Transcriptome profiling of radiata pine branches reveals new insights into reaction wood formation with implications in plant gravitropism

Abstract

BackgroundFormation of compression (CW) and opposite wood (OW) in branches and bent trunks is an adaptive feature of conifer trees in response to various displacement forces, such as gravity, wind, snow and artificial bending. Several previous studies have characterized tracheids, wood and gene transcription in artificially or naturally bent conifer trunks. These studies have provided molecular basis of reaction wood formation in response to bending forces and gravity stimulus. However, little is known about reaction wood formation and gene transcription in conifer branches under gravity stress. In this study SilviScan® technology was used to characterize tracheid and wood traits in radiate pine (Pinus radiata D. Don) branches and genes differentially transcribed in CW and OW were investigated using cDNA microarrays.ResultsCW drastically differed from OW in tracheids and wood traits with increased growth, thicker tracheid walls, larger microfibril angle (MFA), higher density and lower stiffness. However, CW and OW tracheids had similar diameters in either radial or tangential direction. Thus, gravity stress largely influenced wood growth, secondary wall deposition, cellulose microfibril orientation and wood properties, but had little impact on primary wall expansion. Microarray gene transcription revealed about 29% of the xylem transcriptomes were significantly altered in CW and OW sampled in both spring and autumn, providing molecular evidence for the drastic variation in tracheid and wood traits. Genes involved in cell division, cellulose biosynthesis, lignin deposition, and microtubules were mostly up-regulated in CW, conferring its greater growth, thicker tracheid walls, higher density, larger MFA and lower stiffness. However, genes with roles in cell expansion and primary wall formation were differentially transcribed in CW and OW, respectively, implicating their similar diameters of tracheid walls and different tracheid lengths. Interestingly, many genes related to hormone and calcium signalling as well as various environmental stresses were exclusively up-regulated in CW, providing important clues for earlier molecular signatures of reaction wood formation under gravity stimulus.ConclusionsThe first comprehensive investigation of tracheid characteristics, wood properties and gene transcription in branches of a conifer species revealed more accurate and new insights into reaction wood formation in response to gravity stress. The identified differentially transcribed genes with diverse functions conferred or implicated drastic CW and OW variation observed in radiata pine branches. These genes are excellent candidates for further researches on the molecular mechanisms of reaction wood formation with a view to plant gravitropism.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-14-768) contains supplementary material, which is available to authorized users.

Gravitropisms and reaction woods of forest trees – evolution, functions and mechanisms

“…Not surprisingly, large numbers of genes have been described as being differentially expressed in reaction wood vs normal wood in various angiosperm species, including Eucalyptus (Paux et al ., ), tulip tree ( L. tulipifera ) (Jin et al ., ), and poplar (Andersson‐Gunneras et al ., ; Chen et al ., ). In pines, large numbers of genes have been identified that are differentially expressed between compression wood and opposite wood, including cell division, cell wall, hormonal, and cytoskeleton‐related genes (Ramos et al ., ; Villalobos et al ., ; Li et al ., ), A crucial next step for gene expression studies is to describe how the thousands of genes involved in reaction wood development interact to affect changes in wood anatomy.…”

The Cytoskeleton and Its Role in Determining Cellulose Microfibril Angle in Secondary Cell Walls of Woody Tree Species

“…The molecular machinery behind MFA determination is still unclear; however, many quantitative trait loci (QTL) have been identified for wood and fibre properties, including MFA [93][94][95], and some genes have been identified as candidates [95][96][97][98][99]. Reaction wood (RW) has proved to be a useful model system in attempts to better understand the molecular basis of wood formation [100] and several studies have published transcriptomes of angiosperm and gymnosperm RW [101][102][103]. A large number of genes were reported to be highly expressed in RW, among them some encoding arabinogalactan proteins (AGPs), fasciclin-like arabinogalactan proteins (FLAs) and α and β-tubulins [102,[104][105][106][107][108].…”

“…Reaction wood (RW) has proved to be a useful model system in attempts to better understand the molecular basis of wood formation [100] and several studies have published transcriptomes of angiosperm and gymnosperm RW [101][102][103]. A large number of genes were reported to be highly expressed in RW, among them some encoding arabinogalactan proteins (AGPs), fasciclin-like arabinogalactan proteins (FLAs) and α and β-tubulins [102,[104][105][106][107][108].…”

Forest Tree Genomics: Review of Progress

“…differential genes, transcripts or probes (%): The number in parentheses corresponds to the percentage (%) of differential genes (transcripts or probes) relative to the total number of analyzed genes (transcripts or probes). Li, Yang, & Wu, 2013;Ralph et al, 2006;Villalobos et al, 2012) and long-oligonucleotide microarrays (e.g. Hybridization methods used microarray which contains a collection of probes spotted or printed onto a glass surface.…”