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

Kelly Houston (Lead / Corresponding author), Rachel A. Burton, Beata Sznajder, Antoni J. Rafalski, Kanwarpal S. Dhugga, Diane E. Mather, Jillian Taylor, Brian J. Steffenson, Robbie Waugh, Geoffrey B. Fincher

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

Cellulose 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.

Original languageEnglish
Article numbere0130890
Number of pages21
JournalPLoS ONE
Volume10
Issue number7
DOIs
Publication statusPublished - 8 Jul 2015

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cellulose synthase
Genome-Wide Association Study
Hordeum
Cellulose
cellulose
Genes
barley
genes
Cell Wall
Association reactions
Population
Molecular Sequence Annotation
United States Department of Agriculture
Plant Development
genome-wide association study
Atlases
Growth and Development
Cells
cell wall components
Tissue

Cite this

Houston, Kelly ; Burton, Rachel A. ; Sznajder, Beata ; Rafalski, Antoni J. ; Dhugga, Kanwarpal S. ; Mather, Diane E. ; Taylor, Jillian ; Steffenson, Brian J. ; Waugh, Robbie ; Fincher, Geoffrey B. / 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. In: PLoS ONE. 2015 ; Vol. 10, No. 7.
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abstract = "Cellulose 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.",
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Houston, K, Burton, RA, Sznajder, B, Rafalski, AJ, Dhugga, KS, Mather, DE, Taylor, J, Steffenson, BJ, Waugh, R & Fincher, GB 2015, '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', PLoS ONE, vol. 10, no. 7, e0130890. https://doi.org/10.1371/journal.pone.0130890

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. / Houston, Kelly (Lead / Corresponding author); Burton, Rachel A.; Sznajder, Beata; Rafalski, Antoni J.; Dhugga, Kanwarpal S.; Mather, Diane E.; Taylor, Jillian; Steffenson, Brian J.; Waugh, Robbie; Fincher, Geoffrey B.

In: PLoS ONE, Vol. 10, No. 7, e0130890, 08.07.2015.

Research output: Contribution to journalArticle

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T1 - 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

AU - Houston, Kelly

AU - Burton, Rachel A.

AU - Sznajder, Beata

AU - Rafalski, Antoni J.

AU - Dhugga, Kanwarpal S.

AU - Mather, Diane E.

AU - Taylor, Jillian

AU - Steffenson, Brian J.

AU - Waugh, Robbie

AU - Fincher, Geoffrey B.

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