Page 95 - University of Pretoria RESEARCH REVIEW 2016

SYSTEMS GENETICS
UP RESEARCHERS UNRAVEL GENE NETWORKS
Systems genetics is an experimental and statistical approach to understanding the dynamics and interactions of genes and biological processes that act together
to give rise to complex trait variation in plant and animal populations.
In 2016, two research groups, in the Department of Genetics and in the Department of Plant and Soil Sciences, pioneered the use of systems genetics to study the woody biomass production in Eucalyptus trees, and foliar disease interactions in maize. Experimental and statistical methods were used
to analyse and integrate molecular component phenotypes, such as gene expression, and protein or metabolite levels, in populations that vary for these components and for complex traits such as growth, development and defence.
These studies featured the work of two young researchers, Dr Eshchar Mizrachi and Dr Nanette Christie, who have been instrumental in establishing the underlying genomics and statistical methods
for analysing these two biological systems. Both
studies were also performed in collaboration with the Bioinformatics and Systems Biology research groups of Professors Yves van de Peer and Kathleen Marchal at Ghent University in Belgium, both of whom are visiting professors at the Genome Research Institute at UP.
GENE NETWORKS DRIVING WOOD FORMATION IN TREES
How trees produce vast amounts of wood, and how to change the properties of wood to suit various end uses, are questions that have been difficult to pursue in trees due to their large sizes and long life cycles.
The advent of modern genomics technologies, which enable the rapid and simultaneous profiling of thousands of genes, even in difficult to analyse tissues such as wood from mature trees, promises to overcome these hurdles. Together with their Belgian collaborators, Dr Eshchar Mizrachi,
Dr Nanette Christie and Professor Zander Myburg in the Department of Genetics have reported one of the first large-scale, integrated analyses of tens
of thousands of genes in developing Eucalyptus plantation wood. In their paper, published in the prestigious journal Proceedings of the National Academy of Sciences of the United States of America
(Mizrachi et al. PNAS, January 2017), the team described how they used network-based approaches (connecting genes with similar expression and functions) to unravel the molecular basis of wood formation.
In particular, the team pioneered the use of a
systems genetics approach that leverages the power
of genetics in large numbers of trees. For their
project, a collaboration with industry partner Sappi,
the team sampled genetic materials from developing
wood of 156 Eucalyptus trees and profiled the
expression of nearly 30 000 genes in each tree,
allowing them to identify the gene networks
important for the different structural and chemical
properties of wood. This information can now be
used for molecular breeding or genetic engineering
of trees in an effort to develop a new generation
of woody biomass crops supporting a thriving and
sustainable bio-based economy. Eshchar Mizrachi
Nanette Christie and
UP Research Review 2016 | 93
Moloko/Dalila, FABI