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Fine-mapping of a major QTL controlling angular leaf spot resistance in common bean (Phaseolus vulgaris L.).

Keller B, Manzanares C, Jara C, Lobaton JD, Studer B, Raatz B - Theor. Appl. Genet. (2015)

Bottom Line: Additional evaluation of 153 F4, 89 BC1F2 and 139 F4/F5/BC1F3 descendants with markers in the region of the major QTL delimited the region to 418 kbp harboring 36 candidate genes.Among these, 11 serine/threonine protein kinases arranged in a repetitive array constitute promising candidate genes for controlling ALS resistance.Single nucleotide polymorphism markers cosegregating with the major QTL for ALS resistance have been developed and constitute the basis for marker-assisted introgression of ALS resistance into advanced breeding germplasm of common bean.

View Article: PubMed Central - PubMed

Affiliation: Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland, kellebea@alumni.ethz.ch.

ABSTRACT

Key message: A major QTL for angular leaf spot resistance in the common bean accession G5686 was fine-mapped to a region containing 36 candidate genes. Markers have been developed for marker-assisted selection. Common bean (Phaseolus vulgaris L.) is an important grain legume and an essential protein source for human nutrition in developing countries. Angular leaf spot (ALS) caused by the pathogen Pseudocercospora griseola (Sacc.) Crous and U. Braun is responsible for severe yield losses of up to 80%. Breeding for resistant cultivars is the most ecological and economical means to control ALS and is particularly important for yield stability in low-input agriculture. Here, we report on a fine-mapping approach of a major quantitative trait locus (QTL) ALS4.1(GS, UC) for ALS resistance in a mapping population derived from the resistant genotype G5686 and the susceptible cultivar Sprite. 180 F3 individuals of the mapping population were evaluated for ALS resistance and genotyped with 22 markers distributed over 11 genome regions colocating with previously reported QTL for ALS resistance. Multiple QTL analysis identified three QTL regions, including one major QTL on chromosome Pv04 at 43.7 Mbp explaining over 75% of the observed variation for ALS resistance. Additional evaluation of 153 F4, 89 BC1F2 and 139 F4/F5/BC1F3 descendants with markers in the region of the major QTL delimited the region to 418 kbp harboring 36 candidate genes. Among these, 11 serine/threonine protein kinases arranged in a repetitive array constitute promising candidate genes for controlling ALS resistance. Single nucleotide polymorphism markers cosegregating with the major QTL for ALS resistance have been developed and constitute the basis for marker-assisted introgression of ALS resistance into advanced breeding germplasm of common bean.

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One major QTL controls angular leaf spot (ALS) resistance in the G5686 × Sprite population in an evaluation of 180 F3 plants infected with Pseudocercospora griseola (Sacc.) Crous and U. Braun pathotype (race 31-0). aBox plot sorted by the genotypes at Marker50 shows significant correlation (permutation p < 2e−16, 161 observations) to ALS disease scores, explaining 70.4 % of the phenotypic variation for ALS resistance. The horizontal bar (bold) indicates the median, the box represents inter-quartile range, discontinuous lines represent the upper and lower quartile, and outlier samples (>1.5 × inter-quartile range) are depicted by a circle. Letters indicate significant differences between genotypes using permutation tests. b LOD curve with Marker8, 50 and 9 revealed Marker50 at 43,773,443 bp as closest linked with ALS resistance gene. Dashed line represents LOD score threshold for the 5 % significance level
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Fig1: One major QTL controls angular leaf spot (ALS) resistance in the G5686 × Sprite population in an evaluation of 180 F3 plants infected with Pseudocercospora griseola (Sacc.) Crous and U. Braun pathotype (race 31-0). aBox plot sorted by the genotypes at Marker50 shows significant correlation (permutation p < 2e−16, 161 observations) to ALS disease scores, explaining 70.4 % of the phenotypic variation for ALS resistance. The horizontal bar (bold) indicates the median, the box represents inter-quartile range, discontinuous lines represent the upper and lower quartile, and outlier samples (>1.5 × inter-quartile range) are depicted by a circle. Letters indicate significant differences between genotypes using permutation tests. b LOD curve with Marker8, 50 and 9 revealed Marker50 at 43,773,443 bp as closest linked with ALS resistance gene. Dashed line represents LOD score threshold for the 5 % significance level

Mentions: Four markers (Marker7, 8, 50 and 9) were analyzed in the region of ALS4.1. Single QTL analysis by interval mapping showed that Marker50 had the most significant effect on ALS resistance (LOD score of 45.9, Fig. 1a), masking all other QTL effects in the single QTL analysis. In accordance with the reported dominant inheritance of ALS resistance, the Marker50 genotypes GG and GS resulted in resistant phenotypes and SS in susceptible phenotypes (permutation p < 2e−16 including 172 observations, Fig. 1a). However, heterozygous GS genotypes had lower resistance levels indicating some codominance effect. Marker50 showed complete linkage with ALS resistance in the sense of all homozygous plants with genotype GG being resistant. Only three plants with a Sprite SS genotype on this locus (according to all four markers in the region) were evaluated as resistant, suggesting phenotypic escapes or involvement of other loci.Fig. 1


Fine-mapping of a major QTL controlling angular leaf spot resistance in common bean (Phaseolus vulgaris L.).

