Abstract
In Australia, barley (Hordeum vulgare L.) is grown for several end-uses, however, the majority of the grain is produced for the malt export market. Barley cultivars that have recently been released in Australia (e.g. Baudin, Vlamingh, Flagship and Buloke) have improved malt quality, but lack adequate levels of resistance to one or more important foliar pathogens, while Australian cultivars have variable levels of grain dormancy for protection against pre-harvest sprouting (PHS). Additional knowledge of the genetic mechanisms controlling disease resistance (particularly adult plant resistance (APR) or partial resistance) and grain dormancy is required to develop more robust cultivars. In this study, three traits important for adaptation of barley to the northern grain-growing region of Australia (i.e. northern New South Wales and Queensland) were subject to genetic analysis: APR to leaf rust (Puccinia hordei), partial resistance to powdery mildew (Blumeria graminis), and grain dormancy for resistance to PHS. A doubled haploid (DH) barley population derived from a cross between the breeding line ND24260 and cultivar Flagship consisting of 321 lines genotyped with DArT (Diversity Array Technology Pty, Inc.) markers was used to identify genomic regions influencing the expression of these polygenic traits. Phenotype data from multiple environments in Australia and Uruguay, were analysed using both composite interval mapping (CIM) and single-marker genome-wide association analyses to identify novel quantitative trait loci (QTL) for the three traits positioned. QTL were detected on all seven chromosomes, including seven major QTL (i.e. six independent genomic regions) that were critical for expression of the three traits across multiple environments. Two QTL conferring APR in this DH population were detected consistently across four environments; qRphFlag and qRphND (donated by Flagship and ND24260, respectively). qRphFlag was mapped to the short arm of chromosome 5H (5HS), accounting for up to 85% of the phenotypic variation in field environments and 56% under controlled environmental conditions (CEC). qRphND was mapped to chromosome 6HL and had smaller effect. The qRphFlag resistance allele was common in leaf rust resistant cultivars derived from Vada and Emir and has been designated Rph20, the first gene conferring APR to P. hordei to be characterized in barley. Three QTL contributing partial resistance to B. graminis were detected in at least two of the three test environments. All three QTL were donated by Flagship and were mapped to chromosomes 3H, 4H and 5H (5HS) accounting for up to 18.6%, 3.4% and 8.8% phenotypic variation, respectively. The 5HS QTL contributed partial resistance to B. graminis in all field environments and aligned with the genomic region of Rph20. Despite both parental lines being non-dormant, some DH lines displayed moderate to high levels of grain dormancy. Two QTL for grain dormancy were indentified that were detected consistently across three environments; qSDFlag and qSDND (donated by Flagship and ND24260, respectively). qSDFlag was positioned close to the centromeric region of chromosome 5H (accounting for up to 15% of the phenotypic variation), whereas qSDND had larger effect (accounted for up to 35% of the phenotypic variation) and was mapped to chromosome 5HL; positioned proximal and independent to the well-characterized “SD2 region” that is associated with both high levels of dormancy and with inferior malt quality. DH lines were assigned QTL based on marker haplotypes within each of the favourable QTL regions. Based on these haplotypes, three DH lines carrying all six major QTL were identified. However, none of these three DH lines displayed high phenotypic values across multiple environments. Therefore, it appears that additional genes with small effect are required to achieve both high levels of disease resistance and grain dormancy. The implications of these results for breeding programs are discussed. Despite the complex inheritance patterns of these traits, the opportunity remains to accelerate the introgression of multiple target traits into adapted cereal cultivars. Breeding strategies can be built using technologies such as: rapid generation advance under controlled environmental conditions using constant light photoperiod, high-throughput phenotypic screening methods allowing selection for multiple target traits, and application of high-throughput DNA markers for selection of known genes and recovery of the adapted genetic background.
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Claims 18
Claim · model-written summary
QTL for the three traits were detected on all seven barley chromosomes.
