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Genetic architecture of gene expression during xylogenesis in Eucalyptus interspecific hybrids
Xylogenesis is a complex biological process involving thousands of genes that leads to the formation
of woody biomass, which is one of the largest sources of renewable raw materials for many industrial
applications, such as construction, bioenergy, and biomaterials. This process is a strong carbon sink
that needs to be kept under strict regulation at the transcriptional level. Better understanding of the
key regulators underlying environmentally or industrially desirable phenotypes will allow us to
improve woody biomass traits for bioprocessing and biorefinery. Variation in these phenotypes is
associated with many genes segregating at population level, particularly in highly outbred populations
such as Eucalyptus interspecific hybrids. Eucalyptus trees, which have a large capacity to produce
woody tissue with superior structural and chemical qualities and relatively short rotation, are
important models for wood formation research.
In this study, we aimed to characterise the genetic architecture of gene expression during xylogenesis
in an interspecific (E. grandis x E. urophylla) Eucalyptus F2 backcross population and to determine the conservation of the genetic architecture across age. This was done by analysing RNA-seq data
from xylem tissues of 156 and 100 field-grown Eucalyptus trees at juvenile (three years) and rotation
(eight years) age respectively. Transcriptome-derived SNPs were used to construct a gene-based
genetic linkage map for eQTL detection using 236 high confidence markers in highly expressed
genes. We identified co-expression modules for 25,267 genes, which were used to construct a coexpression
network. This network allowed identification of the main biological functions of each
module, and dissemination of transcriptional coordination of metabolic functions and development
during xylogenesis. Global eQTL analyses of co-regulated genes led us to the identification of 22
trans-eQTL hotspots, which are major regulatory perturbations that can change the structure of the
co-expression network. To characterise the genetic architecture of gene expression variation during
xylem development, the co-expression and co-regulation results were integrated into systems genetics
models, which revealed a major shift in the transcriptional regulation architecture from juvenile to
mature age, evidenced by new trans-eQTL hotspots detected in mature trees.
This study provides a new method for rapid genetic dissection of gene expression variation from
population-wide transcriptome data alone and provides insight into the regulation of xylem genes
across age. The observed changes in the genetic architecture of wood formation genes, as well as
those observed in genes related to abiotic stress response, suggests that there are multiple contributing
factors associated with variation in transcript abundance, including developmental or age-related
changes, stress-related changes and other yet unknown biological effects. By combining results from
eQTL and co-expression analyses into systems genetics models, we identified a genetic basis for
coordinated gene expression responses regulating biological processes in xylem. These results will
enable us to analyse the genetic architecture underlying complex wood biorefinery traits and identify
interacting genes and pathways. This can then be used to engineer or breed for complex wood
property traits while avoiding negative effects on plant growth.
Description:
Dissertation (MSc (Bioinformatics))--University of Pretoria, 2019.