Genes For Seed Quality


To understand the molecular mechanisms that determine seed quality and to identify the genes involved in this process.


The yield and economic success of horticultural crops depends to a large degree on the quality of the seed used to grow these crops. High quality seeds are undamaged seeds that have a high level of germination, which will produce uniform, vigorous seedlings without defects under various environmental conditions. Seed quality attributes include dormancy, germination (rate and uniformity), seed and seedling vigour (germination/growth under stress conditions), seedling dry weight, normal embryo- and seedling morphology, as well as the ability to develop into a normal plant. Seed quality is largely established during seed development and maturation, as a result of, often complex, interactions between the genome and the environment. We are trying to dissect these seed processes and their relationship with seed and seedling phenotypes and we hope to identify the regulatory genes and signaling pathways involved. This knowledge will provide us with the means to predict and enhance seed quality. The ultimate aim of the project is to develop markers which can be used for marker assisted breeding.

Our approach

By an innovative combination of physiology, genetics and genomics, the present project aims at identifying genes associated with tomato and Arabidopsis seed quality attributes. We will use the power of natural variation to find the genes responsible for different seed quality traits. This will be done with the help of Recombinant Inbred Line (RIL) populations from Arabidopsis and tomato. The phenotypical and genetical characterization of the different lines of these populations, will allow us to efficiently localize Quantitative Trait Loci (QTL’s). We use advanced imaging techniques to automatically score Arabidopsis seed germination and Arabidopsis and tomato seedling growth. This enables high troughput screens for germination potential under various environmental conditions. The results are used to define and confirm QTL’s. Such a genome position will still harbour many candidate genes and therefore, we will combine the standard QTL analysis with a genomic approach where we use microarrays to narrow the list of candidate genes. RNA from all the lines in the RIL populations will be used to hybridise tiling microarrays which will enable the localisation of so called “expression QTL’s” (eQTL’s). With the help of metabolomics to quantify the different primary metabolites in the different lines we will also localize QTL’s for these compounds (metabolic QTL’s or mQTL’s).

Student projects

  • Unraveling the complex trait of seed quality in tomato: Or how to get better and stronger tomato seeds
  • Genes for Seed Quality in Arabidopsis

Posters presentations

  • Automated scoring of Arabidopsis germination, Leo Willems, annual ALW plant science meeting, Lunteren, NL, 2009
  • Genes for Seed Quality, a physiological genetical genomics approach to find genes for seed quality in tomato,, Rashid Kazmi, annual ALW plant science meeting, Lunteren, NL, 2009
  • Genes for seed quality, Ronny, Joosen, International Conference on Arabidopsis Research (ICAR), Edinburgh, Scotland, 2009
  • Genes for seed quality: A physiological Genetical Genomics Approach, Wilco Ligterink, Plant Genomics and Beyond Conference, Evry, France, 2009

Oral presentations

  • Genes for seed quality, a physiological genetical genomics approach, Wilco Ligterink, Masterclass Natural Variation, Wageningen, 2008
  • Genes for seed quality, a physiological genetical genomics approach, Wilco Ligterink, QTL-MAS, Wageningen, NL, 2009
  • Genes for seed quality, unraveling the complex trait of seed quality in tomato, Wilco Ligterink, SOL 2009, New Delhi, India, 2009
  • Putting omics tools to work, unraveling the complex trait of seed quality by Genetical Genomics, Wilco Ligterink, 3rd ISSS Workshop on the Molecular Aspects of Seed Dormancy and Germination - York, UK, 2010