Conifer forests worldwide are becoming increasingly vulnerable to the effects of climate change. Although the production of phenolic compounds (PCs) has been shown to be modulated by biotic and abiotic stresses, the genetic basis underlying the variation in their constitutive production level remains poorly documented in conifers. We used QTL mapping and RNA-Seq to explore the complex polygenic network underlying the constitutive production of PCs in a white spruce (Picea glauca) full-sib family for 2 years. QTL detection was performed for nine PCs and differentially expressed genes (DEGs) were identified between individuals with high and low PC contents for five PCs exhibiting stable QTLs across time. A total of 17 QTLs were detected for eight metabolites, including one major QTL explaining up to 91.3% of the neolignan-2 variance. The RNA-Seq analysis highlighted 50 DEGs associated with phenylpropanoid biosynthesis, several key transcription factors, and a subset of 137 genes showing opposite expression patterns in individuals with high levels of the flavonoids gallocatechin and taxifolin glucoside. A total of 19 DEGs co-localized with QTLs. Our findings represent a significant step toward resolving the genomic architecture of PC production in spruce and facilitate the functional characterization of genes and transcriptional networks responsible for differences in constitutive production of PCs in conifers.

Additional methodological details are provided in the following publication:  

Laoué J, Depardieu C, Gérardi S, Lamothe M, Bomal C, Azaiez A, Gros-Louis M-C, Laroche J, Boyle B, Hammerbacher A, Isabel N and Bousquet J (2021) Combining QTL
Mapping and Transcriptomics to Decipher the Genetic Architecture of Phenolic Compounds Metabolism in the Conifer White Spruce. Front. Plant Sci. 12:675108. doi: 10.3389/fpls.2021.675108

Raw data files provided herein include:

1) GCAT_WS-3.3.cluseq.fasta: a gene catalog developped by Rigault et al., 2011 which was used as a reference to map reads obtained using RNA-Seq in the associated publication. Further details regarding the development of the gene catalog are provided in the following publication: Rigault P., Boyle B., Lepage P., Cooke JEK, Bousquet J, MacKay JJ. (2011). A white spruce gene catalog for conifer genome analyses. Plant Physiology, 157(1):14-28. doi: 10.1104/pp.111.179663.

2) Concentration_metabolites.xlsx: an excel file reporting concentrations in phenolic compounds for 164 individuals measured in 2014, and 203 individuals measured in 2017 (expressed in mg g-1 dry weight). Phenolic compounds measured were: astringin, catechin, gallocatechin, isorhapontin, neolignan-2 (4-[1,3-dihydroxy-2-[2-hydroxy-4-(3-hydroxypropyl)phenoxy]propyl]- ß-D-xylopyranoside), piceid, procyanidin B1, taxifolin and taxifolin glucoside.