Exploiting copy number variation for rapid improvement of abiotic stress tolerance in crops

Introduction

Copy number variations (CNVs) are a type of intraspecific genetic polymorphisms that involves either the loss or gain of sequences larger than 50 bp, and typically encompassing one or more genes. Upon duplication of a gene, this will initially affect gene expression, while on longer evolutionary timescales this may give rise to an altered or new gene function by the duplicated gene. CNV is abundant in plants, also in crops, and is frequently associated with adaptation and evolution to (a)biotic stress. It often impacts important agronomical traits that could be selected for in crop improvement. Recent analyses suggests that plant genomes are not as stable as always assumed, but highly dynamic, in part through the frequent occurrence of CNVs, even within only a few generations and especially under adverse environmental conditions. It thus appears that it is an important mechanism for plant evolution to their environment and potentially a very interesting tool in plant breeding.

Aim

The aim of this project is to understand the role of CNV in the evolution of plant adaptations to their environment. Therefore, assessing the rate at which these kinds of mutations occur, the (molecular) mechanisms underlying CNV formation and association of copy number variants to important physiological traits are a few key points that are instrumental to understand how this drives plant evolution.

Approach

Copy number variants are studied in a few different plant species that are adapted to diverse environmental conditions; Arabidopsis thaliana (model organism), Noccaea caerulescens (heavy metal hyperaccumulator) and Hirschfeldia incana (extreme photosynthesis) based on whole genome sequence data. Functional analysis is performed on duplicated gene copies to understand the genomic organization and the relevance to particular traits.

Student opportunities

We are open to applications for thesis projects! We have different thesis topics available. Are you interested? Contact Mark.Aarts@wur.nl.