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Summary: Occurrence of stomata on both leaf surfaces (amphistomaty) 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). Individuals 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 amphistomaty 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 amphistomaty in P. trichocarpa involves PtSPCH1 and reflects selection for supporting rapid growth over investment in immunity. [ABSTRACT FROM AUTHOR]

Summary: Spring bud‐break phenology is a critical adaptive feature common to temperate perennial woody plants. Understanding the molecular underpinnings of variation in bud‐break is important for elucidating adaptive evolution and predicting outcomes relating to climate change. Field and controlled growth chamber tests were used to assess population‐wide patterns in bud‐break from wild‐sourced black cottonwood (Populus trichocarpa) genotypes. We conducted a genome‐wide association study (GWAS) with single nucleotide polymorphisms (SNPs) derived from whole genome sequencing to test for loci underlying variation in bud‐break. Bud‐break had a quadratic relationship with latitude, where southern‐ and northern‐most provenances generally broke bud earlier than those from central parts of the species’ range. Reduced winter chilling increased population‐wide variation in bud‐break, whereas greater chilling decreased variation. GWAS uncovered 16 loci associated with bud‐break. Phenotypic changes connected with allelic variation were replicated in an independent set of P. trichocarpa trees. Despite phenotypic similarities, genetic profiles between southern‐ and northern‐most genotypes were dissimilar based on our GWAS‐identified SNPs. We propose that the GWAS‐identified loci underpin the geographical pattern in P. trichocarpa and that variation in bud‐break reflects different selection for winter chilling and heat sum accumulation, both of which can be affected by climate warming. [ABSTRACT FROM AUTHOR]

Populus trichocarpa is widespread across western North America spanning extensive variation in photoperiod, growing season and climate. We investigated trait variation in P. trichocarpa using over 2000 trees from a common garden at Vancouver, Canada, representing replicate plantings of 461 genotypes originating from 136 provenance localities., We measured 40 traits encompassing phenological events, biomass accumulation, growth rates, and leaf, isotope and gas exchange-based ecophysiology traits. With replicated plantings and 29 354 single nucleotide polymorphisms ( SNPs) from 3518 genes, we estimated both broad-sense trait heritability ( H2) and overall population genetic structure from principal component analysis., Populus trichocarpa had high phenotypic variation and moderate/high H2 for many traits. H2 ranged from 0.3 to 0.9 in phenology, 0.3 to 0.8 in biomass and 0.1 to 0.8 in ecophysiology traits. Most traits correlated strongly with latitude, maximum daylength and temperature of tree origin, but not necessarily with elevation, precipitation or heat : moisture indices. Trait H2 values reflected trait correlation strength with geoclimate variables. The population genetic structure had one significant principal component ( PC1) which correlated with daylength and showed enrichment for genes relating to circadian rhythm and photoperiod., Robust relationships between traits, population structure and geoclimate in P. trichocarpa reflect patterns which suggest that range-wide geographical and environment gradients have shaped its genotypic and phenotypic variability. [ABSTRACT FROM AUTHOR]

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 (log BF) 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. [ABSTRACT FROM AUTHOR]

The increasing ecological and economical importance of Populus species and hybrids has stimulated research into the investigation of the natural variation of the species and the estimation of the extent of genetic control over its wood quality traits for traditional forestry activities as well as the emerging bioenergy sector. A realized kinship matrix based on informative, high-density, biallelic single nucleotide polymorphism ( SNP) genetic markers was constructed to estimate trait variance components, heritabilities, and genetic and phenotypic correlations., Seventeen traits related to wood chemistry and ultrastructure were examined in 334 9-yr-old Populus trichocarpa grown in a common-garden plot representing populations spanning the latitudinal range 44° to 58.6°. In these individuals, 9342 SNPs that conformed to Hardy- Weinberg expectations were employed to assess the genomic pair-wise kinship to estimate narrow-sense heritabilities and genetic correlations among traits., The range-wide phenotypic variation in all traits was substantial and several trait heritabilities were > 0.6. In total, 61 significant genetic and phenotypic correlations and a network of highly interrelated traits were identified., The high trait variation, the evidence for moderate to high heritabilities and the identification of advantageous trait combinations of industrially important characteristics should aid in providing the foundation for the enhancement of poplar tree breeding strategies for modern industrial use. [ABSTRACT FROM AUTHOR]