Functional network analysis of genes differentially expressed during xylogenesis insoc1fulwoody Arabidopsis plants

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Many plant genes are known to be involved in the development of cambium and wood, but how the expression and functional interaction of these genes determine the unique biology of wood remains largely unknown. We used thesoc1fulloss of function mutant – the woodiest genotype known in the otherwise herbaceous model plant Arabidopsis – to investigate the expression and interactions of genes involved in secondary growth (wood formation). Detailed anatomical observations of the stem in combination with mRNA sequencing were used to assess transcriptome remodeling during xylogenesis in wild-type and woodysoc1fulplants. To interpret the transcriptome changes, we constructed functional gene association networks of differentially expressed genes using the STRING database. This analysis revealed functionally enriched gene association hubs that are differentially expressed in herbaceous and woody tissues. In particular, we observed the differential expression of genes related to mechanical stress and jasmonate biosynthesis/signaling during wood formation insoc1fulplants that may be an effect of greater tension within woody tissues. Our results suggest that habit shifts from herbaceous to woody life forms observed in many angiosperm lineages could have evolved convergently by genetic changes that modulate the gene expression and interaction network, and thereby redeploy the conserved wood developmental program.

Significance Statement

Arabidopsis plants that are doubly mutant at SOC1 and FUL, which encode MADS-box transcription factors, are somewhat woody. Here we investigated gene expression in stems of this double mutant and identified clusters of interacting genes differentially expressed at stages of secondary growth. Derived woodiness in flowering plants, which has evolved hundreds of times, might have happened by adjusting multiple nodes within such a network, and thus we propose that these transcription factors are potential master regulators of wood development.

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