A genome-wide association study for culm cellulose content in barley reveals candidate genes co-expressed with members of the Cellulose synthase A gene family

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dc.contributor.authorHouston, K.
dc.contributor.authorBurton, R.
dc.contributor.authorSznajder, B.
dc.contributor.authorRafalski, A.
dc.contributor.authorDhugga, K.
dc.contributor.authorMather, D.
dc.contributor.authorTaylor, J.
dc.contributor.authorSteffenson, B.
dc.contributor.authorWaugh, R.
dc.contributor.authorFincher, G.
dc.contributor.editorZabotina, O.
dc.date.issued2015
dc.description.abstractCellulose is a fundamentally important component of cell walls of higher plants. It provides a scaffold that allows the development and growth of the plant to occur in an ordered fashion. Cellulose also provides mechanical strength, which is crucial for both normal development and to enable the plant to withstand both abiotic and biotic stresses. We quantified the cellulose concentration in the culm of 288 two--rowed and 288 six--rowed spring type barley accessions that were part of the USDA funded barley Coordinated Agricultural Project (CAP) program in the USA. When the population structure of these accessions was analysed we identified six distinct populations, four of which we considered to be comprised of a sufficient number of accessions to be suitable for genome-wide association studies (GWAS). These lines had been genotyped with 3072 SNPs so we combined the trait and genetic data to carry out GWAS. The analysis allowed us to identify regions of the genome containing significant associations between molecular markers and cellulose concentration data, including one region cross-validated in multiple populations. To identify candidate genes we assembled the gene content of these regions and used these to query a comprehensive RNA-seq based gene expression atlas. This provided us with gene annotations and associated expression data across multiple tissues, which allowed us to formulate a supported list of candidate genes that regulate cellulose biosynthesis. Several regions identified by our analysis contain genes that are co-expressed with cellulose synthase A (HvCesA) across a range of tissues and developmental stages. These genes are involved in both primary and secondary cell wall development. In addition, genes that have been previously linked with cellulose synthesis by biochemical methods, such as HvCOBRA, a gene of unknown function, were also associated with cellulose levels in the association panel. Our analyses provide new insights into the genes that contribute to cellulose content in cereal culms and to a greater understanding of the interactions between them.
dc.description.statementofresponsibilityKelly Houston, Rachel A. Burton, Beata Sznajder, Antoni J. Rafalski, Kanwarpal S. Dhugga, Diane E. Mather, Jillian Taylor, Brian J. Steffenson, Robbie Waugh, Geoffrey B. Fincher
dc.identifier.citationPLoS ONE, 2015; 10(7):e0130890-1-e0130890-21
dc.identifier.doi10.1371/journal.pone.0130890
dc.identifier.issn1932-6203
dc.identifier.issn1932-6203
dc.identifier.orcidBurton, R. [0000-0002-0638-4709]
dc.identifier.orcidSznajder, B. [0009-0007-6048-2506]
dc.identifier.orcidMather, D. [0000-0001-7506-2589]
dc.identifier.urihttp://hdl.handle.net/2440/94874
dc.language.isoen
dc.publisherPublic Library of Science
dc.relation.grantARC
dc.rights© 2015 Houston et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
dc.source.urihttps://doi.org/10.1371/journal.pone.0130890
dc.subjectCell Wall
dc.subjectHordeum
dc.subjectCellulose
dc.subjectGlycoside Hydrolases
dc.subjectGlucosyltransferases
dc.subjectGenetic Markers
dc.subjectSequence Analysis, RNA
dc.subjectGenetics, Population
dc.subjectGene Expression Regulation, Plant
dc.subjectGenotype
dc.subjectLinkage Disequilibrium
dc.subjectPhenotype
dc.subjectGenes, Plant
dc.subjectMultigene Family
dc.subjectQuantitative Trait Loci
dc.subjectAgriculture
dc.subjectUnited States
dc.subjectGenome-Wide Association Study
dc.titleA genome-wide association study for culm cellulose content in barley reveals candidate genes co-expressed with members of the Cellulose synthase A gene family
dc.typeJournal article
pubs.publication-statusPublished

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