Construction of co-expression network based on natural expression variation of xylogenesis-related transcripts in Eucalyptus tereticornis

Abstract

Natural genetic variation is randomly distributed and gene expression patterns vary widely in natural populations. These variations are an effect of multifactorial genetic perturbations resulting in different phenotypes. Genome-wide analysis can be used to comprehend the genetic basis governing this naturally occurring developmental variation. Secondary growth is a highly complex trait and systems genetics models are presently being applied to understand the molecular architecture of wood formation. In the present study, the natural variation in expression patterns of 18,987 transcripts expressed in the developing xylem tissues were documented across four phenotypes of Eucalyptus tereticornis with distinct holocellulose/klason lignin content. The differentially expressed genes across all the phenotypes were used to construct co-expression networks and sub-network 2 with 380 nodes and 17,711 edges was determined as the network of relevance, including 30 major cell wall biogenesis related transcripts with 2394 interactions and 10 families of transcription factors with 3360 interactions. EYE [EMBRYO YELLOW] was identified as major hub transcript with 173 degrees which interacted with known cell wall biogenesis genes. K-mean clustering was also performed for differentially expressed transcripts and two clusters discriminated the phenotypes based on their holocellulose/klason lignin content. The cluster based networks were enriched with GOs related to cell wall biogenesis and sugar metabolism. The networks developed in the present study enabled identification of critical regulators and novel transcripts whose expression variation could presumably govern the phenotypic variation in wood properties across E. tereticornis.

Xylem Transcriptome Analysis in Contrasting Wood Phenotypes of Eucalyptus urophylla × tereticornis Hybrids

“…The differences in gene transcription between high and low phenotypes were quantified using Log 2 FC, and the results showed a range of −21.6-27.7 for the BD group samples, −21.6-12.9 for CC, −29.2-12.5 for HC, and −27.9-13.1 for LC (Figure 1a), indicating that considerable differences in gene transcription were detected in these groups. Compared to earlier studies in Eucalyptus [15,16,26,28], we found a greater number of xylem-related genes. This is probably due to the highly contrasting phenotypes we selected from within a larger breeding population with a large number of continuously variable phenotypes.…”

Co-expression network of secondary cell wall biogenesis genes in Eucalyptus tereticornis

“…In our earlier publication, we had reported that the expression variation of EYE [EMBRYO YELLOW] could presumably govern the phenotypic variation in wood properties across Eucalyptus tereticornis. Further, gene clusters discriminating the phenotypes were also reported (Dharanishanthi and Ghosh Dasgupta, 2016). However, the differentially expressed transcripts selected for the previous study did not include major transcripts regulating secondary cell-wall biogenesis, necessitating the present study, wherein a specific secondary cell wall related co-expression network was developed to identify major transcripts regulating secondary cell wall biogenesis in wood tissues of E. tereticornis.…”

“…Total RNA from duplicate samples was pooled in equimolar concentration prior to labeling and hybridization. A 8x60K microarray chip was customdesigned in Agilent platform (AMADID: 059849) consisting of 44,817 probes representing 18,987 transcripts (Dharanishanthi and Ghosh Dasgupta, 2016). The size of the probes was sixty base pairs and a minimum of two probes per transcript was designed.…”

Identification and functional evaluation of accessible chromatin associated with wood formation in Eucalyptus grandis

“…Although there is some evidence that several TFs within the Arabidopsis network are functionally conserved in woody plants (Zhong et al ., , ; Kalluri et al ., ; Nakano et al ., ), the presence of woody plant‐specific subgroups of MYB TFs with proven roles in regulating xylem development (Soler et al ., , ) and a large number of novel protein–DNA interactions in model woody plants (Chen et al ., ) suggests that SCW transcriptional networks undergo rewiring in different lineages. Systems genetics and co‐expression network analyses in Eucalyptus , which is emerging as an important model for wood formation, are implicating new genes in certain aspects of wood formation or linking them to lignocellulosic biomass traits (Myburg et al ., ; Dharanishanthi & Dasgupta, ; Mizrachi et al ., ; Pinard et al ., ; Ployet et al ., ). However, the mechanisms by which they are transcriptionally regulated through interactions with CREs in the context of accessible chromatin in developing xylem is not yet understood.…”