Network analysis reveals the relationship among wood properties, gene expression levels and genotypes of natural Populus trichocarpa accessions

• Published in: The New phytologist Vol. 200; no. 3; pp. 727 - 742
• Main Authors: Porth, Ilga, Klápště, Jaroslav, Skyba, Oleksandr, Friedmann, Michael C, Hannemann, Jan, Ehlting, Juergen, El-Kassaby, Yousry A, Mansfield, Shawn D, Douglas, Carl J
• Format: Journal Article
• Language: English
• Published: England New Phytologist Trust 01.11.2013; Wiley Subscription Services, Inc
• Subjects: Algorithms; Bayes Theorem; Bayesian analysis; Cell walls; Chromosome Mapping; Gene Expression; Genes; Genes, Plant; Genetic variability; Genetic variation; Genome, Plant; Genotype; Genotypes; Hierarchies; Lignin; Machine learning; Network analysis; Nucleotides; Phenotype; phenotype prediction; Phenotypes; Phenotypic traits; Plant genetics; Polygenic inheritance; Polymorphism, Single Nucleotide; Populus - genetics; Populus - metabolism; Populus - ultrastructure; Populus trichocarpa; Probability theory; Properties; Proteins; single nucleotide polymorphisms (SNPs); Single-nucleotide polymorphism; T tests; transcriptomics; Ultrastructure; Variability; Wood; Wood - metabolism; Wood - ultrastructure; wood chemistry; wood density; wood properties; phenotype prediction; single nucleotide polymorphisms (SNPs); wood chemistry; wood density; wood properties; transcriptomics; network analysis; Populus trichocarpa
• ISSN: 0028-646X; 1469-8137
• DOI: 10.1111/nph.12419

High-throughput approaches have been widely applied to elucidate the genetic underpinnings of industrially important wood properties. Wood traits are polygenic in nature, but gene hierarchies can be assessed to identify the most important gene variants controlling specific traits within complex networks defining the overall wood phenotype. We tested a large set of genetic, genomic, and phenotypic information in an integrative approach to predict wood properties in Populus trichocarpa. Nine-yr-old natural P. trichocarpa trees including accessions with high contrasts in six traits related to wood chemistry and ultrastructure were profiled for gene expression on 49k Nimblegen (Roche NimbleGen Inc., Madison, WI, USA) array elements and for 28 831 polymorphic single nucleotide polymorphisms (SNPs). Pre-selected transcripts and SNPs with high statistical dependence on phenotypic traits were used in Bayesian network learning procedures with a stepwise K2 algorithm to infer phenotype-centric networks. Transcripts were pre-selected at a much lower logarithm of Bayes factor (logBF) threshold than SNPs and were not accommodated in the networks. Using persistent variables, we constructed cross-validated networks for variability in wood attributes, which contained four to six variables with 94–100% predictive accuracy. Accommodated gene variants revealed the hierarchy in the genetic architecture that underpins substantial phenotypic variability, and represent new tools to support the maximization of response to selection.