A Genome Wide Association Study of arabinoxylan content in 2-row spring barley grain

Ali Saleh Hassan, Kelly Houston, Jelle Lahnstein, Neil Shirley, Julian G. Schwerdt, Michael J. Gidley, Robbie Waugh, Alan Little, Rachel A. Burton (Lead / Corresponding author)

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Abstract

In barley endosperm arabinoxylan (AX) is the second most abundant cell wall polysaccharide and in wheat it is the most abundant polysaccharide in the starchy endosperm walls of the grain. AX is one of the main contributors to grain dietary fibre content providing several health benefits including cholesterol and glucose lowering effects, and antioxidant activities. Due to its complex structural features, AX might also affect the downstream applications of barley grain in malting and brewing. Using a high pressure liquid chromatography (HPLC) method we quantified AX amounts in mature grain in 128 spring 2-row barley accessions. Amounts ranged from ~ 5.2 μg/g to ~ 9 μg/g. We used this data for a Genome Wide Association Study (GWAS) that revealed three significant quantitative trait loci (QTL) associated with grain AX levels which passed a false discovery threshold (FDR) and are located on two of the seven barley chromosomes. Regions underlying the QTLs were scanned for genes likely to be involved in AX biosynthesis or turnover, and strong candidates, including glycosyltransferases from the GT43 and GT61 families and glycoside hydrolases from the GH10 family, were identified. Phylogenetic trees of selected gene families were built based on protein translations and were used to examine the relationship of the barley candidate genes to those in other species. Our data reaffirms the roles of existing genes thought to contribute to AX content, and identifies novel QTL (and candidate genes associated with them) potentially influencing the AX content of barley grain. One potential outcome of this work is the deployment of highly associated single nucleotide polymorphisms markers in breeding programs to guide the modification of AX abundance in barley grain.

Original languageEnglish
Article numbere0182537
Pages (from-to)1-19
Number of pages19
JournalPLoS ONE
Volume12
Issue number8
DOIs
Publication statusPublished - 3 Aug 2017

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arabinoxylan
Genome-Wide Association Study
spring barley
Hordeum
Genes
barley
quantitative trait loci
Endosperm
Quantitative Trait Loci
genes
endosperm
Polysaccharides
polysaccharides
High pressure liquid chromatography
Brewing
genome-wide association study
Glycosyltransferases
glycosyltransferases
malting
Glycoside Hydrolases

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Hassan, A. S., Houston, K., Lahnstein, J., Shirley, N., Schwerdt, J. G., Gidley, M. J., ... Burton, R. A. (2017). A Genome Wide Association Study of arabinoxylan content in 2-row spring barley grain. PLoS ONE, 12(8), 1-19. [e0182537]. https://doi.org/10.1371/journal.pone.0182537
Hassan, Ali Saleh ; Houston, Kelly ; Lahnstein, Jelle ; Shirley, Neil ; Schwerdt, Julian G. ; Gidley, Michael J. ; Waugh, Robbie ; Little, Alan ; Burton, Rachel A. / A Genome Wide Association Study of arabinoxylan content in 2-row spring barley grain. In: PLoS ONE. 2017 ; Vol. 12, No. 8. pp. 1-19.
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abstract = "In barley endosperm arabinoxylan (AX) is the second most abundant cell wall polysaccharide and in wheat it is the most abundant polysaccharide in the starchy endosperm walls of the grain. AX is one of the main contributors to grain dietary fibre content providing several health benefits including cholesterol and glucose lowering effects, and antioxidant activities. Due to its complex structural features, AX might also affect the downstream applications of barley grain in malting and brewing. Using a high pressure liquid chromatography (HPLC) method we quantified AX amounts in mature grain in 128 spring 2-row barley accessions. Amounts ranged from ~ 5.2 μg/g to ~ 9 μg/g. We used this data for a Genome Wide Association Study (GWAS) that revealed three significant quantitative trait loci (QTL) associated with grain AX levels which passed a false discovery threshold (FDR) and are located on two of the seven barley chromosomes. Regions underlying the QTLs were scanned for genes likely to be involved in AX biosynthesis or turnover, and strong candidates, including glycosyltransferases from the GT43 and GT61 families and glycoside hydrolases from the GH10 family, were identified. Phylogenetic trees of selected gene families were built based on protein translations and were used to examine the relationship of the barley candidate genes to those in other species. Our data reaffirms the roles of existing genes thought to contribute to AX content, and identifies novel QTL (and candidate genes associated with them) potentially influencing the AX content of barley grain. One potential outcome of this work is the deployment of highly associated single nucleotide polymorphisms markers in breeding programs to guide the modification of AX abundance in barley grain.",
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Hassan, AS, Houston, K, Lahnstein, J, Shirley, N, Schwerdt, JG, Gidley, MJ, Waugh, R, Little, A & Burton, RA 2017, 'A Genome Wide Association Study of arabinoxylan content in 2-row spring barley grain', PLoS ONE, vol. 12, no. 8, e0182537, pp. 1-19. https://doi.org/10.1371/journal.pone.0182537

A Genome Wide Association Study of arabinoxylan content in 2-row spring barley grain. / Hassan, Ali Saleh; Houston, Kelly; Lahnstein, Jelle; Shirley, Neil; Schwerdt, Julian G.; Gidley, Michael J.; Waugh, Robbie; Little, Alan; Burton, Rachel A. (Lead / Corresponding author).

In: PLoS ONE, Vol. 12, No. 8, e0182537, 03.08.2017, p. 1-19.

Research output: Contribution to journalArticle

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N2 - In barley endosperm arabinoxylan (AX) is the second most abundant cell wall polysaccharide and in wheat it is the most abundant polysaccharide in the starchy endosperm walls of the grain. AX is one of the main contributors to grain dietary fibre content providing several health benefits including cholesterol and glucose lowering effects, and antioxidant activities. Due to its complex structural features, AX might also affect the downstream applications of barley grain in malting and brewing. Using a high pressure liquid chromatography (HPLC) method we quantified AX amounts in mature grain in 128 spring 2-row barley accessions. Amounts ranged from ~ 5.2 μg/g to ~ 9 μg/g. We used this data for a Genome Wide Association Study (GWAS) that revealed three significant quantitative trait loci (QTL) associated with grain AX levels which passed a false discovery threshold (FDR) and are located on two of the seven barley chromosomes. Regions underlying the QTLs were scanned for genes likely to be involved in AX biosynthesis or turnover, and strong candidates, including glycosyltransferases from the GT43 and GT61 families and glycoside hydrolases from the GH10 family, were identified. Phylogenetic trees of selected gene families were built based on protein translations and were used to examine the relationship of the barley candidate genes to those in other species. Our data reaffirms the roles of existing genes thought to contribute to AX content, and identifies novel QTL (and candidate genes associated with them) potentially influencing the AX content of barley grain. One potential outcome of this work is the deployment of highly associated single nucleotide polymorphisms markers in breeding programs to guide the modification of AX abundance in barley grain.

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Hassan AS, Houston K, Lahnstein J, Shirley N, Schwerdt JG, Gidley MJ et al. A Genome Wide Association Study of arabinoxylan content in 2-row spring barley grain. PLoS ONE. 2017 Aug 3;12(8):1-19. e0182537. https://doi.org/10.1371/journal.pone.0182537