Keller B, Manzanares C, Jara C, Lobaton JD, Studer B, Raatz B - Theor. Appl. Genet. (2015)

One major QTL controls angular leaf spot (ALS) resistance in the G5686 × Sprite population in an evaluation of 180 F3 plants infected with Pseudocercospora griseola (Sacc.) Crous and U. Braun pathotype (race 31-0). aBox plot sorted by the genotypes at Marker50 shows significant correlation (permutation p < 2e−16, 161 observations) to ALS disease scores, explaining 70.4 % of the phenotypic variation for ALS resistance. The horizontal bar (bold) indicates the median, the box represents inter-quartile range, discontinuous lines represent the upper and lower quartile, and outlier samples (>1.5 × inter-quartile range) are depicted by a circle. Letters indicate significant differences between genotypes using permutation tests. b LOD curve with Marker8, 50 and 9 revealed Marker50 at 43,773,443 bp as closest linked with ALS resistance gene. Dashed line represents LOD score threshold for the 5 % significance level
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4544502&req=5

Fig1: One major QTL controls angular leaf spot (ALS) resistance in the G5686 × Sprite population in an evaluation of 180 F3 plants infected with Pseudocercospora griseola (Sacc.) Crous and U. Braun pathotype (race 31-0). aBox plot sorted by the genotypes at Marker50 shows significant correlation (permutation p < 2e−16, 161 observations) to ALS disease scores, explaining 70.4 % of the phenotypic variation for ALS resistance. The horizontal bar (bold) indicates the median, the box represents inter-quartile range, discontinuous lines represent the upper and lower quartile, and outlier samples (>1.5 × inter-quartile range) are depicted by a circle. Letters indicate significant differences between genotypes using permutation tests. b LOD curve with Marker8, 50 and 9 revealed Marker50 at 43,773,443 bp as closest linked with ALS resistance gene. Dashed line represents LOD score threshold for the 5 % significance level
Mentions: Four markers (Marker7, 8, 50 and 9) were analyzed in the region of ALS4.1. Single QTL analysis by interval mapping showed that Marker50 had the most significant effect on ALS resistance (LOD score of 45.9, Fig. 1a), masking all other QTL effects in the single QTL analysis. In accordance with the reported dominant inheritance of ALS resistance, the Marker50 genotypes GG and GS resulted in resistant phenotypes and SS in susceptible phenotypes (permutation p < 2e−16 including 172 observations, Fig. 1a). However, heterozygous GS genotypes had lower resistance levels indicating some codominance effect. Marker50 showed complete linkage with ALS resistance in the sense of all homozygous plants with genotype GG being resistant. Only three plants with a Sprite SS genotype on this locus (according to all four markers in the region) were evaluated as resistant, suggesting phenotypic escapes or involvement of other loci.Fig. 1

Bottom Line: Additional evaluation of 153 F4, 89 BC1F2 and 139 F4/F5/BC1F3 descendants with markers in the region of the major QTL delimited the region to 418 kbp harboring 36 candidate genes.Among these, 11 serine/threonine protein kinases arranged in a repetitive array constitute promising candidate genes for controlling ALS resistance.Single nucleotide polymorphism markers cosegregating with the major QTL for ALS resistance have been developed and constitute the basis for marker-assisted introgression of ALS resistance into advanced breeding germplasm of common bean.

View Article: PubMed Central - PubMed

Affiliation: Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland, kellebea@alumni.ethz.ch.

ABSTRACT

Key message: A major QTL for angular leaf spot resistance in the common bean accession G5686 was fine-mapped to a region containing 36 candidate genes. Markers have been developed for marker-assisted selection. Common bean (Phaseolus vulgaris L.) is an important grain legume and an essential protein source for human nutrition in developing countries. Angular leaf spot (ALS) caused by the pathogen Pseudocercospora griseola (Sacc.) Crous and U. Braun is responsible for severe yield losses of up to 80%. Breeding for resistant cultivars is the most ecological and economical means to control ALS and is particularly important for yield stability in low-input agriculture. Here, we report on a fine-mapping approach of a major quantitative trait locus (QTL) ALS4.1(GS, UC) for ALS resistance in a mapping population derived from the resistant genotype G5686 and the susceptible cultivar Sprite. 180 F3 individuals of the mapping population were evaluated for ALS resistance and genotyped with 22 markers distributed over 11 genome regions colocating with previously reported QTL for ALS resistance. Multiple QTL analysis identified three QTL regions, including one major QTL on chromosome Pv04 at 43.7 Mbp explaining over 75% of the observed variation for ALS resistance. Additional evaluation of 153 F4, 89 BC1F2 and 139 F4/F5/BC1F3 descendants with markers in the region of the major QTL delimited the region to 418 kbp harboring 36 candidate genes. Among these, 11 serine/threonine protein kinases arranged in a repetitive array constitute promising candidate genes for controlling ALS resistance. Single nucleotide polymorphism markers cosegregating with the major QTL for ALS resistance have been developed and constitute the basis for marker-assisted introgression of ALS resistance into advanced breeding germplasm of common bean.

Show MeSH
Related in: MedlinePlus