title: 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.
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.
authors.affiliation: The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, United Kingdom.
authors.forename: Kelly
authors.initials: K
authors.lastname: Houston
authors.affiliation: ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food & Wine, The University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia.
authors.forename: Rachel A
authors.initials: RA
authors.lastname: Burton
authors.affiliation: Australian Centre for Plant Functional Genomics, The University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia.
authors.forename: Beata
authors.initials: B
authors.lastname: Sznajder
authors.affiliation: Genetic Discovery Group, DuPont Agricultural Biotechnology, DuPont Pioneer, DuPont Experimental Station, Building E353, Wilmington, DE, 19803, United States of America.
authors.forename: Antoni J
authors.initials: AJ
authors.lastname: Rafalski
authors.affiliation: Genetic Discovery Group, DuPont Agricultural Biotechnology, DuPont Pioneer, 7300 NW 62nd Avenue, Johnston, IA, 50131, United States of America.
authors.forename: Kanwarpal S
authors.initials: KS
authors.lastname: Dhugga
authors.affiliation: Australian Centre for Plant Functional Genomics, The University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia.
authors.forename: Diane E
authors.initials: DE
authors.lastname: Mather
authors.affiliation: ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food & Wine, The University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia.
authors.forename: Jillian
authors.initials: J
authors.lastname: Taylor
authors.affiliation: Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, United States of America.
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Steffenson
authors.affiliation: The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, United Kingdom; Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Scotland, Dundee, DD2 5DA, United Kingdom.
authors.forename: Robbie
authors.initials: R
authors.lastname: Waugh
authors.affiliation: ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food & Wine, The University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia.
authors.forename: Geoffrey B
authors.initials: GB
authors.lastname: Fincher
mesh_terms: D000383:Agriculture; D002473:Cell Wall / Q000378:metabolism; D002482:Cellulose / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D005819:Genetic Markers; D005828:Genetics, Population; D055106:Genome-Wide Association Study; D005838:Genotype; D005964:Glucosyltransferases / Q000235:genetics* / Q000378:metabolism*; D006026:Glycoside Hydrolases / Q000378:metabolism; D001467:Hordeum / Q000235:genetics*; D015810:Linkage Disequilibrium; D005810:Multigene Family; D010641:Phenotype; D040641:Quantitative Trait Loci; D017423:Sequence Analysis, RNA; D014481:United States
chemical_list: D005819:Genetic Markers; D002482:Cellulose; D005964:Glucosyltransferases; C478648:cellulose synthase; D006026:Glycoside Hydrolases