Research

The research group together with our outside collaborators follows a multidisciplinary approach that might be best described as a "Functional Genomic Approach to link Genomics, Genetics and Plant Physiology with Plant Breeding and Agronomy".

We have three main research topics: phosphorus (P) deficiency, Zn biofortification and tolerance to iron (Fe) toxicity plus the cross-cutting theme of understanding root function and architecture in relation to above topics.

Research Topic

P deficiency: Research focuses on genotypic differences in tolerance to P deficiency, targeting mechanisms/genes that enhance internal P utilization efficiency (PUE) or P uptake from low-P soils (sites are located in Japan, South-East Asia, and Madagascar). Within P uptake we differentiate between root growth/architecture and P acquisition efficiency (PAE). We further investigate whether P loading into the grain can be reduced to improve P balances through lower P removal from fields at harvest. Work focuses on rice and in Madagascar has had a very applied variety selection and release component.

Specific Activities

  • Cloning of the Pup1 locus in rice and application of tolerance alleles in marker assisted selection (MAS).

  • Genome-wide association mapping (GWAM) of loci enhancing PUE in diverse rice genebank accessions.

  • Identification of novel loci for P deficiency tolerance in African rice: Oryza glaberrima and interspecific crosses.

  • Agronomic assessment of impacts of enhanced PUE and reduced grain P concentrations on seedling growth and grain yield.

  • Breeding population to select for enhanced P efficiency


Research Topic

Root function and architecture: Whether we are concerned with the uptake of deficient or toxic nutrients, root properties are likely a key factor for observed genotypic differences. We are therefore focusing on root architectural properties and on the interaction of rice roots with their rhizosphere. Both aspects are investigated through modeling, experimental and genetic approaches. Allocation of resources (assimilates or limiting nutrients such as P) between shoot and root is a further topic of interest as we observed a more rapid re-allocation of resources for root growth in varieties adapted to low soil fertility.

Specific Activities

  • Development of a 3-D root growth and P uptake model for upland rice and simulation of costs (P invested in root biomass) and benefits (P uptake) of different root classes.

  • Expansion of above model to simulate the effects of drought and root distribution on P and water uptake.

  • Genotypic differences in lateral root branching (S-type and L-type length and density) as related to P and water uptake.

  • Root exudation and their effects on P solubilization (directly and indirectly through effects on P solubilizing microorganisms).


Research Topic

Fe toxicity: Together with collaborators at AfricaRice and LRI (Madagascar), QTLs associated with tolerance are being mapped and fine mapped. We further try to understand interactions between genotype and site-specific effects that affect the severity of Fe toxicity on one hand and efficacy of tolerance mechanisms on the other. Molecular studies are geared towards identification of candidate genes controlling such tolerance mechanisms.

Specific Activities

  • Phenotypic evaluations of mapping populations under induced Fe toxicity and under field conditions.

  • Physiological studies to identify tolerance mechanisms operating in potential donor and recipient varieties. In tolerant accessions we distinguish Fe excluders, compartmentalizers and accessions with high tissue tolerance.

  • Candidate gene characterization in contrasting lines for compartmentalization and tissue tolerance based on greenhouse studies.


Research Topic

Zn biofortification: Zinc (Zn) malnutrition is a global problem causing infant mortality, delaying infant development and reducing immune system function. Developing crops with higher Zn concentrations in edible parts, a process termed Zn biofortification, is seen as one of the most efficient ways to alleviate Zn malnutrition, especially for rural populations. With partners in Madagascar (FOFIFA, CIRAD) we test high-Zn breeding lines developed by HarvestPlus breeding programs elsewhere, and search for new high-Zn donor to initiate a local breeding program.

Specific Activities

  • Field testing of imported high-Zn breeding lines to assess the feasibility of a fast-track variety release.

  • Screening of gene bank accessions from the 3K panel (SNP-Seek) for potential high-Zn donors, combined with GWAS analyses.

  • Development of a Genomic Prediction model from above panel and prediction of grain Zn concentrations among 3 K accessions to identify superior donors.

  • Physiological studies to determine whether high grain Zn is due to efficient uptake or translocation of Zn.