A genome wide analysis of key genes controlling diastatic power activity in UK barley (DPGENES)

SP Hoad, Joanne Russell, Mark Looseley, Micha Bayer, Hazel Bull, Luke Ramsay, William Thomas, Allan Booth, Jenny Morris, Pete Hedley, Linde Hess, James Brosnan

Research output: Book/ReportCommissioned report

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Abstract

Diastatic Power (DP) is an important quality trait for malt used in adjunct brewing and distilling. Substantial genetic variation for DP exists within UK elite barley cultivars, but breeding progress has been slow due to the limited demand, compared to the overall barley market, and difficulties in assessing DP. The aim of this project was to develop a suite of genetic markers and robust phenotypic screening methods to identify differences in barley malt diastase activity that can be used by breeders, testing authorities, and maltsters for the early identification and promotion of new varieties for the grain distilling market. To do this, we first identified subsets of barley accessions that contrast for diastase activity using pre-existing data for both spring and winter germplasm. These subsets were the basis for marker development (A) and phenotypic screening protocols (B).
(A) Twelve high DP and twelve low DP pools of DNA for spring and winter lines were sequenced using a gene enrichment approach, generating over 84,000 polymorphic SNP markers. Using allele frequency differences between low and high DP pools, we identified 66 and 32 SNPs that distinguished between high and low DP in the winters and springs, respectively. For each chromosome region, we chose the marker that showed the highest differentiation between pools, several of these were collocated with known diastase genes, or genes which were annotated with a putative diastase function. Eight KASP marker assays (marker favoured by UK and European breeders) were designed from the SNPs identified from the winters and five for springs. These were tested on a large set of winter and spring germplasm, and a strong correlation (r = 0.92) between genotype and true DP was observed. Further validation was carried out using independent germplasm, supplied by UK and European breeders, which were genotyped, DP predicted and confirmed where possible by micro-malting at Scotch Whisky Research Institute (SWRI).
(B) The subsets selected were sown under a range of conditions expected to differentiate between high and low DP lines. Winter and spring lines were trialled under both standard and high nitrogen fertiliser treatments, and yield data showed little difference between high and low DP varieties, but in contrast grain nitrogen differed between subsets considerably, at both rates of nitrogen. Based on these initially findings an improved assessment protocol to complement the markers in an integrated screening package enable breeders to produce new varieties that are specifically targeted at the production of high DP malt.
Original languageEnglish
PublisherAgriculture and Horticulture Development Board
Commissioning bodyAgriculture and Horticulture Development Board
Number of pages20
EditionPR583
Publication statusPrint publication - Oct 2017

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barley
genome
winter
malt
germplasm
genes
new variety
screening
Scotch whisky
markets
malting
brewing
nitrogen
gene frequency
complement
fertilizer application
nitrogen fertilizers
chromosomes
genetic variation
genetic markers

