Genotype x Environment interaction. Seed tubers will be planted at multiple experimental field sites. Data collected from field measurements will be combined with sprouting and metabolic data to model the impact of physiological age on crop performance. Models developed during this project will be evaluated and applied in improved decision support systems for crop management and to reduce the yield gap in potato production.

This project offers multiple choices of hands-on and theoretical work for an MSc (BSc) thesis, including:

  • Analysing sprouting dynamics of seed tubers under different storage temperature treatments (winter-spring)
  • Analysing tissue-specific metabolite profiles of seed tubers, and linking the changes to sprouting dynamics
  • Modelling the physiological ageing process of seed tubers
  • Analysing field crop performance of seed tubers at three field locations (summer)
  • Analysing crop performance in relation to sprouting and metabolic dynamics of seed tubers
  • Modelling the impact of physiological age on crop performance
  • Analysing the effect of different seed tuber origins on crop performance

Collaboration

Crop Systems Analysis (CSA) group and Plant Production System (PPS) group, Wageningen University

Required courses in consultation

General: MAT-20306 Advanced statistics

Courses CSA: CSA-30306 Advanced crop physiology; CSA-30806 Research methods in Crop Science

Courses PPS: PPS-30306 Quantitative Analysis of Land Use Systems (QUALUS); PPS-30806 Analysing Sustainability of Farming Systems

Location

Wageningen Unifarm; Multiple field locations in The Netherlands

Duration

01/01/2021 - 31/10/2023

Contact of supervisors

Chunmei Zou (chunmei.zou@wur.nl), Prof. Dr. Paul Struik (paul.struik@wur.nl), Dr. Ir. Willemien Lommen (willemien.lommen@wur.nl), Prof. Dr. Martin van Ittersum (PPS, martin.vanittersum@wur.nl)

Effects of seedling size on yield and yield components of transplanted hybrid potato seedlings

Background:

Hybrid breeding in potato is a relatively novel and very promising technology, through which new potato cultivars can be developed and propagated much more rapidly than through conventional breeding.  Hybrid ware crops can be established in the field through different pathways such as field transplanting of nursery generated seedlings, direct sowing and use of seedling tubers.  Field transplanting of hybrid potato seedlings involves production of seedlings in a greenhouse nursery and transplanting into the field. Various factors affect seedling establishment and ultimately potato yield of transplanted potato. Among these factors, the contribution of seedling size to yield and yield components has not been quantified. Moreover, the optimal seedling size for field transplanting has not been determined. As part of a PhD project on the development of a resilient cropping system for field transplanted hybrid potato, a study will be conducted to assess the effects of seedling size on growth and development as well as yield of hybrid potato.

Objectives:

  • To assess the impact of transplant seedling size on tuber yield and tuber size distribution

    • Using intermediate and final harvests
    • To describe the effects of seedling size on yield components

      • Plant biomass
      • Ground cover
    • To define the optimal seedling size for field transplanting through:

      • Analysis of seedling performance under field conditions through observations of growth and development
      • Using greenhouse climate data such as temperature, radiation, days after sowing, growth stages, etc.

The project work will mainly involve managing trials, lab work (processing plant biomass during harvests), data collection and analysis. The field work will start mid-May 2021and end around September, 2021. We are therefore looking for enthusiastic Plant Science students (or students from other related studies programmes) to support our research through an MSc thesis during the trial period. Our ideal candidate is one who is keen on conducting field trials on agronomy research and has experience in field work and knowledge in data collection and analysis.

Contact:

If you are interested, please get in touch with Olivia Kacheyo (olivia.kacheyo@wur.nl).

Influence of seedling size on factors affecting (mitigating) transplant shock

Background:

Hybrid breeding in potato is a relatively novel and very promising technology, through which new potato cultivars can be developed and propagated much more rapidly than in conventional  breeding.  Hybrid ware crops can be established in the field through different pathways such as field transplanting of nursery generated seedlings, direct sowing and use of seedling tubers. Field transplanting of hybrid potato seedlings involves production of seedlings in a greenhouse nursery and transplanting into the field. Seedlings however face a transplanting shock during their acclimatisation period in the field. Little is known on the factors contributing to the transplanting shock in hybrid potato and what can be done to reduce the shock. As part of a PhD project on the development of a resilient cropping system for field transplanted hybrid potato, a study will be conducted to understand the transplant shock and the factors that contribute to the shock. Hybrid potato seedlings will be observed under both greenhouse and field conditions.

Objectives:

  • To define the effects of seedling development stage on seedling establishment and the duration of transplant shock period under field conditions
  • To define the optimal seedling size for field transplanting through observation of seedling growth and development under nursery conditions and performance under field conditions
  • To define effects of seedling treatments on seedling establishment
  • To define length of transplant shock period for seedling treatments based on data collected

The project work will mainly involve managing trials, lab work (processing plant biomass during harvests), data collection and analysis. The greenhouse work will start mid-March 2021 and will be followed by  field work from mid-May to June/July 2021. We are therefore looking for enthusiastic Plant Science students (or students from other related studies programmes) to support our research through a BSc or MSc thesis during the period. Our ideal candidate is one who is keen on conducting field trials on agronomy research and has experience in field work and knowledge in data collection and analysis.

Contact:

If you are interested, please get in touch with Olivia Kacheyo (olivia.kacheyo@wur.nl).

