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Association mapping of spot blotch resistance in wild barley.

Roy JK, Smith KP, Muehlbauer GJ, Chao S, Close TJ, Steffenson BJ - Mol. Breed. (2010)

Bottom Line: A high frequency of resistance was found in the WBDC as 95% (302/318) of the accessions exhibited low infection responses.These QTL were found on chromosomes 1H, 2H, 3H, 5H, and 7H and explained from 2.3 to 3.9% of the phenotypic variance.This study demonstrates that AM is an effective technique for identifying and mapping QTL for disease resistance in a wild crop progenitor.

View Article: PubMed Central - PubMed

ABSTRACT
Spot blotch, caused by Cochliobolus sativus, is an important foliar disease of barley. The disease has been controlled for over 40 years through the deployment of cultivars with durable resistance derived from the line NDB112. Pathotypes of C. sativus with virulence for the NDB112 resistance have been detected in Canada; thus, many commercial cultivars are vulnerable to spot blotch epidemics. To increase the diversity of spot blotch resistance in cultivated barley, we evaluated 318 diverse wild barley accessions comprising the Wild Barley Diversity Collection (WBDC) for reaction to C. sativus at the seedling stage and utilized an association mapping (AM) approach to identify and map resistance loci. A high frequency of resistance was found in the WBDC as 95% (302/318) of the accessions exhibited low infection responses. The WBDC was genotyped with 558 Diversity Array Technology (DArT((R))) and 2,878 single nucleotide polymorphism (SNP) markers and subjected to structure analysis before running the AM procedure. Thirteen QTL for spot blotch resistance were identified with DArT and SNP markers. These QTL were found on chromosomes 1H, 2H, 3H, 5H, and 7H and explained from 2.3 to 3.9% of the phenotypic variance. Nearly half of the identified QTL mapped to chromosome bins where spot blotch resistance loci were previously reported, offering some validation for the AM approach. The other QTL mapped to unique genomic regions and may represent new spot blotch resistance loci. This study demonstrates that AM is an effective technique for identifying and mapping QTL for disease resistance in a wild crop progenitor. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-010-9402-8) contains supplementary material, which is available to authorized users.

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Related in: MedlinePlus

Triangular linkage disequilibrium (LD) matrix plot of nine DArT® markers on chromosome 1H in the Wild Barley Diversity Collection (WBDC). The plots were produced using pairwise R2 estimates of LD with the computer program, Haploview (Barrett et al. 2005). In the figure, the pairwise R2 values are given inside the boxes. The solid back boxes represent a pairwise R2 value of 1.0
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Fig3: Triangular linkage disequilibrium (LD) matrix plot of nine DArT® markers on chromosome 1H in the Wild Barley Diversity Collection (WBDC). The plots were produced using pairwise R2 estimates of LD with the computer program, Haploview (Barrett et al. 2005). In the figure, the pairwise R2 values are given inside the boxes. The solid back boxes represent a pairwise R2 value of 1.0

Mentions: To determine the extent of LD at QTL detected in this study, we identified all of the markers in LD (R2 > 0.2) with the marker associated with spot blotch resistance. We then characterized the size of this region in cM and determined whether the other markers in LD were significantly associated with spot blotch resistance. Of the 12 QTL identified and mapped in this study, three had at least one adjacent marker in LD with the most significant marker associated with the trait. Strong LD (R2 ≥ 0.96) was found for the QTL-identifying marker bPb-2813 on chromosome 1H at 59.7 cM. Three other flanking markers (bPb-0468, bPb-7325, and bPb-7859) at the same location were in strong LD (R2 range of 0.96–1.0) with bPb-2813 (Fig. 3). These three markers also showed highly significant associations with spot blotch resistance (P = 0.003–0.006). Additionally, the above-mentioned four markers also were in strong LD with bPb-2967, a marker significantly associated (P = 0.000; R2 range of 0.96–1.0) with spot blotch resistance on chromosome 1H at 60.7 cM. Although the QTL detected by markers bPb-2813 and bPb-2967 were 1.0 cM apart, we considered these five adjacent markers to be detecting the same QTL because they have strong LD with each other and are all significantly associated with spot blotch resistance. On chromosome 5H, the QTL-identifying marker at 276.8 cM (11_20189) exhibited moderate LD (R2 = 0.39) with one flanking marker (data not shown); however, this flanking marker was not significantly associated with spot blotch resistance. The QTL-identifying marker on chromosome 7H at 107.4 cM (12_30004) had moderate to strong LD (R2 range of 0.11–1.0) with seven other markers at the same position (data not shown). Two of these markers (12_31215 and 12_30563) showed a highly significant association with spot blotch resistance (P = 0.003 and 0.008, respectively).Fig. 3


Association mapping of spot blotch resistance in wild barley.