Cite this

Hoad, SP., Joanne Russell, Mark Looseley, Micha Bayer, Hazel Bull, Luke Ramsay, ... James Brosnan (2017). A genome wide analysis of key genes controlling diastatic power activity in UK barley (DPGENES). (PR583 ed.) Agriculture and Horticulture Development Board.
Hoad, SP ; Joanne Russell ; Mark Looseley ; Micha Bayer ; Hazel Bull ; Luke Ramsay ; William Thomas ; Allan Booth ; Jenny Morris ; Pete Hedley ; Linde Hess ; James Brosnan. / A genome wide analysis of key genes controlling diastatic power activity in UK barley (DPGENES). PR583 ed. Agriculture and Horticulture Development Board, 2017. 20 p.
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abstract = "Diastatic Power (DP) is an important quality trait for malt used in adjunct brewing and distilling. Substantial genetic variation for DP exists within UK elite barley cultivars, but breeding progress has been slow due to the limited demand, compared to the overall barley market, and difficulties in assessing DP. The aim of this project was to develop a suite of genetic markers and robust phenotypic screening methods to identify differences in barley malt diastase activity that can be used by breeders, testing authorities, and maltsters for the early identification and promotion of new varieties for the grain distilling market. To do this, we first identified subsets of barley accessions that contrast for diastase activity using pre-existing data for both spring and winter germplasm. These subsets were the basis for marker development (A) and phenotypic screening protocols (B).(A) Twelve high DP and twelve low DP pools of DNA for spring and winter lines were sequenced using a gene enrichment approach, generating over 84,000 polymorphic SNP markers. Using allele frequency differences between low and high DP pools, we identified 66 and 32 SNPs that distinguished between high and low DP in the winters and springs, respectively. For each chromosome region, we chose the marker that showed the highest differentiation between pools, several of these were collocated with known diastase genes, or genes which were annotated with a putative diastase function. Eight KASP marker assays (marker favoured by UK and European breeders) were designed from the SNPs identified from the winters and five for springs. These were tested on a large set of winter and spring germplasm, and a strong correlation (r = 0.92) between genotype and true DP was observed. Further validation was carried out using independent germplasm, supplied by UK and European breeders, which were genotyped, DP predicted and confirmed where possible by micro-malting at Scotch Whisky Research Institute (SWRI).(B) The subsets selected were sown under a range of conditions expected to differentiate between high and low DP lines. Winter and spring lines were trialled under both standard and high nitrogen fertiliser treatments, and yield data showed little difference between high and low DP varieties, but in contrast grain nitrogen differed between subsets considerably, at both rates of nitrogen. Based on these initially findings an improved assessment protocol to complement the markers in an integrated screening package enable breeders to produce new varieties that are specifically targeted at the production of high DP malt.",
author = "SP Hoad and {Joanne Russell} and {Mark Looseley} and {Micha Bayer} and {Hazel Bull} and {Luke Ramsay} and {William Thomas} and {Allan Booth} and {Jenny Morris} and {Pete Hedley} and {Linde Hess} and {James Brosnan}",
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Hoad, SP, Joanne Russell, Mark Looseley, Micha Bayer, Hazel Bull, Luke Ramsay, William Thomas, Allan Booth, Jenny Morris, Pete Hedley, Linde Hess & James Brosnan 2017, A genome wide analysis of key genes controlling diastatic power activity in UK barley (DPGENES). PR583 edn, Agriculture and Horticulture Development Board.

A genome wide analysis of key genes controlling diastatic power activity in UK barley (DPGENES). / Hoad, SP; Joanne Russell; Mark Looseley; Micha Bayer; Hazel Bull; Luke Ramsay; William Thomas; Allan Booth; Jenny Morris; Pete Hedley; Linde Hess; James Brosnan.

PR583 ed. Agriculture and Horticulture Development Board, 2017. 20 p.

Research output: Book/ReportCommissioned report

TY - BOOK

T1 - A genome wide analysis of key genes controlling diastatic power activity in UK barley (DPGENES)

