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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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Effects of QTLs ALS10.1DG, UC, GS, ALS9.1GS and ALS5.2UC, GS on angular leaf spot (ALS) resistance in the G5686 × Sprite population infected with Pseudocercospora griseola (Sacc.) Crous and U. Braun pathotype (race 31-0). a Marker17 (ALS10.1) localized on chromosome Pv010 showed significant correlation with ALS resistance (p = 0.003, 52 observations) within the subpopulation of the F3 G5686 × Sprite population with homozygous SS genotypes at Marker50 (ALS4.1GS, UC). b In the same subpopulation, Marker33 (ALS9.1) on Pv09 showed a weak correlation with ALS resistance (p = 0.062, 47 observations). c Marker31 (ALS5.2) localized on Pv05 showed significant influence on ALS resistance (permutation p < 0.05, 130 observations) evaluating the whole F3 population. For each genotype, 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 TukeyHSD (Marker17) and permutation tests (Marker31)
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Fig2: Effects of QTLs ALS10.1DG, UC, GS, ALS9.1GS and ALS5.2UC, GS on angular leaf spot (ALS) resistance in the G5686 × Sprite population infected with Pseudocercospora griseola (Sacc.) Crous and U. Braun pathotype (race 31-0). a Marker17 (ALS10.1) localized on chromosome Pv010 showed significant correlation with ALS resistance (p = 0.003, 52 observations) within the subpopulation of the F3 G5686 × Sprite population with homozygous SS genotypes at Marker50 (ALS4.1GS, UC). b In the same subpopulation, Marker33 (ALS9.1) on Pv09 showed a weak correlation with ALS resistance (p = 0.062, 47 observations). c Marker31 (ALS5.2) localized on Pv05 showed significant influence on ALS resistance (permutation p < 0.05, 130 observations) evaluating the whole F3 population. For each genotype, 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 TukeyHSD (Marker17) and permutation tests (Marker31)

Mentions: Marker17, linked to ALS10.1 localized on chromosome Pv010 at around 38.01 Mbp, showed weak linkage with ALS resistance (permutation p < 0.1, 169 observations). Considering only plants with homozygous SS genotypes at Marker50, correlation of Marker17 with ALS resistance was significant (p = 0.003 including 52 observations, Fig. 2a). Marker17 explained 18.2 % of phenotypic variation in those selected plants. Analysis of further markers at the beginning of Pv010, MarkerA1 (p = 0.010, 40 observations) and MarkerA4 (p = 0.044, 40 observations) at 7.15 and 9.73 Mbp, respectively, also resulted in a weak but significant correlation with ALS resistance considering only susceptible SS genotypes at Marker50.Fig. 2


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)

Effects of QTLs ALS10.1DG, UC, GS, ALS9.1GS and ALS5.2UC, GS on angular leaf spot (ALS) resistance in the G5686 × Sprite population infected with Pseudocercospora griseola (Sacc.) Crous and U. Braun pathotype (race 31-0). a Marker17 (ALS10.1) localized on chromosome Pv010 showed significant correlation with ALS resistance (p = 0.003, 52 observations) within the subpopulation of the F3 G5686 × Sprite population with homozygous SS genotypes at Marker50 (ALS4.1GS, UC). b In the same subpopulation, Marker33 (ALS9.1) on Pv09 showed a weak correlation with ALS resistance (p = 0.062, 47 observations). c Marker31 (ALS5.2) localized on Pv05 showed significant influence on ALS resistance (permutation p < 0.05, 130 observations) evaluating the whole F3 population. For each genotype, 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 TukeyHSD (Marker17) and permutation tests (Marker31)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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Fig2: Effects of QTLs ALS10.1DG, UC, GS, ALS9.1GS and ALS5.2UC, GS on angular leaf spot (ALS) resistance in the G5686 × Sprite population infected with Pseudocercospora griseola (Sacc.) Crous and U. Braun pathotype (race 31-0). a Marker17 (ALS10.1) localized on chromosome Pv010 showed significant correlation with ALS resistance (p = 0.003, 52 observations) within the subpopulation of the F3 G5686 × Sprite population with homozygous SS genotypes at Marker50 (ALS4.1GS, UC). b In the same subpopulation, Marker33 (ALS9.1) on Pv09 showed a weak correlation with ALS resistance (p = 0.062, 47 observations). c Marker31 (ALS5.2) localized on Pv05 showed significant influence on ALS resistance (permutation p < 0.05, 130 observations) evaluating the whole F3 population. For each genotype, 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 TukeyHSD (Marker17) and permutation tests (Marker31)
Mentions: Marker17, linked to ALS10.1 localized on chromosome Pv010 at around 38.01 Mbp, showed weak linkage with ALS resistance (permutation p < 0.1, 169 observations). Considering only plants with homozygous SS genotypes at Marker50, correlation of Marker17 with ALS resistance was significant (p = 0.003 including 52 observations, Fig. 2a). Marker17 explained 18.2 % of phenotypic variation in those selected plants. Analysis of further markers at the beginning of Pv010, MarkerA1 (p = 0.010, 40 observations) and MarkerA4 (p = 0.044, 40 observations) at 7.15 and 9.73 Mbp, respectively, also resulted in a weak but significant correlation with ALS resistance considering only susceptible SS genotypes at Marker50.Fig. 2

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