Genetic architecture of gene expression during xylogenesis in Eucalyptus interspecific hybrids

Abstract

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.