Genetic effect in leaf and xylem transcriptome variations among Eucalyptus urophylla x grandis hybrids in field conditions

Abstract

To assess the genetic and environmental components of gene-expression variation among trees we used RNA-seq technology and Eucalyptus urophylla x grandis hybrid clones tested in field conditions. Leaf and xylem transcriptomes of three 20 month old clones differing in terms of growth, repeated in two blocks, were investigated. Transcriptomes were very similar between ramets. The number of expressed genes was significantly (P<0.05) higher in leaf (25,665±634) than in xylem (23,637±1,241). A pairwise clone comparisons approach showed that 4.5 to 14 % of the genes were diffe­rentially expressed (false discovery rate [FDR]<0.05) in leaf and 7.1 to 16 % in xylem. An assessment of among clone variance components revealed significant results in leaf and xylem in 3431 (248) genes (at FDR<0.2) and 160 (3) (at FDR<0.05), respectively. These two complementary approa­ches displayed correlated results. A focus on the phenylpro­panoid, cellulose and xylan pathways revealed a large majo­rity of low expressed genes and a few highly expressed ones, with RPKM values ranging from nearly 0 to 600 in leaf and 10,000 in xylem. Out of the 115 genes of these pathways, 45 showed differential expression for at least one pair of geno­type, five of which displaying also clone variance compo­nents. These preliminary results are promising in evaluating whether gene expression can serve as possible ‘intermediate phenotypes’ that could improve the accuracy of selection of grossly observable traits.

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

“…Due to advances in high-throughput sequencing technologies, researchers have conducted some transcriptome sequencing (RNA-seq) to discover functional genes and try to reveal molecular mechanisms of complex traits in Eucalyptus (Nakahama et al, 2018;Vaillant et al, 2018;Zhang et al, 2022). For example, Zhang et al ( 2022) performed RNA-seq to identify the co-expressed genes during the callus maturation and shoot regeneration of Eucalyptus, and found a number of potentially functional genes associated with reproductive capacity.…”

“…Due to advances in high-throughput sequencing technologies, researchers have conducted some transcriptome sequencing (RNA-seq) to discover functional genes and try to reveal molecular mechanisms of complex traits in Eucalyptus ( Nakahama et al., 2018 ; Vaillant et al., 2018 ; Zhang et al., 2022 ). For example, Zhang et al.…”