The influence of crop management practices and seedling “treatments” on yield and yield components of hybrid potato

Description:

Hybrid breeding in potato is a relatively novel and very promising technology, through which new potato cultivars can be developed and propagated much more rapidly.  Hybrid ware can be established in the field through different pathways such as field transplanting of nursery generated seedlings, direct sowing and use of seedling tubers.  Field transplanting of hybrid potato seedlings involves production of seedlings in a greenhouse nursery and transplanting into the field. The establishment and  development of a hybrid ware crop from field transplanted seedlings is influenced by various factors including transplanting shock and crop management practices.

As part of the PhD project to develop a resilient cropping system for field transplanted hybrid potato, studies will be conducted on the influence of various seedling sizes as well as other seedling conditions on seedling establishment and their influence on transplant shock. Additionally, we will define the influence of crop management factors on yield and yield components of field transplanted hybrid potato. The crop management factors include, but are not limited to, fertiliser application and management, tillage practices as well as weeding.

The project work will mainly involve managing of field trials, lab work (processing plant biomass during destructive harvests), data collection and analysis. The work will start from May 2021 till the end of the project in 2024 and various topics on transplant growth and development as well as transplant crop management will be explored. We are therefore looking for enthusiastic Plant Sciences students (or students from other related studies programmes) to support our research through an MSc thesis during the trial period. Our ideal candidate is one who is keen on conducting field trials on agronomy research and has experience in field work and knowledge in data collection and analysis.

Contact:

If you are interested, please get in touch with Olivia Kacheyo (olivia.kacheyo@wur.nl).

Lateral root length accumulation in monocot and dicot species

Description:

Fibrous root systems (formed by monocots) and tap root systems (formed by dicots) are distinct in many aspects. However, both types of root systems produce lateral roots. Recently, it has been demonstrated that lateral roots significantly influence water and nutrient capture, and in many environments capture the majority of water and nutrients acquired by the plant. Lateral roots do not take up more nutrients and water per root length, but their proportionally greater root length when compared to axial roots translates into greater capture of soil resources.

It is known that lateral roots generally comprise the majority of the total root length. However, it is unknown how the proportional length of lateral roots to axial roots changes throughout plant development and between species. Presumably, the ratio of axial to lateral root length is dynamic in response to plant maturity and the development of axial (shoot-borne) roots at different developmental stages. This project will characterize root length in terms of the proportion of axial and lateral roots in several different dicot and monocot plant species from germination to 8 weeks of growth.

Types of work:

You will conduct a series of experiments in the growth chamber using several different plant species. Projects will involve measuring root morphology, image analysis, and development of a conceptual framework for root length accumulation in different root classes across species.

Location:

Wageningen (WUR Crop Systems Analysis)

Contact:

Dr. Hannah Schneider, Centre for Crop Systems Analysis-CSA, hannah.schneider@wur.nl

Spatial and temporal responses of root traits to soil compaction stress

Description:

Root traits have important roles in the capture of nutrients and water, particularly in environments where root growth is impeded due to compacted soils. Several root traits have been identified that enable roots to penetrate compacted, hard soils to explore greater volumes of soil and therefore acquire more nutrients and water and improve plant growth.

In response to abiotic stress, some root traits are plastic and alter their phenotype in response to environmental conditions. The expression of plasticity in several root traits may be an adaptive response  to stress if it is beneficial for the capture of soil resources. However, little is known about the spatial and temporal plastic response of anatomical and architectural root traits to compaction stress.  

This project will explore the phenotypic plasticity of roots to compaction stress, particularly spatial and temporal responses of root traits to compacted soil layers. You will characterize root anatomical and architectural responses to compaction including changes in phenotypic expression of specific root traits and the duration of these changes along the growing root as the root grows through layers of compacted and non-compacted soils. The expression of root traits presumably has a direct influence on plant growth and nutrient acquisition and therefore plant performance in compacted soils. Understanding spatial and temporal root phenotypic responses to compacted soils is an important step in understanding root plasticity and improving root traits for more productive crops.

Types of work:

You will conduct a series of experiments in the growth chamber using a set of diverse genotypes. Plants will be grown under various compaction regimes (i.e. varying bulk density and the depth and number of compacted layers) and root responses will be assessed. Projects will involve microscopy, image analysis, and development of a conceptual framework for root adaptation to compaction stress.

Location:

Wageningen (WUR Crop Systems Analysis)

Contact:

Dr. Hannah Schneider, Centre for Crop Systems Analysis-CSA, hannah.schneider@wur.nl

The potential of pest and disease suppression in an intercrop system

Description:

Pesticides and fungicides are often the farmer’s main means of crop protection. However, with more restriction being put in place on the use of these products, and the development of fungicide-resistance among pathogens, alternative protection measures need to be explored. Intercropping has many benefits, among one is the potential to reduce pests and diseases, and could thus be a alternative disease management practice. This MSc thesis project will focus on the potential of a potato-based intercrop system for pest and/or disease suppression. We will explore how intercropping affects different stages of the epidemiology, and which mechanisms play a role in disease suppression. Students can participate in a planned field experiment to monitor various aspects of pest and/or disease in potato.

In this project you will explore the potential of intercropping potato for pest/disease control. The current aim of the project is to focus on Phytophthora infestans, but we are open to include other diseases or pests (e.g. Colorado potato beetle, aphids, Alternaria), depending on your interest. Different aspects of the disease can be measured, for example incoming spores, disease progress or disease severity. Aspect of the canopy with reference to disease can be measured, such as microclimate, or the morphological or physiological characteristics of the potato plants.

Starting date:

April/May 2021

Contact:

If you have questions do not hesitate to contact us: Zohralyn Homulle (zohralyn.homulle@wur.nl) and/or Bob Douma (bob.douma@wur.nl, 0317-482140).