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

doi: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

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 journal › Article › peer-review

63 Citations (Scopus)

217 Downloads (Pure)

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 language	English
Article number	907
Number of pages	15
Journal	BMC Genomics
Volume	15
DOIs	https://doi.org/10.1186/1471-2164-15-907
Publication status	Published - 17 Oct 2014

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1186/1471-2164-15-907

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" 2014 Houston et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated."
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Aref#d: 20552. Manipulating Lignin to Improve Biofuel Conversion of Plant Biomass (joint with University of York)
Halpin, C. (Investigator)
20/04/09 → 19/10/14
Project: Research

Identification of genes involved in (1,3;1,4)-β-glucan synthesis in barley (Hordeum vulgare)
Schreiber, M. (Author), Halpin, C. (Supervisor) & Waugh, R. (Supervisor), 2016
Student thesis: Doctoral Thesis › Doctor of Philosophy

Cite this

@article{06a0df4a414d42f48f3221edec3212ed,

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",

year = "2014",

month = oct,

day = "17",

doi = "10.1186/1471-2164-15-907",

language = "English",

volume = "15",

journal = "BMC Genomics",

issn = "1471-2164",

publisher = "Springer Verlag",

}

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

SN - 1471-2164

VL - 15

JO - BMC Genomics

JF - BMC Genomics

M1 - 907

ER -

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

UN SDGs

Access to Document

Fingerprint

Aref#d: 20552. Manipulating Lignin to Improve Biofuel Conversion of Plant Biomass (joint with University of York)

Identification of genes involved in (1,3;1,4)-β-glucan synthesis in barley (Hordeum vulgare)

Cite this

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

UN SDGs

Access to Document

Fingerprint

Projects

Aref#d: 20552. Manipulating Lignin to Improve Biofuel Conversion of Plant Biomass (joint with University of York)

Student theses

Identification of genes involved in (1,3;1,4)-β-glucan synthesis in barley (Hordeum vulgare)

Cite this