Project

Constructing the genetic regulatory network controlling zinc use efficiency in Arabidopsis

My research aim involves the identification of genes related to an increased efficiency in the use of Zn by some plants, enabling some genotypes to grow and yield in Zn deficient soils and to improve the uptake of this micronutrient resulting in biofortified varieties of plants.

I work with the model plant for genetic studies: Arabidopsis thaliana. I use 360 Arabidopsis accessions collected at different regions in the world as a source of natural genetic variation for Genome Wide Association Mapping (GWA) studies. With this kind of analysis we can identify genes responsible for a better performance under Zn deficiency conditions (for example). In addition to this, I am also investigating 3 mutant lines with a differential response to Zn nutrition. I am going to use a re-sequencing and microarray approach to clone the genes responsible for the phenotypes observed. Following, the genes cloned will be further characterized.

Thesis topic: Constructing the genetic regulatory network controlling zinc use efficiency in Arabidopsis

Supervisors:

Ana Carolina A. L. Campos and Mark Aarts

Zinc is one of the most common crop micronutrient deficiencies, mainly as a result of an increased pH in soils. Notably, 50% of cultivated soils in India and Turkey, a third of cultivated soils in China, and most soils in Western Australia are classed as Zn-deficient (Broadley et al., 2007). Deficiencies of essential minerals affect both the quality and quantity of plant-derived food components, thereby negatively affecting a large portion of the world's human population for whom plants serve as the major dietary source of essential minerals.

As a consequence of coping with low nutrient availability certain plant genotypes are able to grow and yield under nutrient deficiency. This ability is named NUE (nutrient use efficiency). Currently the genetic basis for NUE is not well understood. We use Arabidopsis thaliana to further investigate this. In this study we use the Arabidopsis Hap Map collection, comprised of 360 well-genotyped accessions collected in different parts of the world. This collection is a source of genetic variation that can be used as a powerful tool to identify genes controlling NUE in Arabidopsis. Therefore, this research focuses on understanding the genetic variation in the ability of Arabidopsis to respond to low Zn availability with a minimal reduction in growth.

20 Arabidopsis accessions grown in hydroponics using a ½ strength Hoagland’s solution with optimal (2 µM) (A); and low (0 µM) Zn (B). Zn Use Efficiency (%) calculated based on the plant shoot dry biomass (C).
20 Arabidopsis accessions grown in hydroponics using a ½ strength Hoagland’s solution with optimal (2 µM) (A); and low (0 µM) Zn (B). Zn Use Efficiency (%) calculated based on the plant shoot dry biomass (C).

Key-objectives:

  1. Identification of regulatory and structural genes involved in controlling Zn use efficiency in Arabidopsis.
  2. To understand the role of some of these genes in relation to plant growth.
  3. To extrapolate this information to Brassica.

Used skills:

Basic genetics and molecular biology skills, bioinformatics, some statistical analysis to interpret the results.

Requirements:

Genetic Analysis Tools and Concepts (GEN30306) and Plant Biotechnology (GEN20806) are good preparations.

Reference:

Broadley, M. R., White, P. J., Hammond, J. P., Zelko, I., and Lux, A.  2007  Zinc in plants. 173: 677-702.

Assuncao AGLD, Herrero E, Lin Y, Huettel B, Talukdar S, Smaczniak C et al. Arabidopsis thaliana transcription factors bZIP19 and bZIP23 regulate the adaptation to zinc deficiency. PNAS Early Edition. 2010 jun;107(22):10296-10301.