- Taxon
- barley
.jpg?width=60)
Hordeum vulgaret0 - Outcome
- QTLe1
- Qualifier
- detected on all seven chromosomese1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
.jpg?width=500)
Verbatim
e1“QTL were detected on all seven chromosomes”
t0“barley population”
Claim · model-written summary
Seven major QTL, representing six independent genomic regions, were critical for expression of the three traits across multiple environments.
- Taxon
- barleyHordeum vulgaret0
- Outcome
- major QTLe1
- Value
- sevene1
- Qualifier
- six independent genomic regionse1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“seven major QTL (i.e. six independent genomic regions) that were critical for expression of the three traits across multiple environments”
t0“barley population”
Claim · model-written summary
qRphFlag on chromosome 5HS accounted for up to 85% of the phenotypic variation for leaf rust resistance in field environments.
- Taxon
- barleyHordeum vulgaret0
- Gene
- qRphFlage1
- Outcome
- phenotypic variatione1
- Value
- 85%e1
- Setting
- field environmentse1
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“qRphFlag was mapped to the short arm of chromosome 5H (5HS), accounting for up to 85% of the phenotypic variation in field environments and 56% under controlled environmental conditions (CEC)”
t0“barley population”
Claim · model-written summary
qRphFlag on chromosome 5HS accounted for up to 56% of the phenotypic variation under controlled environmental conditions.
- Taxon
- barleyHordeum vulgaret0
- Gene
- qRphFlage1
- Outcome
- phenotypic variatione1
- Value
- 56%e1
- Setting
- controlled environmental conditionse1
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“qRphFlag was mapped to the short arm of chromosome 5H (5HS), accounting for up to 85% of the phenotypic variation in field environments and 56% under controlled environmental conditions (CEC)”
t0“barley population”
Claim · model-written summary
qRphND on chromosome 6HL had a smaller effect than qRphFlag.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“qRphND was mapped to chromosome 6HL and had smaller effect”
t0“barley population”
Claim · model-written summary
Three QTL contributed partial resistance to Blumeria graminis (powdery mildew) detected in at least two of the three test environments.
- Taxon
- barleyHordeum vulgaret0
- Interactor
- B. graminis
Blumeria graminise1pathogen - Outcome
- partial resistance to B. graminise1
- Direction
- increaseinferrede1
- Qualifier
- detected in at least two of the three test environmentse1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“Three QTL contributing partial resistance to B. graminis were detected in at least two of the three test environments”
t0“barley population”
Claim · model-written summary
A QTL on chromosome 3H, donated by Flagship, accounted for up to 18.6% of the phenotypic variation.
- Taxon
- barleyHordeum vulgaret0
- Material
- Flagshipe1
- Outcome
- phenotypic variatione1
- Value
- 18.6%e1
- Qualifier
- chromosomes 3He1
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“All three QTL were donated by Flagship and were mapped to chromosomes 3H, 4H and 5H (5HS) accounting for up to 18.6%, 3.4% and 8.8% phenotypic variation, respectively”
t0“barley population”
Claim · model-written summary
A QTL on chromosome 4H, donated by Flagship, accounted for up to 3.4% of the phenotypic variation.
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“All three QTL were donated by Flagship and were mapped to chromosomes 3H, 4H and 5H (5HS) accounting for up to 18.6%, 3.4% and 8.8% phenotypic variation, respectively”
t0“barley population”
Claim · model-written summary
A QTL on chromosome 5HS, donated by Flagship, accounted for up to 8.8% of the phenotypic variation.
- Taxon
- barleyHordeum vulgaret0
- Material
- Flagshipe1
- Outcome
- phenotypic variatione1
- Value
- 8.8%e1
- Qualifier
- 5HSe1
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“All three QTL were donated by Flagship and were mapped to chromosomes 3H, 4H and 5H (5HS) accounting for up to 18.6%, 3.4% and 8.8% phenotypic variation, respectively”
t0“barley population”
Claim · model-written summary
The 5HS QTL contributed partial resistance to B. graminis in all field environments and aligned with the genomic region of Rph20.
