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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 K, Burton RA, Sznajder B, Rafalski AJ, Dhugga KS, Mather DE, Taylor J, Steffenson BJ, Waugh R, Fincher GB - PLoS ONE (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, United Kingdom.

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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Related in: MedlinePlus

Manhattan plots of culm cellulose content (mg cellulose / mg dry weight) genome wide association scans (GWAS) using the Kinship relationship model.The-log10 (p-values) from a genome-wide scan are plotted against the position on each of the 7 barley chromosomes. Manhattan plots are displayed for those populations which had associations that passed the significance threshold set by FDR p > 0.05 (-log10P >3.0), i.e. populations 3 and 5. Manhattan plots of the  models are provided for comparison. (A) Population 3 Kinship model. (B) Population 5 Kinship model. (C) Population 3 Null model. (D) Population 5 Null model.
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pone.0130890.g003: Manhattan plots of culm cellulose content (mg cellulose / mg dry weight) genome wide association scans (GWAS) using the Kinship relationship model.The-log10 (p-values) from a genome-wide scan are plotted against the position on each of the 7 barley chromosomes. Manhattan plots are displayed for those populations which had associations that passed the significance threshold set by FDR p > 0.05 (-log10P >3.0), i.e. populations 3 and 5. Manhattan plots of the models are provided for comparison. (A) Population 3 Kinship model. (B) Population 5 Kinship model. (C) Population 3 Null model. (D) Population 5 Null model.

Mentions: GWAS on each of the four largest subpopulations individually (subpopulations 2, 3, 4 and 5), detected nine regions containing significant associations (using a FDR corrected adjusted p value of −log10 p ≥3.0 with adjusted p≤0.05) with cellulose concentration (Table 3, S4 Table, Fig 3). Significant associations were detected in the two two-rowed subpopulations (subpopulations 3 and 5) but not in the two six-rowed subpopulations (subpopulations 2 and 4). The largest subpopulation, subpopulation 5, was the germplasm in which we detected most associations, and several had adjusted p values of p≤0.001 (−log10 p ≥5.69) (Table 3,S4 Table). A further significant association was identified in subpopulation 3. GWAS was not carried out on populations one and six due to the small number of individuals in each. When considering the PCoA (Fig 1) it is quite clear that the two rowed subpopulations, subpopulations 3 (dominated by N2), and 5 (mostly consisting of WA and MT) are almost as distinct from each other as they are from the six rowed subpopulations 2 and 4.


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 K, Burton RA, Sznajder B, Rafalski AJ, Dhugga KS, Mather DE, Taylor J, Steffenson BJ, Waugh R, Fincher GB - PLoS ONE (2015)

Manhattan plots of culm cellulose content (mg cellulose / mg dry weight) genome wide association scans (GWAS) using the Kinship relationship model.The-log10 (p-values) from a genome-wide scan are plotted against the position on each of the 7 barley chromosomes. Manhattan plots are displayed for those populations which had associations that passed the significance threshold set by FDR p > 0.05 (-log10P >3.0), i.e. populations 3 and 5. Manhattan plots of the  models are provided for comparison. (A) Population 3 Kinship model. (B) Population 5 Kinship model. (C) Population 3 Null model. (D) Population 5 Null model.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4496100&req=5

pone.0130890.g003: Manhattan plots of culm cellulose content (mg cellulose / mg dry weight) genome wide association scans (GWAS) using the Kinship relationship model.The-log10 (p-values) from a genome-wide scan are plotted against the position on each of the 7 barley chromosomes. Manhattan plots are displayed for those populations which had associations that passed the significance threshold set by FDR p > 0.05 (-log10P >3.0), i.e. populations 3 and 5. Manhattan plots of the models are provided for comparison. (A) Population 3 Kinship model. (B) Population 5 Kinship model. (C) Population 3 Null model. (D) Population 5 Null model.
Mentions: GWAS on each of the four largest subpopulations individually (subpopulations 2, 3, 4 and 5), detected nine regions containing significant associations (using a FDR corrected adjusted p value of −log10 p ≥3.0 with adjusted p≤0.05) with cellulose concentration (Table 3, S4 Table, Fig 3). Significant associations were detected in the two two-rowed subpopulations (subpopulations 3 and 5) but not in the two six-rowed subpopulations (subpopulations 2 and 4). The largest subpopulation, subpopulation 5, was the germplasm in which we detected most associations, and several had adjusted p values of p≤0.001 (−log10 p ≥5.69) (Table 3,S4 Table). A further significant association was identified in subpopulation 3. GWAS was not carried out on populations one and six due to the small number of individuals in each. When considering the PCoA (Fig 1) it is quite clear that the two rowed subpopulations, subpopulations 3 (dominated by N2), and 5 (mostly consisting of WA and MT) are almost as distinct from each other as they are from the six rowed subpopulations 2 and 4.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, United Kingdom.

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.

No MeSH data available.


Related in: MedlinePlus