Genetic architecture of transcription factor expression variation in developing secondary xylem of Eucalyptus grandis x E. urophylla

Abstract

The xylem secondary cell walls (SCW) are a strong carbon sink in woody plants and part of an irreversible developmental commitment which ends in programmed cell death. The biosynthetic processes involved in fibre SCW wall formation are guided by intrinsic developmental programmes and extrinsic signals, such as mechanical stress in woody stems, which are tightly co-ordinated. The model plants Arabidopsis and Populus have been used to study many of the transcription factors which are involved in the complex network responsible for the regulation of the formation of SCW. It is thought that variation in the expression of SCW transcription factor genes will affect cell wall deposition and wood properties in commercially important wood fibre crops such as Eucalyptus tree species and hybrids. To date the transcriptional control of SCW deposition in woody plants has not been fully resolved nor is it known which components of the transcriptional network regulating SCW exhibit natural variation in expression, or what the genetic architecture of such regulatory variation might be. In this study expression quantitative trait locus (eQTL) mapping and expression correlation analyses was performed for SCW-related transcription factor (transcription factor) homologs predicted in the Eucalyptus grandis genome. The expression of 353 candidate xylem-expressed transcription factor genes was quantified in the immature xylem of 156 and 127 F2 backcross progeny of an E. grandis x E. urophylla F1 hybrid respectively using Illumina RNA-Seq expression profiling. Many of the SCW related transcription factor genes shared trans-acting eQTLs or had shared cis- and trans-eQTLs, indicating the presence of polymorphisms affecting the expression of these SCW transcription factors and their downstream targets in the transcriptional network. Using information from expression correlation across 283 individuals and from shared transcription factor eQTLs, regulatory modules of the Eucalyptus SCW transcriptional network were partially reconstructed allowing the identification of known and novel candidate transcription factor genes and their genetic interactions that represent novel targets for functional studies in woody plants.