A genome wide association scan for (1,3;1,4)-β-glucan content in the grain of contemporary 2-row Spring and Winter barleys

Kelly Houston, Joanne Russell, Miriam Schreiber, Claire Halpin, Helena Oakey, Jennifer M. Washington, Allan Booth, Neil Shirley, Rachel A. Burton, Geoffrey B. Fincher, Robbie Waugh (Lead / Corresponding author)

    Research output: Contribution to journalArticle

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    Abstract

    Background: (1,3;1,4)-β-Glucan is an important component of the cell walls of barley grain as it affects processability during the production of alcoholic beverages and has significant human health benefits when consumed aboverecommended threshold levels. This leads to diametrically opposed quality requirements for different applications as low levels of (1,3;1,4)-β-glucan are required for brewing and distilling and high levels for positive impacts on humanhealth.
    Results: We quantified grain (1,3;1,4)-β-glucan content in a collection of 399 2-row Spring-type, and 204 2-row Winter-type elite barley cultivars originating mainly from north western Europe. We combined these data with genotypic information derived using a 9 K Illumina iSelect SNP platform and subsequently carried out a Genome Wide Association Scan (GWAS). Statistical analysis accounting for residual genetic structure within the germplasm collection allowed us to identify significant associations between molecular markers and the phenotypic data. By anchoring the regions that contain these associations to the barley genome assembly we catalogued genes underlying the associations. Based on gene annotations and transcript abundance data we identified candidate genes.
    Conclusions: We show that a region of the genome on chromosome 2 containing a cluster of CELLULOSE SYNTHASE-LIKE (Csl) genes, including CslF3, CslF4, CslF8, CslF10, CslF12 and CslH, as well as a region on chromosome 1H containingCslF9, are associated with the phenotype in this germplasm. We also observed that several regions identified by GWAS contain glycoside hydrolases that are possibly involved in (1,3;1,4)-β-glucan breakdown, together with other genes that might participate in (1,3;1,4)-β-glucan synthesis, re-modelling or regulation. This analysis provides new opportunities for understanding the genes related to the regulation of (1,3;1,4)-β-glucan content in cereal grains.
    Original languageEnglish
    Article number907
    Number of pages15
    JournalBMC Genomics
    Volume15
    DOIs
    Publication statusPublished - 17 Oct 2014

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    Genome-Wide Association Study
    Hordeum
    Genes
    Genome
    Molecular Sequence Annotation
    Alcoholic Beverages
    Chromosomes, Human, Pair 2
    Genetic Structures
    Glycoside Hydrolases
    Insurance Benefits
    Cell Wall
    Single Nucleotide Polymorphism
    (1-3)-(1-4)-glucan
    Chromosomes
    Phenotype

    Cite this

    Houston, Kelly ; Russell, Joanne ; Schreiber, Miriam ; Halpin, Claire ; Oakey, Helena ; Washington, Jennifer M. ; Booth, Allan ; Shirley, Neil ; Burton, Rachel A. ; Fincher, Geoffrey B. ; Waugh, Robbie. / A genome wide association scan for (1,3;1,4)-β-glucan content in the grain of contemporary 2-row Spring and Winter barleys. In: BMC Genomics. 2014 ; Vol. 15.
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    title = "A genome wide association scan for (1,3;1,4)-β-glucan content in the grain of contemporary 2-row Spring and Winter barleys",
    abstract = "Background: (1,3;1,4)-β-Glucan is an important component of the cell walls of barley grain as it affects processability during the production of alcoholic beverages and has significant human health benefits when consumed aboverecommended threshold levels. This leads to diametrically opposed quality requirements for different applications as low levels of (1,3;1,4)-β-glucan are required for brewing and distilling and high levels for positive impacts on humanhealth.Results: We quantified grain (1,3;1,4)-β-glucan content in a collection of 399 2-row Spring-type, and 204 2-row Winter-type elite barley cultivars originating mainly from north western Europe. We combined these data with genotypic information derived using a 9 K Illumina iSelect SNP platform and subsequently carried out a Genome Wide Association Scan (GWAS). Statistical analysis accounting for residual genetic structure within the germplasm collection allowed us to identify significant associations between molecular markers and the phenotypic data. By anchoring the regions that contain these associations to the barley genome assembly we catalogued genes underlying the associations. Based on gene annotations and transcript abundance data we identified candidate genes.Conclusions: We show that a region of the genome on chromosome 2 containing a cluster of CELLULOSE SYNTHASE-LIKE (Csl) genes, including CslF3, CslF4, CslF8, CslF10, CslF12 and CslH, as well as a region on chromosome 1H containingCslF9, are associated with the phenotype in this germplasm. We also observed that several regions identified by GWAS contain glycoside hydrolases that are possibly involved in (1,3;1,4)-β-glucan breakdown, together with other genes that might participate in (1,3;1,4)-β-glucan synthesis, re-modelling or regulation. This analysis provides new opportunities for understanding the genes related to the regulation of (1,3;1,4)-β-glucan content in cereal grains.",
    author = "Kelly Houston and Joanne Russell and Miriam Schreiber and Claire Halpin and Helena Oakey and Washington, {Jennifer M.} and Allan Booth and Neil Shirley and Burton, {Rachel A.} and Fincher, {Geoffrey B.} and Robbie Waugh",
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    Houston, K, Russell, J, Schreiber, M, Halpin, C, Oakey, H, Washington, JM, Booth, A, Shirley, N, Burton, RA, Fincher, GB & Waugh, R 2014, 'A genome wide association scan for (1,3;1,4)-β-glucan content in the grain of contemporary 2-row Spring and Winter barleys', BMC Genomics, vol. 15, 907. https://doi.org/10.1186/1471-2164-15-907

