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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.

No MeSH data available.


Related in: MedlinePlus

Co-expression of two groups of genes (HvCesA9, HvCobra1, HvCslF6, and HvChitinase, HvGT1) identified by GWAS as putatively linked to culm cellulose content with HvCesA genes known to be involved in primary and secondary cell wall development.Transcript abundance across a range of tissues shown in fragment per kilobase of exon per million fragments mapped (FPKM) for group 1, primary cell wall including HvCesA1, HvCesA2, and HvCesA6 (A) for reference, and group 2, secondary cell wall including HvCesA4, HvCesA7 and HvCesA8 for reference (B). Abbreviations for tissues/ developmental stages as follows; EMB = Embryo tissues (germinating), ROO = Root (10cm seedlings), LEA = Shoot (10cm seedlings), INF1 = Inflorescence (0.5cm), INF2 = Inflorescence (1–1.5cm), NOD = Tillers (3rd internode), CAR5 = Grain (5 Days Post Anthesis—DPA), CAR15 = Grain (15 DPA), ETI = Etiolated (10 day seedlings), LEM = Lemma (6 weeks Days After Planting—DAP), LOD = Lodicule (42 DAP), PAL = Palea (42 DAP), EPI = Epidermis (28 DAP), RAC = Rachis (35 DAP), ROO2 = Root (28 DAP seedling), SEN = Senescing leaf (63 DAP).
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pone.0130890.g004: Co-expression of two groups of genes (HvCesA9, HvCobra1, HvCslF6, and HvChitinase, HvGT1) identified by GWAS as putatively linked to culm cellulose content with HvCesA genes known to be involved in primary and secondary cell wall development.Transcript abundance across a range of tissues shown in fragment per kilobase of exon per million fragments mapped (FPKM) for group 1, primary cell wall including HvCesA1, HvCesA2, and HvCesA6 (A) for reference, and group 2, secondary cell wall including HvCesA4, HvCesA7 and HvCesA8 for reference (B). Abbreviations for tissues/ developmental stages as follows; EMB = Embryo tissues (germinating), ROO = Root (10cm seedlings), LEA = Shoot (10cm seedlings), INF1 = Inflorescence (0.5cm), INF2 = Inflorescence (1–1.5cm), NOD = Tillers (3rd internode), CAR5 = Grain (5 Days Post Anthesis—DPA), CAR15 = Grain (15 DPA), ETI = Etiolated (10 day seedlings), LEM = Lemma (6 weeks Days After Planting—DAP), LOD = Lodicule (42 DAP), PAL = Palea (42 DAP), EPI = Epidermis (28 DAP), RAC = Rachis (35 DAP), ROO2 = Root (28 DAP seedling), SEN = Senescing leaf (63 DAP).

Mentions: We were interested to see if any of the candidate genes from the GWAS were co-expressed, as this could provide further evidence for their being responsible for the association peaks identified. This is particularly relevant for understanding variation in cellulose content, because the synthesis of cellulose is likely to involve a number of co-factors and interacting proteins. The co-expression analysis allowed us to prioritise genes on our list of potential candidates in Table 3. We extended the number of tissues and developmental stages for which we compared candidate gene expression to sixteen (our unpublished data). When we considered the data for the 14 candidate genes from the nine regions highlighted in Table 3, we observed that five could be classified into two groups of co-expressed genes, groups 1 and 2, which are strongly co-expressed based on pairwise regression analysis between each gene across these 16 tissues with members of the CesA gene family (Fig 4). The output from the regression analysis can be found in S5 Table. Group 1 genes comprised HvCobra1, HvCslF6, and HvCesA9 (a close ortholog /paralog of HvCesA6), and formed a co-expression complex across the 16 different tissues with HvCesA1, HvCesA2, and HvCesA6, genes previously implicated in primary cell wall cellulose biosynthesis [9]. Group 2 genes, HvChitinase and HvUDP-glucosyltransferase (HvGT), were co-expressed with genes important for secondary cell wall development, namely HvCesA4, HvCesA7, and HvCesA8. Where possible we compared the coexpression of the rice orthologs of these genes, however there was no ortholog of HvCslF9 or HvChitinase1. Across both species we observed that genes in group 1 showed a higher and more significant degree of coexpression than those in group 2, with the expression of the candidate genes in barley showing a higher correlation to the known primary and secondary cell wall genes than their rice orthologs (S5 Table).