AU - Hoad, SP

AU - Joanne Russell

AU - Mark Looseley

AU - Micha Bayer

AU - Hazel Bull

AU - Luke Ramsay

AU - William Thomas

AU - Allan Booth

AU - Jenny Morris

AU - Pete Hedley

AU - Linde Hess

AU - James Brosnan

PY - 2017/10

Y1 - 2017/10

N2 - Diastatic Power (DP) is an important quality trait for malt used in adjunct brewing and distilling. Substantial genetic variation for DP exists within UK elite barley cultivars, but breeding progress has been slow due to the limited demand, compared to the overall barley market, and difficulties in assessing DP. The aim of this project was to develop a suite of genetic markers and robust phenotypic screening methods to identify differences in barley malt diastase activity that can be used by breeders, testing authorities, and maltsters for the early identification and promotion of new varieties for the grain distilling market. To do this, we first identified subsets of barley accessions that contrast for diastase activity using pre-existing data for both spring and winter germplasm. These subsets were the basis for marker development (A) and phenotypic screening protocols (B).(A) Twelve high DP and twelve low DP pools of DNA for spring and winter lines were sequenced using a gene enrichment approach, generating over 84,000 polymorphic SNP markers. Using allele frequency differences between low and high DP pools, we identified 66 and 32 SNPs that distinguished between high and low DP in the winters and springs, respectively. For each chromosome region, we chose the marker that showed the highest differentiation between pools, several of these were collocated with known diastase genes, or genes which were annotated with a putative diastase function. Eight KASP marker assays (marker favoured by UK and European breeders) were designed from the SNPs identified from the winters and five for springs. These were tested on a large set of winter and spring germplasm, and a strong correlation (r = 0.92) between genotype and true DP was observed. Further validation was carried out using independent germplasm, supplied by UK and European breeders, which were genotyped, DP predicted and confirmed where possible by micro-malting at Scotch Whisky Research Institute (SWRI).(B) The subsets selected were sown under a range of conditions expected to differentiate between high and low DP lines. Winter and spring lines were trialled under both standard and high nitrogen fertiliser treatments, and yield data showed little difference between high and low DP varieties, but in contrast grain nitrogen differed between subsets considerably, at both rates of nitrogen. Based on these initially findings an improved assessment protocol to complement the markers in an integrated screening package enable breeders to produce new varieties that are specifically targeted at the production of high DP malt.

AB - Diastatic Power (DP) is an important quality trait for malt used in adjunct brewing and distilling. Substantial genetic variation for DP exists within UK elite barley cultivars, but breeding progress has been slow due to the limited demand, compared to the overall barley market, and difficulties in assessing DP. The aim of this project was to develop a suite of genetic markers and robust phenotypic screening methods to identify differences in barley malt diastase activity that can be used by breeders, testing authorities, and maltsters for the early identification and promotion of new varieties for the grain distilling market. To do this, we first identified subsets of barley accessions that contrast for diastase activity using pre-existing data for both spring and winter germplasm. These subsets were the basis for marker development (A) and phenotypic screening protocols (B).(A) Twelve high DP and twelve low DP pools of DNA for spring and winter lines were sequenced using a gene enrichment approach, generating over 84,000 polymorphic SNP markers. Using allele frequency differences between low and high DP pools, we identified 66 and 32 SNPs that distinguished between high and low DP in the winters and springs, respectively. For each chromosome region, we chose the marker that showed the highest differentiation between pools, several of these were collocated with known diastase genes, or genes which were annotated with a putative diastase function. Eight KASP marker assays (marker favoured by UK and European breeders) were designed from the SNPs identified from the winters and five for springs. These were tested on a large set of winter and spring germplasm, and a strong correlation (r = 0.92) between genotype and true DP was observed. Further validation was carried out using independent germplasm, supplied by UK and European breeders, which were genotyped, DP predicted and confirmed where possible by micro-malting at Scotch Whisky Research Institute (SWRI).(B) The subsets selected were sown under a range of conditions expected to differentiate between high and low DP lines. Winter and spring lines were trialled under both standard and high nitrogen fertiliser treatments, and yield data showed little difference between high and low DP varieties, but in contrast grain nitrogen differed between subsets considerably, at both rates of nitrogen. Based on these initially findings an improved assessment protocol to complement the markers in an integrated screening package enable breeders to produce new varieties that are specifically targeted at the production of high DP malt.

M3 - Commissioned report

BT - A genome wide analysis of key genes controlling diastatic power activity in UK barley (DPGENES)

PB - Agriculture and Horticulture Development Board

ER -

Hoad SP, Joanne Russell, Mark Looseley, Micha Bayer, Hazel Bull, Luke Ramsay et al. A genome wide analysis of key genes controlling diastatic power activity in UK barley (DPGENES). PR583 ed. Agriculture and Horticulture Development Board, 2017. 20 p.