Limits...
Genetic mapping of a new race specific resistance allele effective to Puccinia hordei at the Rph9/Rph12 locus on chromosome 5HL in barley.

Dracatos PM, Khatkar MS, Singh D, Park RF - BMC Plant Biol. (2014)

Bottom Line: Marker-trait association analysis of RphC in the CI 9214/Stirling DH population using 4,500 DArT-seq markers identified a highly significant (-log10Pvalue > 17) single peak on the long arm of chromosome 5H (5HL).RphC is an allele of Rph12 (Rph9.z) and is therefore designated Rph9.am.Bioinformatic analysis using sequence arrays from DArT-seq markers in linkage disequilibrium with Rph9.am identified possible candidates for further gene cloning efforts and marker development at the Rph9/Rph12/Rph9.am locus.

View Article: PubMed Central - PubMed

Affiliation: The University of Sydney, Plant Breeding Institute Cobbitty, Private Bag 4011, Narellan, 2567, NSW, Australia. peter.dracatos@sydney.edu.au.

ABSTRACT

Background: Barley is an important cereal crop cultivated for malt and ruminant feed and in certain regions it is used for human consumption. It is vulnerable to numerous foliar diseases including barley leaf rust caused by the pathogen Puccinia hordei.

Results: A temporarily designated resistance locus RphCantala (RphC) identified in the Australian Hordeum vulgare L. cultivar 'Cantala' displayed an intermediate to low infection type (";12 = N") against the P. hordei pathotype 253P- (virulent on Rph1, Rph2, Rph4, Rph6, Rph8 and RphQ). Phenotypic assessment of a 'CI 9214' (susceptible) x 'Stirling' (RphC) (CI 9214/Stirling) doubled haploid (DH) population at the seedling stage using P. hordei pathotype 253P-, confirmed that RphC was monogenically inherited. Marker-trait association analysis of RphC in the CI 9214/Stirling DH population using 4,500 DArT-seq markers identified a highly significant (-log10Pvalue > 17) single peak on the long arm of chromosome 5H (5HL). Further tests of allelism determined that RphC was genetically independent of Rph3, Rph7, Rph11, Rph13 and Rph14, and was an allele of Rph12 (Rph9.z), which also maps to 5HL.

Conclusion: Multipathotype tests and subsequent pedigree analysis determined that 14 related Australian barley varieties (including 'Stirling' and 'Cantala') carry RphC and that the likely source of this resistance is via a Czechoslovakian landrace LV-Kvasice-NA-Morave transferred through common ancestral cultivars 'Hanna' and 'Abed Binder'. RphC is an allele of Rph12 (Rph9.z) and is therefore designated Rph9.am. Bioinformatic analysis using sequence arrays from DArT-seq markers in linkage disequilibrium with Rph9.am identified possible candidates for further gene cloning efforts and marker development at the Rph9/Rph12/Rph9.am locus.

Show MeSH

Related in: MedlinePlus

Marker trait association analysis scans using Fisher’s exact test Vertical axis represents -log10 (P) values of the P-value of the marker trait association. The peaks above minimum threshold of 2 (P-value = 0.03) can be considered as significantly associated. The colours blue and red were used to differentiate between chromosomes (1H-7H). (A) Chromosome-wise plot and (B) genome-wide manhattan plot of chromosome 5HL derived from marker-trait association (MTA) analysis using Fisher’s exact test on 2 X 2 count table for seedling resistance to Puccinia hordei pathotype 253P- (binary scoring data) in the CI9214/Stirling doubled haploid population using 4, 500 DArT-seq markers. The –log10 of P-values were plotted against the positions on the physical Bowman genome assembly [20]. The peaks above minimum threshold of 2 (P-value = 0.03) can be considered as significantly associated.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4302584&req=5

