ORCID Profile
0000-0003-2302-696X
Current Organisation
University of Victoria
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Publisher: Wiley
Date: 29-07-2013
DOI: 10.1111/NPH.12419
Abstract: 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 P opulus 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 N imblegen (Roche NimbleGen Inc., Madison, WI, USA) array elements and for 28 831 polymorphic single nucleotide polymorphisms ( SNP s). Pre‐selected transcripts and SNP s with high statistical dependence on phenotypic traits were used in Bayesian network learning procedures with a stepwise K 2 algorithm to infer phenotype‐centric networks. Transcripts were pre‐selected at a much lower logarithm of B ayes factor (log BF ) threshold than SNP s 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.
Publisher: Wiley
Date: 22-04-2014
DOI: 10.1111/NPH.12815
Abstract: In order to uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions of black cottonwood ( Populus trichocarpa ) from much of its range in western North America. Extensive data from large‐scale trait phenotyping (with spatial and temporal replications within a common garden) and genotyping (with a 34 K Populus single nucleotide polymorphism ( SNP ) array) of all accessions were used for gene discovery in a genome‐wide association study ( GWAS ). We performed GWAS with 40 biomass, ecophysiology and phenology traits and 29 355 filtered SNP s representing 3518 genes. The association analyses were carried out using a Unified Mixed Model accounting for population structure effects among accessions. We uncovered 410 significant SNPs using a Bonferroni‐corrected threshold ( P 1.7 × 10 −6 ). Markers were found across 19 chromosomes, explained 1–13% of trait variation, and implicated 275 unique genes in trait associations. Phenology had the largest number of associated genes (240 genes), followed by biomass (53 genes) and ecophysiology traits (25 genes). The GWAS results propose numerous loci for further investigation. Many traits had significant associations with multiple genes, underscoring their genetic complexity. Genes were also identified with multiple trait associations within and/or across trait categories. In some cases, traits were genetically correlated while in others they were not.
Publisher: Public Library of Science (PLoS)
Date: 23-11-2015
Publisher: Wiley
Date: 11-07-2019
DOI: 10.1111/NPH.15911
Abstract: Occurrence of stomata on both leaf surfaces ( histomaty) promotes higher stomatal conductance and photosynthesis while simultaneously increasing exposure to potential disease agents in black cottonwood (Populus trichocarpa). A genome-wide association study (GWAS) with 2.2M single nucleotide polymorphisms generated through whole-genome sequencing found 280 loci associated with variation in adaxial stomatal traits, implicating genes regulating stomatal development and behavior. Strikingly, numerous loci regulating plant growth and response to biotic and abiotic stresses were also identified. The most significant locus was a poplar homologue of SPEECHLESS (PtSPCH1). In iduals possessing PtSPCH1 alleles associated with greater adaxial stomatal density originated primarily from environments with shorter growing seasons (e.g. northern latitudes, high elevations) or with less precipitation. PtSPCH1 was expressed in developing leaves but not developing stem xylem. In developing leaves, RNA sequencing showed patterns of coordinated expression between PtSPCH1 and other GWAS-identified genes. The breadth of our GWAS results suggests that the evolution of histomaty is part of a larger, complex response in plants. Suites of genes underpin this response, retrieved through genetic association to adaxial stomata, and show coordinated expression during development. We propose that the occurrence of histomaty in P. trichocarpa involves PtSPCH1 and reflects selection for supporting rapid growth over investment in immunity.
Publisher: Wiley
Date: 26-07-2013
DOI: 10.1111/NPH.12422
Abstract: Establishing links between phenotypes and molecular variants is of central importance to accelerate genetic improvement of economically important plant species. Our work represents the first genome‐wide association study to the inherently complex and currently poorly understood genetic architecture of industrially relevant wood traits. Here, we employed an Illumina Infinium 34 K single nucleotide polymorphism ( SNP ) genotyping array that generated 29 233 high‐quality SNP s in c . 3500 broad‐based candidate genes within a population of 334 unrelated P opulus trichocarpa in iduals to establish genome‐wide associations. The analysis revealed 141 significant SNP s ( α ≤ 0.05) associated with 16 wood chemistry/ultrastructure traits, in idually explaining 3–7% of the phenotypic variance. A large set of associations (41% of all hits) occurred in candidate genes preselected for their suggested a priori involvement with secondary growth. For ex le, an allelic variant in the FRA 8 ortholog explained 21% of the total genetic variance in fiber length, when the trait's heritability estimate was considered. The remaining associations identified SNP s in genes not previously implicated in wood or secondary wall formation. Our findings provide unique insights into wood trait architecture and support efforts for population improvement based on desirable allelic variants.
No related grants have been discovered for Jürgen Ehlting.