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)

Co-expression of two groups of genes (HvCesA9, HvCobra1, HvCslF6, and HvChitinase, HvGT1) identified by GWAS as putatively linked to culm cellulose content with HvCesA genes known to be involved in primary and secondary cell wall development.Transcript abundance across a range of tissues shown in fragment per kilobase of exon per million fragments mapped (FPKM) for group 1, primary cell wall including HvCesA1, HvCesA2, and HvCesA6 (A) for reference, and group 2, secondary cell wall including HvCesA4, HvCesA7 and HvCesA8 for reference (B). Abbreviations for tissues/ developmental stages as follows; EMB = Embryo tissues (germinating), ROO = Root (10cm seedlings), LEA = Shoot (10cm seedlings), INF1 = Inflorescence (0.5cm), INF2 = Inflorescence (1–1.5cm), NOD = Tillers (3rd internode), CAR5 = Grain (5 Days Post Anthesis—DPA), CAR15 = Grain (15 DPA), ETI = Etiolated (10 day seedlings), LEM = Lemma (6 weeks Days After Planting—DAP), LOD = Lodicule (42 DAP), PAL = Palea (42 DAP), EPI = Epidermis (28 DAP), RAC = Rachis (35 DAP), ROO2 = Root (28 DAP seedling), SEN = Senescing leaf (63 DAP).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0130890.g004: Co-expression of two groups of genes (HvCesA9, HvCobra1, HvCslF6, and HvChitinase, HvGT1) identified by GWAS as putatively linked to culm cellulose content with HvCesA genes known to be involved in primary and secondary cell wall development.Transcript abundance across a range of tissues shown in fragment per kilobase of exon per million fragments mapped (FPKM) for group 1, primary cell wall including HvCesA1, HvCesA2, and HvCesA6 (A) for reference, and group 2, secondary cell wall including HvCesA4, HvCesA7 and HvCesA8 for reference (B). Abbreviations for tissues/ developmental stages as follows; EMB = Embryo tissues (germinating), ROO = Root (10cm seedlings), LEA = Shoot (10cm seedlings), INF1 = Inflorescence (0.5cm), INF2 = Inflorescence (1–1.5cm), NOD = Tillers (3rd internode), CAR5 = Grain (5 Days Post Anthesis—DPA), CAR15 = Grain (15 DPA), ETI = Etiolated (10 day seedlings), LEM = Lemma (6 weeks Days After Planting—DAP), LOD = Lodicule (42 DAP), PAL = Palea (42 DAP), EPI = Epidermis (28 DAP), RAC = Rachis (35 DAP), ROO2 = Root (28 DAP seedling), SEN = Senescing leaf (63 DAP).
Mentions: We were interested to see if any of the candidate genes from the GWAS were co-expressed, as this could provide further evidence for their being responsible for the association peaks identified. This is particularly relevant for understanding variation in cellulose content, because the synthesis of cellulose is likely to involve a number of co-factors and interacting proteins. The co-expression analysis allowed us to prioritise genes on our list of potential candidates in Table 3. We extended the number of tissues and developmental stages for which we compared candidate gene expression to sixteen (our unpublished data). When we considered the data for the 14 candidate genes from the nine regions highlighted in Table 3, we observed that five could be classified into two groups of co-expressed genes, groups 1 and 2, which are strongly co-expressed based on pairwise regression analysis between each gene across these 16 tissues with members of the CesA gene family (Fig 4). The output from the regression analysis can be found in S5 Table. Group 1 genes comprised HvCobra1, HvCslF6, and HvCesA9 (a close ortholog /paralog of HvCesA6), and formed a co-expression complex across the 16 different tissues with HvCesA1, HvCesA2, and HvCesA6, genes previously implicated in primary cell wall cellulose biosynthesis [9]. Group 2 genes, HvChitinase and HvUDP-glucosyltransferase (HvGT), were co-expressed with genes important for secondary cell wall development, namely HvCesA4, HvCesA7, and HvCesA8. Where possible we compared the coexpression of the rice orthologs of these genes, however there was no ortholog of HvCslF9 or HvChitinase1. Across both species we observed that genes in group 1 showed a higher and more significant degree of coexpression than those in group 2, with the expression of the candidate genes in barley showing a higher correlation to the known primary and secondary cell wall genes than their rice orthologs (S5 Table).

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