Student projects
Students interested to join my research team are welcome. Have a look at the student projects below or contact me by mail to discuss your topic of interest.
Distribution and variation of downy mildew resistance genes
in natural populations of wild lettuce
Lettuce downy mildew is one of the most serious diseases of lettuce (Lactuca sativa). It is caused by the oomycete Bremia lactucae, a pathogen notorious for its capability to rapidly overcome host resistance.
As a result most lettuce cultivars lack nowadays adequate resistance to new Bremia races. Natural populations of related Lactuca species are regarded as important sources of novel genetic resistance.
This project aims to evaluated Bremia resistance in wild Lactuca populations from Central Asia, which are currently underrepresented in gene bank centres, by combining phenotypic and genotypic analyses.
You will:
- analyse biogeographical distribution and population structures of wild lettuce species.
- explore natural variation in disease resistance with pathogen assays.
- determine frequency and genetic variation in resistance genes across wild lettuce populations.
- perform phylogenetic and population genetic studies.
Skill development: DNA barcoding, Gene variant analysis, Population genetics, Plant phenotyping, Pathogens assays
Requirements: Basic knowledge of plant-microbe interactions and molecular biology
Similarities between plant immunity and self-incompatibility
Self-incompatibility (SI) is a genetic mechanism in plants to prevent inbreeding and to promote outcrossing.
In the mustard family (Brassicaceae), SI is determined by two recognition determinants;
the pistil receptor-like kinase SRK and the pollen ligand SCR. Self-pollen recognition via SRK induces a response that resembles an immune reaction. Brassicaceae contain besides SRK, multiple homologous RLKs of unknown function. Many of these are expressed during diverse plant-biotic interactions, suggesting key roles in plant defense. Here, we hypothesise that SRK evolved from a defense gene, and underwent neofunctionalization.
You will:
- investigate natural sequence variation of SRK and related genes in cabbage crops and wild relatives.
- perform phylogenetic analyses to study gene relationships.
- quantify expression of SRK and related RLK genes during biotic interactions.
- characterize mutant plants with pathogens to detect changes in disease susceptibility.
Skill development: Comparative genomics, Functional characterization, Disease assays with plant pathogens
Requirements: Basic knowledge of bioinformatics, molecular biology and evolutionary biology
Dissecting Xanthomonas black rot resistance in cabbage
Black rot, caused by the bacterium Xanthomonas campestris campestris (Xcc), is one of the most destructive diseases of cabbage. Currently grown cultivars do not provide adequate resistance, and no resistance genes have been cloned so far. This project aims to unravel novel defense mechanisms during early bacterial attack.
You will:
- explore natural variation in black rot resistance using bio-panels of cabbage (Brassica spp.) and diverse wild relatives.
- quantify expression of candidate genes in differential Xcc-Brassica interactions.
- characterize candidate genes for resistance against black rot.
- set-up new methods for gene-silencing in Brassica, and test mutants with Xcc to detect changes in disease susceptibility.
Skill development: Molecular biology techniques (DNA/RNA isolation, cloning, qPCR), Plant phenotyping, Pathogens assays
Requirements: Basic knowledge of plant-microbe interactions and molecular biology
Evolutionary dynamics of plant resistance genes
Plant receptor genes (RLK/Ps) underwent a dramatic expansion in comparison to many other gene families, indicating their importance for plant immunity to diverse pathogens. Gene duplication via polyploidy and small-scale local duplication events is a major evolutionary force driving gene expansion and variability. This project aims to identify the genetic diversity among RLK/Ps in plants via comparative evolutionary genomics.
You will:
- determine natural sequence variation of RLK/Ps in genomes of crops and wild relatives.
- investigate gene presence/absence variations (PAVs), copy number variations (CNVs)
- determine distribution of single nucleotide polymorphisms (SNPs) in gene sequences.
- assess the evolution of RLK/Ps in plants via phylogenetic and synteny analysis across genomes.
Skill development: Bioinformatics, Phylogenetic analyses, Comparative genomics
Requirements: Affinity and experience with bioinformatics and molecular evolution
Ecotypic variability in Lamb’s lettuce populations (Valerianella spp. L)
Lamb’s lettuce (Valerianella locusta; veldsla) is a leafy vegetable that is often used in mixed salads.
It belongs to the family Caprifoliaceae and is thus not, as suggested by its name, related to lettuce
(Lactuca sativa, Asteraceae). Cultivars of Lamb’s lettuce are supposed to have narrow genetic diversity, largely because breeding programs have much relied on identical germplasm collections.
