C·I·B core team members receive prestigous grant to uncover the influence of epigenetic variation on functional genomics

C·I·B core team members, Jaco Le Roux and Cang Hui recently received a NRF-Blue Skies Concept grant to investigate the role of environmentally induced epigenetic variation on gene expression. Environmental stimuli may alter DNA biochemically so that these new so-called epigenetic variants could differ dramatically in their levels of gene expression (transcriptomes). However, this link is not straight forward since actual gene variation could also lead to drastic differences in transcriptomes.

Pennisetum setaceum (fountain grass)

The proposed research will use Pennisetum setaceum (fountain grass) as a study system to investigate how environmental change(s) induce differences in gene expression. Previous research by Dr Le Roux showed that fountain grass has little or no genetic diversity in South Africa, making it an ideal study system to study the influences of ‘pure’ epigenetic diversity. By sampling populations across a steep environmental gradient (e.g. dry and hot Northern Cape to more mesic and cool Western Cape areas) the current research project will identify which genes are expressed using next-generation sequencing of whole transcriptomes. Whole and annotated genome sequences are available for many members of the grass family, including rice and maize, making gene function annotation, i.e. functional genomics, in fountain grass particularly feasible. Different populations will also be characterized for epigenetic variation to be linked to any differences observed in gene expression among these populations.

If a link between epigenome variation and gene expression is found the next question that arises is to which extent environmentally-induced epigenetic changes are imprinted, i.e. partially heritable. For this, populations obtained from across the environmental gradient will have to be grown in a common garden and re-assessed for epigenetic variation and gene expression.

This research will allow researchers to not only better understand the mechanisms underlying phenotypic plasticity but also the capacity of species to cope with global environmental changes such as climate change.

The Blue Skies Research Programme is a highly competitive programme funded by the National Research Foundation (NRF), which provides space for novel fundamental enquiry, curiosity-driven and basic research.