Evidence map›Paper›PMID 31747881›Full record

ArticleBMC genomics2019

Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa.

Fernando P Guerra, Haktan Suren, Jason Holliday, James H Richards, Oliver Fiehn, Randi Famula, Brian J Stanton, Richard Shuren, Robert Sykes, Mark F Davis and 1 more

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PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.

0numbers the graph read from it
0cells of the map it votes in
11citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

11 citing papers in PubMed.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Fernando P GuerraDepartment of Plant Sciences, University of California at Davis, 262C Robbins Hall, Mail Stop 4, Davis, CA, 95616, USA.
Haktan SurenDepartment of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
Jason HollidayDepartment of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
James H RichardsDepartment of Land, Air and Water Resources, University of California, Davis, CA, 95616, USA.
Oliver FiehnDepartment of Molecular and Cellular Biology & Genome Center, University of California, Davis, CA, 95616, USA.
Randi FamulaDepartment of Plant Sciences, University of California at Davis, 262C Robbins Hall, Mail Stop 4, Davis, CA, 95616, USA.
Brian J StantonBiological Research Group, GreenWood Resources, Portland, OR, 97201, USA.
Richard ShurenBiological Research Group, GreenWood Resources, Portland, OR, 97201, USA.
Robert SykesNational Renewable Energy Laboratory, Golden, CO, 80401, USA.
Mark F DavisNational Renewable Energy Laboratory, Golden, CO, 80401, USA.
David B NealeDepartment of Plant Sciences, University of California at Davis, 262C Robbins Hall, Mail Stop 4, Davis, CA, 95616, USA. dbneale@ucdavis.edu.

Funding

National Science Foundation Plant Genome Research Program 1054444USDA National Institute of Food and Agriculture 2011-68005-30407
6 · The paper itself

Abstract

backgroundPopulus trichocarpa is an important forest tree species for the generation of lignocellulosic ethanol. Understanding the genomic basis of biomass production and chemical composition of wood is fundamental in supporting genetic improvement programs. Considerable variation has been observed in this species for complex traits related to growth, phenology, ecophysiology and wood chemistry. Those traits are influenced by both polygenic control and environmental effects, and their genome architecture and regulation are only partially understood. Genome wide association studies (GWAS) represent an approach to advance that aim using thousands of single nucleotide polymorphisms (SNPs). Genotyping using exome capture methodologies represent an efficient approach to identify specific functional regions of genomes underlying phenotypic variation.

resultsWe identified 813 K SNPs, which were utilized for genotyping 461 P. trichocarpa clones, representing 101 provenances collected from Oregon and Washington, and established in California. A GWAS performed on 20 traits, considering single SNP-marker tests identified a variable number of significant SNPs (p-value < 6.1479E-8) in association with diameter, height, leaf carbon and nitrogen contents, and δ

conclusionsSNP-markers within genes associated with traits of importance for biomass production were detected. They contribute to characterize the genomic architecture of P. trichocarpa biomass required to support the development and application of marker breeding technologies.

Indexed as

Genome, PlantQuantitative Trait, HeritableCaliforniaCarbonExome SequencingGenetic MarkersGenome-Wide Association StudyLigninMetabolic Networks and PathwaysMetabolomeNitrogenPlant LeavesPolymorphism, Single NucleotidePopulusWoodCarbonGenetic MarkersLigninlignocelluloseNitrogenCelluloseGrowthGWASLigninPopulusSequence captureStable isotopesWood metabolome

Identifiers

PMID31747881
PMCPMC6864938

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.