Fig3: Marker trait association analysis scans using Fisher’s exact test Vertical axis represents -log10 (P) values of the P-value of the marker trait association. The peaks above minimum threshold of 2 (P-value = 0.03) can be considered as significantly associated. The colours blue and red were used to differentiate between chromosomes (1H-7H). (A) Chromosome-wise plot and (B) genome-wide manhattan plot of chromosome 5HL derived from marker-trait association (MTA) analysis using Fisher’s exact test on 2 X 2 count table for seedling resistance to Puccinia hordei pathotype 253P- (binary scoring data) in the CI9214/Stirling doubled haploid population using 4, 500 DArT-seq markers. The –log10 of P-values were plotted against the positions on the physical Bowman genome assembly [20]. The peaks above minimum threshold of 2 (P-value = 0.03) can be considered as significantly associated.

Mentions: A total of 61 representative genotypes of the CI 9214/Stirling DH population from both resistant and susceptible phenotypic classes were selected for genetic mapping of RphC and subsequently genotyped using 10,258 DArT-seq marker loci. A genetic map was constructed and contained nine linkage groups spanning 4,246 cM using over 4,500 DArT-seq markers, which include the RphC binary phenotype as a marker. Based on the known positions of flanking markers on the consensus ‘Bowman’ , ‘Morex’ and ‘Barke’ genetic maps, RphC was mapped to chromosome 5HL between 129–134 cM (Figure 2). RphC co-segregated with two DArT markers (DART4872 and DART7508) and was 1.8 cM distal to the flanking markers DART2682, DART5867 and DART7413 and 3.9 cM proximal to DART6236 and DART214 (Figure 2). Further genome-wide marker-trait association demonstrated that DArT sequences only on 5HL were associated with RphC phenotypic scores indicated by two significant peaks [−log10(P-value) of 17.5], across the entire genome, at approximately 506 Mb on 5HL (Figures 3A and 3B) and correlated with LD mapping results of RphC (Additional file 1). Further linkage disequilibrium analysis identified that the 2nd peak at 430 Mb was due to incorrect map position of a single DArT marker (data not shown).Figure 2


Genetic mapping of a new race specific resistance allele effective to Puccinia hordei at the Rph9/Rph12 locus on chromosome 5HL in barley.

Dracatos PM, Khatkar MS, Singh D, Park RF - BMC Plant Biol. (2014)

Marker trait association analysis scans using Fisher’s exact test Vertical axis represents -log10 (P) values of the P-value of the marker trait association. The peaks above minimum threshold of 2 (P-value = 0.03) can be considered as significantly associated. The colours blue and red were used to differentiate between chromosomes (1H-7H). (A) Chromosome-wise plot and (B) genome-wide manhattan plot of chromosome 5HL derived from marker-trait association (MTA) analysis using Fisher’s exact test on 2 X 2 count table for seedling resistance to Puccinia hordei pathotype 253P- (binary scoring data) in the CI9214/Stirling doubled haploid population using 4, 500 DArT-seq markers. The –log10 of P-values were plotted against the positions on the physical Bowman genome assembly [20]. The peaks above minimum threshold of 2 (P-value = 0.03) can be considered as significantly associated.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4302584&req=5