    A genome wide association scan for (1,3;1,4)-β-glucan content in the grain of contemporary 2-row Spring and Winter barleys. / Houston, Kelly; Russell, Joanne; Schreiber, Miriam; Halpin, Claire; Oakey, Helena; Washington, Jennifer M.; Booth, Allan; Shirley, Neil; Burton, Rachel A.; Fincher, Geoffrey B.; Waugh, Robbie (Lead / Corresponding author).

    In: BMC Genomics, Vol. 15, 907, 17.10.2014.

    Research output: Contribution to journalArticle

    TY - JOUR

    T1 - A genome wide association scan for (1,3;1,4)-β-glucan content in the grain of contemporary 2-row Spring and Winter barleys

    AU - Houston, Kelly

    AU - Russell, Joanne

    AU - Schreiber, Miriam

    AU - Halpin, Claire

    AU - Oakey, Helena

    AU - Washington, Jennifer M.

    AU - Booth, Allan

    AU - Shirley, Neil

    AU - Burton, Rachel A.

    AU - Fincher, Geoffrey B.

    AU - Waugh, Robbie

    PY - 2014/10/17

    Y1 - 2014/10/17

    N2 - Background: (1,3;1,4)-β-Glucan is an important component of the cell walls of barley grain as it affects processability during the production of alcoholic beverages and has significant human health benefits when consumed aboverecommended threshold levels. This leads to diametrically opposed quality requirements for different applications as low levels of (1,3;1,4)-β-glucan are required for brewing and distilling and high levels for positive impacts on humanhealth.Results: We quantified grain (1,3;1,4)-β-glucan content in a collection of 399 2-row Spring-type, and 204 2-row Winter-type elite barley cultivars originating mainly from north western Europe. We combined these data with genotypic information derived using a 9 K Illumina iSelect SNP platform and subsequently carried out a Genome Wide Association Scan (GWAS). Statistical analysis accounting for residual genetic structure within the germplasm collection allowed us to identify significant associations between molecular markers and the phenotypic data. By anchoring the regions that contain these associations to the barley genome assembly we catalogued genes underlying the associations. Based on gene annotations and transcript abundance data we identified candidate genes.Conclusions: We show that a region of the genome on chromosome 2 containing a cluster of CELLULOSE SYNTHASE-LIKE (Csl) genes, including CslF3, CslF4, CslF8, CslF10, CslF12 and CslH, as well as a region on chromosome 1H containingCslF9, are associated with the phenotype in this germplasm. We also observed that several regions identified by GWAS contain glycoside hydrolases that are possibly involved in (1,3;1,4)-β-glucan breakdown, together with other genes that might participate in (1,3;1,4)-β-glucan synthesis, re-modelling or regulation. This analysis provides new opportunities for understanding the genes related to the regulation of (1,3;1,4)-β-glucan content in cereal grains.

    AB - Background: (1,3;1,4)-β-Glucan is an important component of the cell walls of barley grain as it affects processability during the production of alcoholic beverages and has significant human health benefits when consumed aboverecommended threshold levels. This leads to diametrically opposed quality requirements for different applications as low levels of (1,3;1,4)-β-glucan are required for brewing and distilling and high levels for positive impacts on humanhealth.Results: We quantified grain (1,3;1,4)-β-glucan content in a collection of 399 2-row Spring-type, and 204 2-row Winter-type elite barley cultivars originating mainly from north western Europe. We combined these data with genotypic information derived using a 9 K Illumina iSelect SNP platform and subsequently carried out a Genome Wide Association Scan (GWAS). Statistical analysis accounting for residual genetic structure within the germplasm collection allowed us to identify significant associations between molecular markers and the phenotypic data. By anchoring the regions that contain these associations to the barley genome assembly we catalogued genes underlying the associations. Based on gene annotations and transcript abundance data we identified candidate genes.Conclusions: We show that a region of the genome on chromosome 2 containing a cluster of CELLULOSE SYNTHASE-LIKE (Csl) genes, including CslF3, CslF4, CslF8, CslF10, CslF12 and CslH, as well as a region on chromosome 1H containingCslF9, are associated with the phenotype in this germplasm. We also observed that several regions identified by GWAS contain glycoside hydrolases that are possibly involved in (1,3;1,4)-β-glucan breakdown, together with other genes that might participate in (1,3;1,4)-β-glucan synthesis, re-modelling or regulation. This analysis provides new opportunities for understanding the genes related to the regulation of (1,3;1,4)-β-glucan content in cereal grains.

    U2 - 10.1186/1471-2164-15-907

    DO - 10.1186/1471-2164-15-907

    M3 - Article

    C2 - 25326272

    VL - 15

    JO - BMC Genomics

    JF - BMC Genomics

    SN - 1471-2164

    M1 - 907

    ER -