- Taxon
- barleyHordeum vulgaret0
- Interactor
- B. graminisBlumeria graminise1pathogen
- Outcome
- partial resistance to B. graminise1
- Direction
- increaseinferrede1
- Qualifier
- aligned with the genomic region of Rph20e1
- Setting
- all field environmentse1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“The 5HS QTL contributed partial resistance to B. graminis in all field environments and aligned with the genomic region of Rph20”
t0“barley population”
Claim · model-written summary
The qRphFlag resistance allele is Rph20, the first gene conferring adult plant resistance to Puccinia hordei characterized in barley.
- Taxon
- barleyHordeum vulgaret0
- Interactor
- Puccinia hordei
Puccinia hordeie2pathogen - Gene
- Rph20e1
- Outcome
- APR to P. hordeie1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“has been designated Rph20, the first gene conferring APR to P. hordei to be characterized in barley”
e2“APR to leaf rust (Puccinia hordei)”
t0“barley population”
Claim · model-written summary
The qRphFlag resistance allele was common in leaf rust resistant cultivars derived from Vada and Emir.
- Taxon
- barleyHordeum vulgaret0
- Material
- leaf rust resistant cultivarse1
- Gene
- qRphFlage1
- Outcome
- qRphFlag resistance allelee1
- Qualifier
- common in leaf rust resistant cultivars derived from Vada and Emire1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“The qRphFlag resistance allele was common in leaf rust resistant cultivars derived from Vada and Emir”
t0“barley population”
Claim · model-written summary
Some DH lines displayed moderate to high levels of grain dormancy although both parental lines were non-dormant.
- Taxon
- barleyHordeum vulgaret0
- Material
- DH linese1
- Outcome
- grain dormancye1
- Qualifier
- moderate to high levelse1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“Despite both parental lines being non-dormant, some DH lines displayed moderate to high levels of grain dormancy”
t0“barley population”
Claim · model-written summary
qSDFlag, close to the centromeric region of chromosome 5H, accounted for up to 15% of the phenotypic variation in grain dormancy.
- Taxon
- barleyHordeum vulgaret0
- Gene
- qSDFlage1
- Outcome
- phenotypic variatione1
- Value
- 15%e1
- Qualifier
- close to the centromeric region of chromosome 5He1
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“qSDFlag was positioned close to the centromeric region of chromosome 5H (accounting for up to 15% of the phenotypic variation)”
t0“barley population”
Claim · model-written summary
qSDND, mapped to chromosome 5HL, had a larger effect and accounted for up to 35% of the phenotypic variation in grain dormancy.
- Taxon
- barleyHordeum vulgaret0
- Gene
- qSDNDe1
- Outcome
- phenotypic variatione1
- Value
- 35%e1
- Qualifier
- larger effecte1
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“qSDND had larger effect (accounted for up to 35% of the phenotypic variation) and was mapped to chromosome 5HL”
t0“barley population”
Claim · model-written summary
None of three DH lines carrying all six major QTL displayed high phenotypic values across multiple environments.
- Taxon
- barleyHordeum vulgaret0
- Material
- three DH lines carrying all six major QTLe1
- Outcome
- high phenotypic valuese2
- Qualifier
- across multiple environmentse2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“three DH lines carrying all six major QTL were identified”
e2“none of these three DH lines displayed high phenotypic values across multiple environments”
t0“barley population”
Claim · model-written summary
Additional genes with small effect appear to be required to achieve both high disease resistance and grain dormancy in barley.
- Taxon
- barleyHordeum vulgaret0
- Outcome
- high levels of disease resistance and grain dormancye1
- Qualifier
- additional genes with small effect are requirede1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“it appears that additional genes with small effect are required to achieve both high levels of disease resistance and grain dormancy”
t0“barley population”
Claim · model-written summary
Breeding strategies can accelerate the introgression of multiple target traits into adapted cereal cultivars.
Verbatim
e1“the opportunity remains to accelerate the introgression of multiple target traits into adapted cereal cultivars”