
Project
Understanding and preventing Somaclonal Variation in plant tissue culture
Clonal propagation through plant tissue culture is widely used for the multiplication of many crops because of its efficiency and the preservation of genetic and phenotypic uniformity. However, in-vitro clonal propagation, especially after prolonged tissue culture, often results in undesired heritable variability, called somaclonal variation (SV), which is a major problem for plant propagators who require uniformity in their clones.
Somaclonal variation (SV) can pose a serious problem in any propagation program, in which it is important to produce uniform and homogeneous offspring. Moreover, with the increased usage of tissue culture steps in breeding programs (e.g. CRISPR-based genome editing, doubled-haploid production), SV is also a serious threat to modern breeding. SV can lead to small or large phenotypic changes, which can become apparent already during the in-vitro propagation process or worse, later in the life cycle of regenerated plants. This leads to plants that are not true-to-type, reduced quality, and subsequently leads to large losses. Unfortunately, no good solution has yet been found for this problem, mostly due to the broad spectrum of adverse phenotypes, the fluctuating frequency of occurrence, and the diverse in-vitro culture protocols used. However, it’s clear that SV is caused by the in-vitro culture step in the propagation and regeneration of plant material and that, amongst others, epigenetic changes in the plant’s genome occurring during in-vitro culture are causing this problem.
In this project we will address the problem of SV, starting with detailed investigation of the genetic and epigenetic changes that are associated with occurrence of SV in multiple in-vitro plant culture systems. We expect that this will shed light on underlying molecular causes and will result in identification of generic molecular signatures for early detection of SV. Besides this inventory of molecular causes, we will perform a dedicated chemical genomics screen for compounds that can suppress the occurrence of SV, which can be implemented by involved companies in their tissue culture routine.
This project is very timely due to the increasing importance of tissue culture in novel breeding programs, recent advances in (epi)genome sequence technologies, and available information about structural variation in genomes, together facilitating an in-depth understanding of the molecular causes of SV.