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

Abstract

An investigation of the effects of two important post-transcriptional regulatory mechanisms, gene transcription and alternative splicing (AS), on the wood formation of Eucalyptusurophylla × tereticornis, an economic tree species widely planted in southern China, was carried out. We performed RNA-seq on E. urophylla × tereticornis hybrids with highly contrasting wood basic density (BD), cellulose content (CC), hemicellulose content (HC), and lignin content (LC). Signals of strong differentially expressed genes (DEGs) and differentially spliced genes (DSGs) were detected in all four groups of wood properties, suggesting that gene transcription and selective splicing may have important regulatory roles in wood properties. We found that there was little overlap between DEGs and DSGs in groups of the same trait. Furthermore, the key DEGs and DSGs that were detected simultaneously in the four groups tended to be enriched in different Gene Ontology terms, Kyoto Encyclopedia of Genes and Genomes pathways, and transcription factors. These results implied that regulation of gene transcription and AS is controlled by independent regulatory systems in wood formation. Lastly, we detected transcript levels of known wood biosynthetic genes and found that 79 genes encoding mainly enzymes or proteins such as UGT, LAC, CAD, and CESA may be involved in the positive or negative regulation of wood properties. This study reveals potential molecular mechanisms that may regulate wood formation and will contribute to the genetic improvement of Eucalyptus.

High-density genetic linkage mapping reveals low stability of QTLs across environments for economic traits in Eucalyptus

“…The developing xylem tissues of 23 progenies were collected for RNA extraction in mid-July 2018 which is the period for most-active tree growth in Guangdong, China. In a parallel study, 17 of 23 progenies were used to study the effects of gene expression and alternative splicing on wood formation in Eucalyptus ( Zhu et al., 2022 ). The RNA-seq libraries of 23 progenies with contrasting phenotypes were constructed using VAHTS™ Stranded mRNA-seq Library Prep Kit (Vazyme Biotech, China) and were sequenced using the Nextseq-500 platform (Illumina, USA).…”