- Populus trichocarpa. - A GWAS performed on 20 traits, considering single SNP-marker tests identified a variable number of significant SNPs (p-value <. - The number of significant SNPs ranged from 2 to 220 per trait. - 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - Full list of author information is available at the end of the article. - Different ap- proaches (candidate gene or GWAS) as well as genotyping platforms have been used, with single SNP- markers accounting for, in general, a low percentage of the phenotypic variation (1–8%) in studied traits. - In the present study, we employ sequence capture for genotyping and performing a GWAS in a P. - trichocarpa population of 461 clones from 101 provenances collected from the Pacific Northwest (Oregon and Washington) in the United States. - The association population was generated with germplasm collected from the southern part of the P. - This approach complements our previous phenotypic characterization of the same association population [5] by identifying SNPs underlying traits of growth, ecophysiology and wood quality, the primary traits targeted for the develop- ment of genetically improved clones suitable for dedi- cated biomass and bioenergy plantations. - The association population used in this study con- sisted of 461 clones (from 101 provenances), comprising part of the natural distribution range of P. - trichocarpa in the Pacific Northwest of the United States. - with high heritability should reveal a large number of significant SNP-markers.. - trichocarpa genome in the association population, and after filtering, a set of 813,280 SNPs was used for association analyses (Table 2). - The number of selected SNPs was propor- tional to chromosome size, ranging from 29,287 to 100, 299 SNPs, for chromosomes 9 and 1, respectively (Table 2, Fig. - Taking advantage of the full gen- ome assembly, genotyping methodologies such as those based on sequence capture can target entire exons or genes across the genome, avoiding bias arising by a priori selection of candidate loci [23, 25]. - In comparison to similar preceding studies that used SNP array plat- forms the number of SNPs in our ana- lyses represent an increase in the power of applied genomic scanning. - The estimated extent of LD decay predicted in our study is higher than the observed by Wegrzyn et al. - [18] (r 2 0.2 at ~ 0.5 kbp) and Wang et al .[28] (r 2 0.2 at ~ 8 kbp) for P. - Distinct methodolo- gies, number of markers, population sizes, genetic ori- gins and standard errors among the studies may account for the different findings. - Fig- ure 2a and c depicts the number of associations detected per chromosome for a selected set of traits. - A detailed Table 1 Summary statistics for traits studied in the Populus trichocarpa association population. - H 2 c ” were extracted from Guerra et al. - The lowest number of associations was observed for chromosome 16. - The pro- portion of significant SNPs of the total analyzed, ranged from 0.02 ‰ to 0.50 ‰ for leaf C content on chromo- some 10, along with δ 15 N on chromosomes 6 and 10, and leaf N content on chromosome 5 (Additional file 1:. - In the case of growth traits, 2 and 148 associations were detected for DBH and h, re- spectively. - Similarly, in the case of wood metabolites, considering a selected subset of those with the top five highest heritability estimates, no significant associations meeting the adjusted p-value were identified for Adeno- sine (Ade), Hydroxybenzoic Acid (HbA), Galactinol (Gal), Galactonic Acid (GAc) and Alpha tocopherol (Toc). - For genes in the Energy/Metabolism functional class, a representative was one (Potri.015G119700) encoding a Domain of unknown func- tion (PGG), which was associated with DBH. - leaf C-content and δ 15 N) a relatively higher number of SNPs were identified. - of multiple SNPs associated with phenotypes is particu- larly interesting in the context of the development of models for genomic selection, where large numbers of markers are utilized to predict the genetic merit of indi- viduals [32]. - Differences among traits in terms of the number of significant SNP-markers suggest the differen- tial effect of both the variable number of SNPs influen- cing each trait and the individual impact of some SNPs.. - Finally, another factor influencing the number of significant as- sociated SNPs (and their effect on phenotypes) deals with the complexity of analyzing thousands of single. - 2 Number of significant single-SNPs (left) and sliding windows (right) associated with a selected set of traits for growth (a), stable isotopes parameters (c), chemical components of wood (b) and selected metabolites (c). - For example, it has been sug- gested that the general applicability of the traditional false discovery ratio (FDR) [34] may suffer from several problems when applied to association analysis of a single trait [35]. - A variable number of windows per chromosome were detected among the phenotypes (Fig. - The total number of significant windows ranged from 6 for HbA, to 192 for N content (Additional file 1: Table. - However, for traits such as DBF, C:N, δ 15 N, and Toc, the most relevant chromosomes in terms of the number of significant win- dows included to 6, 4, 5 and 10, respectively. - Some of the detected genes en- coding proteins with roles in Protein Synthesis/Modification were those expressing Similar to Threonyl-tRNA Synthetase (Potri.008G145600), Interleukin-1 Receptor-Associated Kin- ase 4 (Potri.008G145900) and Leucine Rich Repeat (LRR1) (Potri.005G015700) associated with wood C5-sugars, C6- sugars and height, respectively. - An example of the genes dealing with proteins belonging to the Energy/Metabolism class were Exostosin Heparan Sulfate Glycosyltransferase- Related (Potri.010G197900) and Similar to Aldehyde De- hydrogenase 1 Precursor (Potri.012G078700), associated with δ 15 N and DBF, respectively. - Mutation of members of the XNR gene family produced sensitivity to N starva- tion in