Haplotypes at the Phg-2 Locus Are Determining Pathotype-Specificity of Angular Leaf Spot Resistance in Common Bean

Abstract

Angular leaf spot (ALS) is one of the most devastating diseases of common bean (Phaseolus vulgaris L.) and causes serious yield losses worldwide. ALS resistance is reportedly pathotype-specific, but little is known about the efficacy of resistance loci against different pathotypes. Here, we report on ALS resistance evaluations of 316 bean lines under greenhouse and field conditions at multiple sites in Colombia and Uganda. Surprisingly, genome-wide association studies revealed only two of the five previously described resistance loci to be significantly associated with ALS resistance. Phg-2 on chromosome eight was crucial for ALS resistance in all trials, while the resistance locus Phg-4 on chromosome 4 was effective against one particular pathotype. Further dissection of Phg-2 uncovered an unprecedented diversity of functional haplotypes for a resistance locus in common bean. DNA sequence-based clustering identified eleven haplotype groups at Phg-2. One haplotype group conferred broad-spectrum ALS resistance, six showed pathotype-specific effects, and the remaining seven did not exhibit clear resistance patterns. Our research highlights the importance of ALS pathotype-specificity for durable resistance management strategies in common bean. Molecular markers co-segregating with resistance loci and haplotypes will increase breeding efficiency for ALS resistance and allow to react faster to future changes in pathogen pressure and composition.

Keywords: Pseudocercospora griseola; angular leaf spot (ALS); common bean (Phaseolus vulgaris L.); food security; genome-wide association studies (GWAS); pathotype-specificity; plant breeding; plant pathology.

Figure 1

Frequency distributions of disease scores for angular leaf spot (ALS), evaluated in greenhouse (blue) and field trials (green) using the extBALSIT panel containing 316 common bean lines. ALS was scored on a scale from 1 to 9, where 1 is resistant and 9 is highly susceptible. The greenhouse trials were conducted with five different pathotypes, determined by their origin (COL and UG) and race (63–63, 63–47, 61–63, 13–63, and 30–0). Field trials in Colombia (Darien and Quilichao) and Uganda (Kawanda) were inoculated with mixtures of pathotypes previously collected at the corresponding sites. For Darien and Quilichao, the average ALS score from both evaluation years is shown.

Figure 2

Manhattan plots of the genome-wide association studies (GWAS) for angular leaf spot (ALS) resistance in the extBALSIT panel. The greenhouse trials were conducted with five different pathotypes, determined by their origin (COL and UG) and race (63–63, 63–47, 61–63, 13–63, and 30–0). Field trials in Colombia (Darien and Quilichao) and Uganda (Kawanda) were inoculated with mixtures of pathotypes, previously collected at the corresponding sites. On the x-axis, the genomic position of the markers is given. On the y-axis, the negative logarithm to the base 10 of the P-value, representing the significance value, is given. In order to correct for multiple testing, the significance threshold was adjusted through the Bonferroni method, and the new significance threshold is depicted by the black horizontal line.

Figure 3

Dendrogram of hierarchical clustering at the Phg-2 locus. The common bean lines of the extBALSIT panel were clustered according to similarity of their SNP data in the 61.15–62.93 Mbp interval on Chr 8 and divided into eleven haplotype groups. Haplotype groups were named according to the gene pool of the lines (M, Mesoamerican; A, Andean; and M/A = mixed) and numbered. Below the haplotype names, the number of common bean lines in each haplotype group is given and well known ALS resistant common bean lines as well as the reference genome line (G19833) contained in the haplotype groups are indicated. On the y-axis, the Euclidian distance between clusters is shown.

Figure 4

Haplotype groups at the Phg-2 locus and their ALS response, as evaluated in greenhouse and field trials using the extBALSIT panel. For each trial, the ALS response, scored on a scale from 1 (resistant) to 9 (susceptible), is shown for each of the eleven haplotype groups.

Figure 5

Candidate SNPs for marker-assisted selection of Phg-2 haplotypes. Shown is the phenotypic distribution of ALS scores of the two alleles at the SNPs, which are specific for the functional haplotypes M1 (A) and M2 (B). The SNPs on chromosome 8 at position 61,901,182 bp and 62,188,623 bp of the Pv2.1 reference genome that co-segregated with the haplotype groups M1 and M2, respectively, were used. On the y-axis, ALS response scored on a scale from 1 to 9 is shown, whereas scores below 3 (dashed line) are considered resistant. On the x-axis, greenhouse and field trials are indicated, and for each trial, the ALS-resistance response of the two alleles of the SNP is plotted.