Fig3: Marker trait association analysis scans using Fisher’s exact test Vertical axis represents -log10 (P) values of the P-value of the marker trait association. The peaks above minimum threshold of 2 (P-value = 0.03) can be considered as significantly associated. The colours blue and red were used to differentiate between chromosomes (1H-7H). (A) Chromosome-wise plot and (B) genome-wide manhattan plot of chromosome 5HL derived from marker-trait association (MTA) analysis using Fisher’s exact test on 2 X 2 count table for seedling resistance to Puccinia hordei pathotype 253P- (binary scoring data) in the CI9214/Stirling doubled haploid population using 4, 500 DArT-seq markers. The –log10 of P-values were plotted against the positions on the physical Bowman genome assembly [20]. The peaks above minimum threshold of 2 (P-value = 0.03) can be considered as significantly associated.
Mentions: A total of 61 representative genotypes of the CI 9214/Stirling DH population from both resistant and susceptible phenotypic classes were selected for genetic mapping of RphC and subsequently genotyped using 10,258 DArT-seq marker loci. A genetic map was constructed and contained nine linkage groups spanning 4,246 cM using over 4,500 DArT-seq markers, which include the RphC binary phenotype as a marker. Based on the known positions of flanking markers on the consensus ‘Bowman’ , ‘Morex’ and ‘Barke’ genetic maps, RphC was mapped to chromosome 5HL between 129–134 cM (Figure 2). RphC co-segregated with two DArT markers (DART4872 and DART7508) and was 1.8 cM distal to the flanking markers DART2682, DART5867 and DART7413 and 3.9 cM proximal to DART6236 and DART214 (Figure 2). Further genome-wide marker-trait association demonstrated that DArT sequences only on 5HL were associated with RphC phenotypic scores indicated by two significant peaks [−log10(P-value) of 17.5], across the entire genome, at approximately 506 Mb on 5HL (Figures 3A and 3B) and correlated with LD mapping results of RphC (Additional file 1). Further linkage disequilibrium analysis identified that the 2nd peak at 430 Mb was due to incorrect map position of a single DArT marker (data not shown).Figure 2

Bottom Line: Marker-trait association analysis of RphC in the CI 9214/Stirling DH population using 4,500 DArT-seq markers identified a highly significant (-log10Pvalue > 17) single peak on the long arm of chromosome 5H (5HL).RphC is an allele of Rph12 (Rph9.z) and is therefore designated Rph9.am.Bioinformatic analysis using sequence arrays from DArT-seq markers in linkage disequilibrium with Rph9.am identified possible candidates for further gene cloning efforts and marker development at the Rph9/Rph12/Rph9.am locus.

View Article: PubMed Central - PubMed

Affiliation: The University of Sydney, Plant Breeding Institute Cobbitty, Private Bag 4011, Narellan, 2567, NSW, Australia. peter.dracatos@sydney.edu.au.

ABSTRACT

Background: Barley is an important cereal crop cultivated for malt and ruminant feed and in certain regions it is used for human consumption. It is vulnerable to numerous foliar diseases including barley leaf rust caused by the pathogen Puccinia hordei.

Results: A temporarily designated resistance locus RphCantala (RphC) identified in the Australian Hordeum vulgare L. cultivar 'Cantala' displayed an intermediate to low infection type (";12 = N") against the P. hordei pathotype 253P- (virulent on Rph1, Rph2, Rph4, Rph6, Rph8 and RphQ). Phenotypic assessment of a 'CI 9214' (susceptible) x 'Stirling' (RphC) (CI 9214/Stirling) doubled haploid (DH) population at the seedling stage using P. hordei pathotype 253P-, confirmed that RphC was monogenically inherited. Marker-trait association analysis of RphC in the CI 9214/Stirling DH population using 4,500 DArT-seq markers identified a highly significant (-log10Pvalue > 17) single peak on the long arm of chromosome 5H (5HL). Further tests of allelism determined that RphC was genetically independent of Rph3, Rph7, Rph11, Rph13 and Rph14, and was an allele of Rph12 (Rph9.z), which also maps to 5HL.

Conclusion: Multipathotype tests and subsequent pedigree analysis determined that 14 related Australian barley varieties (including 'Stirling' and 'Cantala') carry RphC and that the likely source of this resistance is via a Czechoslovakian landrace LV-Kvasice-NA-Morave transferred through common ancestral cultivars 'Hanna' and 'Abed Binder'. RphC is an allele of Rph12 (Rph9.z) and is therefore designated Rph9.am. Bioinformatic analysis using sequence arrays from DArT-seq markers in linkage disequilibrium with Rph9.am identified possible candidates for further gene cloning efforts and marker development at the Rph9/Rph12/Rph9.am locus.

Show MeSH
Related in: MedlinePlus