Saccharomyces cerevisiae [44] and morphological alterations in Arabidopsis thaliana [45, 46]. - Thus, asso- ciation of XRN4 with leaf δ 15 N, an indicator of N use ef- ficiency [47], could be related to the N metabolism and mobilization at leaves, particularly during the last third of the growing season, when sampling was done. - Association analyses of the chemical composition of P.. - trichocarpa wood was previously performed in the same population by our group [18] using a candidate gene ap- proach. - We carried out a comparison between the re- sults from both studies considering the 40 candidate genes utilized by Wegrzyn et al. - Association results in the present study were significant only under a p-value <. - For this trait, we also de- tected SNPs in TUA5 gene, which were not identified by Wegrzyn et al. - In the case of lignin content, mem- bers of the cellulose synthase gene family (CesA2B and CesA1A) were differentially detected (differentially) in both studies. - Finally, for the S:G ratio, our analyses detected SNPs in Laccase LAC1A, Phenylalanine Ammonia-Lyase PAL5 genes, which were not identified by Wegrzyn et al. - In spite of the genotypes and wood chemical characterization methods were mostly the same in both studies, distinct trial sites (the first in Westport, Oregon, and the second in Davis, California), sampling height or differential presence of juvenile wood, among other fac- tors, might explain the differences in the findings re- ported previously [18] and those described in the present work.. - At the same time, the genome-wide scale applied for the association analyses re- vealed a large number of SNPs which could be utilized to develop genomic selection schemes. - The upshot will be the estimation of paren- tal hybridization values and an earlier, more precise genotypic selection from segregating F1 hybrid populations, that together will increase the overall magnitude of the real- ized genetic gain per unit of time.. - These represented 101 prove- nances, within 14 river systems located west of the. - Blocks were considered to control a north–south variation in the trial, associated with non-homogenous soil condi- tions. - The clonal trial was already characterized by Guerra et al. - A brief description about their measurements is indicated in the following subsections.. - 5 Venn diagrams for the comparison between the present study (blue circles) and the one carried out by Wegrzyn et al .[18] (green circles).. - Numbers in circles indicate the number of genes containing significant SNPs (p <. - the genetic cluster, clone within cluster, cluster x block and residual, respectively, and σ 2 ee’ is the covariance be- tween residuals of the same clone in two blocks.. - Data used in the phenotypic characterization is avail- able at the TreeGenes platform (http://dendrome.ucda- vis.edu/treegenes/) under the accession number TGDR050.. - at age two, were measured in October 2010, as described by Guerra et al. - These corre- sponded to those with the highest estimates of heritabil- ities according to Guerra et al. - Additionally, a complimentary second subset of leaves, collected in August 2012, was utilized for measuring leaf area and dry biomass to estimate the specific leaf area (SLA) and N content per SLA ratio (NArea), according to Easlon et al. - trichocarpa (corresponding to assembly version 2.0 of the black cottonwood genome) were used to de- sign oligonucleotide baits, complementary to short gen- omic regions that targeted exons, promoter, and intergenic control regions, as described by Zhou et al.. - The baits targeted more than 39,000 of the 40,668 annotated protein-coding transcripts of the P. - As the cumula- tive length of the predicted exons exceeded the available baits, following bait design in eArray, we looped through the gene list, selecting one bait for each gene at each pass, until the maximum number of baits (i.e. - Sequences of the prepared libraries are available at the Sequence Read Archive (http://www.. - The distributions of the different traits were checked for departures from normality. - Clonal means were adjusted by Best Linear Unbiased Predictor, using Proc MIXED in the software SAS v9.2 (SAS Institute, Cary, NC, USA), in order to correct a significant block effect observed across the trial area. - As- sociations were adjusted for multiple testing, using the Bonferroni correction, in the package Stats in R [58].. - We set the number of trees (ntree) grown as 2000 and averaged 50 repeats per trait in our estimates.. - Multiple-SNP testing for each trait was carried out using an overlapping sliding-window analysis on associ- ation results, based on the number of the significant as- sociations (p-value <. - To this end, Poisson tests were carried out by comparing the rate of total sig- nificant SNPs and the total number of SNPs with the similar rate for the tested window using the probability formula below.. - Where lambda ( ℷ ) is the average number of significant SNPs, e is the constant Euler ’ s number and k is the aver- age number of significant SNPs for the window being tested. - Empirical p-values were recorded for each win- dow per trait and then were adjusted by Bonferroni (0.05/number of tested windows) and reported for each trait. - It was expressed in terms of the squared correlation of allele frequencies r 2 . - Additional file 1: Table S1. - a Number of significant single SNP-markers.. - Additional file 2: Table S5. - We would like to thank the California Agricultural Experiment Station for the provided support and two anonymous reviewers for their helpful comments on earlier version of the manuscript.. - Sequences of the prepared libraries for exome capture are available at the Sequence Read Archive (http://www.ncbi.nlm.nih.gov/Traces/sra/) under the accession number SRA058855. - Data used in the phenotypic characterization is available at the TreeGenes platform (http://dendrome.ucdavis.edu/. - 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