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

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dc.contributor.authorGuerra, Fernando P.en
dc.contributor.authorSuren, Haktanen
dc.contributor.authorHolliday, Jason A.en
dc.contributor.authorRichards, James H.en
dc.contributor.authorFiehn, Oliveren
dc.contributor.authorFamula, Randien
dc.contributor.authorStanton, Brian J.en
dc.contributor.authorShuren, Richarden
dc.contributor.authorSykes, Roberten
dc.contributor.authorDavis, Mark F.en
dc.contributor.authorNeale, David B.en
dc.contributor.departmentForest Resources and Environmental Conservationen
dc.date.accessioned2019-12-16T13:49:28Zen
dc.date.available2019-12-16T13:49:28Zen
dc.date.issued2019-11-20en
dc.date.updated2019-11-24T05:18:52Zen
dc.description.abstractBackground Populus 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. Results We 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 δ15N. The number of significant SNPs ranged from 2 to 220 per trait. Additionally, multiple-marker analyses by sliding-windows tests detected between 6 and 192 significant windows for the analyzed traits. The significant SNPs resided within genes that encode proteins belonging to different functional classes as such protein synthesis, energy/metabolism and DNA/RNA metabolism, among others. Conclusions SNP-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.en
dc.description.versionPublished versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationBMC Genomics. 2019 Nov 20;20(1):875en
dc.identifier.doihttps://doi.org/10.1186/s12864-019-6160-9en
dc.identifier.urihttp://hdl.handle.net/10919/95989en
dc.language.isoenen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.holderThe Author(s)en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.titleExome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpaen
dc.title.serialBMC Genomicsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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