Roy JK, Smith KP, Muehlbauer GJ, Chao S, Close TJ, Steffenson BJ - Mol. Breed. (2010)

Triangular linkage disequilibrium (LD) matrix plot of nine DArT® markers on chromosome 1H in the Wild Barley Diversity Collection (WBDC). The plots were produced using pairwise R2 estimates of LD with the computer program, Haploview (Barrett et al. 2005). In the figure, the pairwise R2 values are given inside the boxes. The solid back boxes represent a pairwise R2 value of 1.0
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2908432&req=5

Fig3: Triangular linkage disequilibrium (LD) matrix plot of nine DArT® markers on chromosome 1H in the Wild Barley Diversity Collection (WBDC). The plots were produced using pairwise R2 estimates of LD with the computer program, Haploview (Barrett et al. 2005). In the figure, the pairwise R2 values are given inside the boxes. The solid back boxes represent a pairwise R2 value of 1.0
Mentions: To determine the extent of LD at QTL detected in this study, we identified all of the markers in LD (R2 > 0.2) with the marker associated with spot blotch resistance. We then characterized the size of this region in cM and determined whether the other markers in LD were significantly associated with spot blotch resistance. Of the 12 QTL identified and mapped in this study, three had at least one adjacent marker in LD with the most significant marker associated with the trait. Strong LD (R2 ≥ 0.96) was found for the QTL-identifying marker bPb-2813 on chromosome 1H at 59.7 cM. Three other flanking markers (bPb-0468, bPb-7325, and bPb-7859) at the same location were in strong LD (R2 range of 0.96–1.0) with bPb-2813 (Fig. 3). These three markers also showed highly significant associations with spot blotch resistance (P = 0.003–0.006). Additionally, the above-mentioned four markers also were in strong LD with bPb-2967, a marker significantly associated (P = 0.000; R2 range of 0.96–1.0) with spot blotch resistance on chromosome 1H at 60.7 cM. Although the QTL detected by markers bPb-2813 and bPb-2967 were 1.0 cM apart, we considered these five adjacent markers to be detecting the same QTL because they have strong LD with each other and are all significantly associated with spot blotch resistance. On chromosome 5H, the QTL-identifying marker at 276.8 cM (11_20189) exhibited moderate LD (R2 = 0.39) with one flanking marker (data not shown); however, this flanking marker was not significantly associated with spot blotch resistance. The QTL-identifying marker on chromosome 7H at 107.4 cM (12_30004) had moderate to strong LD (R2 range of 0.11–1.0) with seven other markers at the same position (data not shown). Two of these markers (12_31215 and 12_30563) showed a highly significant association with spot blotch resistance (P = 0.003 and 0.008, respectively).Fig. 3

Bottom Line: A high frequency of resistance was found in the WBDC as 95% (302/318) of the accessions exhibited low infection responses.These QTL were found on chromosomes 1H, 2H, 3H, 5H, and 7H and explained from 2.3 to 3.9% of the phenotypic variance.This study demonstrates that AM is an effective technique for identifying and mapping QTL for disease resistance in a wild crop progenitor.

View Article: PubMed Central - PubMed

ABSTRACT
Spot blotch, caused by Cochliobolus sativus, is an important foliar disease of barley. The disease has been controlled for over 40 years through the deployment of cultivars with durable resistance derived from the line NDB112. Pathotypes of C. sativus with virulence for the NDB112 resistance have been detected in Canada; thus, many commercial cultivars are vulnerable to spot blotch epidemics. To increase the diversity of spot blotch resistance in cultivated barley, we evaluated 318 diverse wild barley accessions comprising the Wild Barley Diversity Collection (WBDC) for reaction to C. sativus at the seedling stage and utilized an association mapping (AM) approach to identify and map resistance loci. A high frequency of resistance was found in the WBDC as 95% (302/318) of the accessions exhibited low infection responses. The WBDC was genotyped with 558 Diversity Array Technology (DArT((R))) and 2,878 single nucleotide polymorphism (SNP) markers and subjected to structure analysis before running the AM procedure. Thirteen QTL for spot blotch resistance were identified with DArT and SNP markers. These QTL were found on chromosomes 1H, 2H, 3H, 5H, and 7H and explained from 2.3 to 3.9% of the phenotypic variance. Nearly half of the identified QTL mapped to chromosome bins where spot blotch resistance loci were previously reported, offering some validation for the AM approach. The other QTL mapped to unique genomic regions and may represent new spot blotch resistance loci. This study demonstrates that AM is an effective technique for identifying and mapping QTL for disease resistance in a wild crop progenitor. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-010-9402-8) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus