Canadian Forest Service Publications
Genetic architecture of wood properties based on association analysis and co-expression networks in white spruce. Lamara, M.; Raherison, E.; Lenz, P.; Beaulieu, J.; Bousquet, J.; MacKay, J. 2016. New Phytol. 210:240-255.
Issued by: Laurentian Forestry Centre
Catalog ID: 36609
CFS Availability: PDF (request by e-mail)
Available from the Journal's Web site. †
† This site may require a fee
Association studies are widely utilized to analyze complex traits but their ability to disclose genetic architectures is often limited by statistical constraints, and functional insights are usually minimal in nonmodel organisms like forest trees.
We developed an approach to integrate association mapping results with co-expression networks. We tested single nucleotide polymorphisms (SNPs) in 2652 candidate genes for statistical associations with wood density, stiffness, microfibril angle and ring width in a population of 1694 white spruce trees (Picea glauca).
Associations mapping identified 229–292 genes per wood trait using a statistical significance level of P < 0.05 to maximize discovery. Over-representation of genes associated for nearly all traits was found in a xylem preferential co-expression group developed in independent experiments. A xylem co-expression network was reconstructed with 180 wood associated genes and several known MYB and NAC regulators were identified as network hubs. The network revealed a link between the gene PgNAC8, wood stiffness and microfibril angle, as well as considerable within-season variation for both genetic control of wood traits and gene expression. Trait associations were distributed throughout the network suggesting complex interactions and pleiotropic effects.
Our findings indicate that integration of association mapping and co-expression networks enhances our understanding of complex wood traits.
Plain Language Summary
In this study of white spruce, the researchers set out to determine which portions of the tree’s genome could be related to certain wood characteristics, including its density, stiffness and fibre quality. They developed a new approach in order to demonstrate the interaction between various genomic regions and identify gene networks that control the expression of those wood characteristics.
This new knowledge on white spruce - a species that is highly valued for the quality of its wood and high plantation yield - will help in the selection of better specimens for the production of seedlings for reforestation purposes.