This narrow genetic diversity limits the potential to cope with environmental changes, including bacterial blight - an emerging disease caused by the bacterium Acidovorax valerianellae. Safeguarding germplasm of natural populations of Lamb’s lettuce and closely related wild relatives will benefit breeding of more future-proof cultivars. This project aims to explore genetic and ecotypic variability in Valerianella, both in cultivars and wild relatives.
You will:
- collect seeds of wild Valerianella species in The Netherlands.
- characterize morphologic differences across cultivars and wild ecotypes.
- assess genetic variation by SCoT marker genotyping in Valerianella, incl. cultivars and ecotypes.
- develop pathogen assays to characterize natural variation in blight resistance.
- analyse phenotypic and population genetic data.
Skill development: DNA barcoding, Gene variant analysis, Population genetics, Plant phenotyping, Pathogens assays
Requirements: Basic knowledge of plant-microbe interactions and molecular biology
Are grasses with low genetic diversity more susceptible to infection by fungal pathogens?
Pathogenic fungi are of great economic importance as they cause serious losses in the production of grasses, such as cereal crops and turf-grasses. To prevent these losses, fungicides are applied. The diversity-disease hypothesis (Elton 1958) suggests that greater plant diversity results in a lower severity of plant diseases.
The severity of pathogens in a population may depend not only on the diversity of co-occurring species, but also on the degree of genotypic variation within species. Grass species in natural systems are often found in near monocultures, which can be the effect of intraspecific variation in which individual plants cope in diverse ways with pathogen attack. To test this hypothesis and gain mechanistic understanding on the interaction between intraspecific genetic diversity and plant pathogens we want (1) to analyse within-species genetic variation of grass species in monoculture and polyculture and (2) test if the degree of genetic variation is related to the disease incidence.
You will:
- perform fieldwork in monoculture and polyculture grasslands
- monitor grass-pathogen interactions
- genotype genetic diversity of grasses
- explore population dynamics
Skill development: Genotyping grass species, Identification of grasses and pathogenic fungi (Puccinia)
Requirements: Basic knowledge of plant-microbe interactions
Student projects
Students interested to join my research team are welcome. Have a look at the student projects below or contact me by mail to discuss your topic of interest.
Distribution and variation of downy mildew resistance genes
in natural populations of wild lettuce
Lettuce downy mildew is one of the most serious diseases of lettuce (Lactuca sativa). It is caused by the oomycete Bremia lactucae, a pathogen notorious for its capability to rapidly overcome host resistance.
As a result most lettuce cultivars lack nowadays adequate resistance to new Bremia races. Natural populations of related Lactuca species are regarded as important sources of novel genetic resistance.
This project aims to evaluated Bremia resistance in wild Lactuca populations from Central Asia, which are currently underrepresented in gene bank centres, by combining phenotypic and genotypic analyses.
You will:
- analyse biogeographical distribution and population structures of wild lettuce species.
- explore natural variation in disease resistance with pathogen assays.
- determine frequency and genetic variation in resistance genes across wild lettuce populations.
- perform phylogenetic and population genetic studies.
Skill development: DNA barcoding, Gene variant analysis, Population genetics, Plant phenotyping, Pathogens assays
Requirements: Basic knowledge of plant-microbe interactions and molecular biology
Similarities between plant immunity and self-incompatibility
Self-incompatibility (SI) is a genetic mechanism in plants to prevent inbreeding and to promote outcrossing.
In the mustard family (Brassicaceae), SI is determined by two recognition determinants;
the pistil receptor-like kinase SRK and the pollen ligand SCR. Self-pollen recognition via SRK induces a response that resembles an immune reaction. Brassicaceae contain besides SRK, multiple homologous RLKs of unknown function. Many of these are expressed during diverse plant-biotic interactions, suggesting key roles in plant defense. Here, we hypothesise that SRK evolved from a defense gene, and underwent neofunctionalization.
You will:
- investigate natural sequence variation of SRK and related genes in cabbage crops and wild relatives.
- perform phylogenetic analyses to study gene relationships.
- quantify expression of SRK and related RLK genes during biotic interactions.
- characterize mutant plants with pathogens to detect changes in disease susceptibility.
