From d029d5d7f8ead1f1de8d318045004a4a6f68f5fb Mon Sep 17 00:00:00 2001
From: Bonface
Date: Fri, 9 Feb 2024 09:41:28 -0600
Subject: Update dataset RTF Files.
---
general/datasets/PoplarPublish/acknowledgment.rtf | 1 +
general/datasets/PoplarPublish/platform.rtf | 1 +
general/datasets/PoplarPublish/processing.rtf | 1 +
general/datasets/PoplarPublish/summary.rtf | 8 ++++++++
4 files changed, 11 insertions(+)
create mode 100644 general/datasets/PoplarPublish/acknowledgment.rtf
create mode 100644 general/datasets/PoplarPublish/platform.rtf
create mode 100644 general/datasets/PoplarPublish/processing.rtf
create mode 100644 general/datasets/PoplarPublish/summary.rtf
(limited to 'general/datasets/PoplarPublish')
diff --git a/general/datasets/PoplarPublish/acknowledgment.rtf b/general/datasets/PoplarPublish/acknowledgment.rtf
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index 0000000..b137fef
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+++ b/general/datasets/PoplarPublish/acknowledgment.rtf
@@ -0,0 +1 @@
+We thank L. E. Gunter, M. S. Azam, E. Drewes, N. Farzaneh, L. Liao, E. Moreno, L. Muenter and L. Quamme for data monitoring, collection and image presentation. We also thank anonymous reviewers for their suggestions and revisions in improving the manuscript. This work was supported by the Genome British Columbia Applied Genomics Innovation Program (Project 103BIO) and Genome Canada Large-Scale Applied Research Project (Project 168BIO) funds to R.D.G., J.E., Q.C.B.C., Y.A.E-K., S.D.M. and C.J.D. and by funds within the BioEnergy Science Center, a US Department of Energy Bioenergy Research Facility under contract DE–AC05–00OR22725.
diff --git a/general/datasets/PoplarPublish/platform.rtf b/general/datasets/PoplarPublish/platform.rtf
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+++ b/general/datasets/PoplarPublish/platform.rtf
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+Illumina iSelect Infinium 34K Populus SNP genotyping array
diff --git a/general/datasets/PoplarPublish/processing.rtf b/general/datasets/PoplarPublish/processing.rtf
new file mode 100644
index 0000000..9a6b788
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+++ b/general/datasets/PoplarPublish/processing.rtf
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+http://bioenergycenter.org/besc/gwas/
diff --git a/general/datasets/PoplarPublish/summary.rtf b/general/datasets/PoplarPublish/summary.rtf
new file mode 100644
index 0000000..ab9c38a
--- /dev/null
+++ b/general/datasets/PoplarPublish/summary.rtf
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+Full article available here.
+
+
+ - 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 SNPs 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<1.79106). 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.
+
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