Skill development: Comparative genomics, Functional characterization, Disease assays with plant pathogens
Requirements: Basic knowledge of bioinformatics, molecular biology and evolutionary biology
Dissecting Xanthomonas black rot resistance in cabbage
Black rot, caused by the bacterium Xanthomonas campestris campestris (Xcc), is one of the most destructive diseases of cabbage. Currently grown cultivars do not provide adequate resistance, and no resistance genes have been cloned so far. This project aims to unravel novel defense mechanisms during early bacterial attack.
You will:
- explore natural variation in black rot resistance using bio-panels of cabbage (Brassica spp.) and diverse wild relatives.
- quantify expression of candidate genes in differential Xcc-Brassica interactions.
- characterize candidate genes for resistance against black rot.
- set-up new methods for gene-silencing in Brassica, and test mutants with Xcc to detect changes in disease susceptibility.
Skill development: Molecular biology techniques (DNA/RNA isolation, cloning, qPCR), Plant phenotyping, Pathogens assays
Requirements: Basic knowledge of plant-microbe interactions and molecular biology
Evolutionary dynamics of plant resistance genes
Plant receptor genes (RLK/Ps) underwent a dramatic expansion in comparison to many other gene families, indicating their importance for plant immunity to diverse pathogens. Gene duplication via polyploidy and small-scale local duplication events is a major evolutionary force driving gene expansion and variability. This project aims to identify the genetic diversity among RLK/Ps in plants via comparative evolutionary genomics.
You will:
- determine natural sequence variation of RLK/Ps in genomes of crops and wild relatives.
- investigate gene presence/absence variations (PAVs), copy number variations (CNVs)
- determine distribution of single nucleotide polymorphisms (SNPs) in gene sequences.
- assess the evolution of RLK/Ps in plants via phylogenetic and synteny analysis across genomes.
Skill development: Bioinformatics, Phylogenetic analyses, Comparative genomics
Requirements: Affinity and experience with bioinformatics and molecular evolution
Ecotypic variability in Lamb’s lettuce populations (Valerianella spp. L)
Lamb’s lettuce (Valerianella locusta; veldsla) is a leafy vegetable that is often used in mixed salads.
It belongs to the family Caprifoliaceae and is thus not, as suggested by its name, related to lettuce
(Lactuca sativa, Asteraceae). Cultivars of Lamb’s lettuce are supposed to have narrow genetic diversity, largely because breeding programs have much relied on identical germplasm collections.
This narrow genetic diversity limits the potential to cope with environmental changes, including bacterial blight - an emerging disease caused by the bacterium Acidovorax valerianellae. Safeguarding germplasm of natural populations of Lamb’s lettuce and closely related wild relatives will benefit breeding of more future-proof cultivars. This project aims to explore genetic and ecotypic variability in Valerianella, both in cultivars and wild relatives.
You will:
- collect seeds of wild Valerianella species in The Netherlands.
- characterize morphologic differences across cultivars and wild ecotypes.
- assess genetic variation by SCoT marker genotyping in Valerianella, incl. cultivars and ecotypes.
- develop pathogen assays to characterize natural variation in blight resistance.
- analyse phenotypic and population genetic data.
Skill development: DNA barcoding, Gene variant analysis, Population genetics, Plant phenotyping, Pathogens assays
Requirements: Basic knowledge of plant-microbe interactions and molecular biology
Are grasses with low genetic diversity more susceptible to infection by fungal pathogens?
Pathogenic fungi are of great economic importance as they cause serious losses in the production of grasses, such as cereal crops and turf-grasses. To prevent these losses, fungicides are applied. The diversity-disease hypothesis (Elton 1958) suggests that greater plant diversity results in a lower severity of plant diseases.
The severity of pathogens in a population may depend not only on the diversity of co-occurring species, but also on the degree of genotypic variation within species. Grass species in natural systems are often found in near monocultures, which can be the effect of intraspecific variation in which individual plants cope in diverse ways with pathogen attack. To test this hypothesis and gain mechanistic understanding on the interaction between intraspecific genetic diversity and plant pathogens we want (1) to analyse within-species genetic variation of grass species in monoculture and polyculture and (2) test if the degree of genetic variation is related to the disease incidence.
You will:
- perform fieldwork in monoculture and polyculture grasslands
- monitor grass-pathogen interactions
- genotype genetic diversity of grasses
- explore population dynamics
Skill development: Genotyping grass species, Identification of grasses and pathogenic fungi (Puccinia)
Requirements: Basic knowledge of plant-microbe interactions