Genome-Wide Association Studies of Anthracnose and Angular Leaf Spot Resistance in Common Bean (Phaseolus vulgaris L.)

Abstract

The common bean (Phaseolus vulgaris L.) is the world's most important legume for human consumption. Anthracnose (ANT; Colletotrichum lindemuthianum) and angular leaf spot (ALS; Pseudocercospora griseola) are complex diseases that cause major yield losses in common bean. Depending on the cultivar and environmental conditions, anthracnose and angular leaf spot infections can reduce crop yield drastically. This study aimed to estimate linkage disequilibrium levels and identify quantitative resistance loci (QRL) controlling resistance to both ANT and ALS diseases of 180 accessions of common bean using genome-wide association analysis. A randomized complete block design with four replicates was performed for the ANT and ALS experiments, with four plants per genotype in each replicate. Association mapping analyses were performed for ANT and ALS using a mixed linear model approach implemented in TASSEL. A total of 17 and 11 significant statistically associations involving SSRs were detected for ANT and ALS resistance loci, respectively. Using SNPs, 21 and 17 significant statistically associations were obtained for ANT and angular ALS, respectively, providing more associations with this marker. The SSR-IAC167 and PvM95 markers, both located on chromosome Pv03, and the SNP scaffold00021_89379, were associated with both diseases. The other markers were distributed across the entire common bean genome, with chromosomes Pv03 and Pv08 showing the greatest number of loci associated with ANT resistance. The chromosome Pv04 was the most saturated one, with six markers associated with ALS resistance. The telomeric region of this chromosome showed four markers located between approximately 2.5 Mb and 4.4 Mb. Our results demonstrate the great potential of genome-wide association studies to identify QRLs related to ANT and ALS in common bean. The results indicate a quantitative and complex inheritance pattern for both diseases in common bean. Our findings will contribute to more effective screening of elite germplasm to find resistance alleles for marker-assisted selection in breeding programs.

Fig 1. Linkage disequilibrium (r²) due to the genetic distance in bp, with SSRs markers.

Thresholds corresponding to Bonferroni corrections and FDR are shown on a logarithmic scale with significant associations (in LD) and non-significant vectors above and below, respectively.

Fig 2. Allele pair linkage disequilibrium (r²) across the entire common bean genome for the full group of genotypes, due to the genetic distance in bp, with SNP markers.

Fig 3. Representative map of the genome positions of markers associated with ANT and ALS resistance.

SSR and SNP markers were located on the reference genome (Schmutz et al., 2014) using the Phytozome v1.0 BLAST tool (http://www.phytozome.net/). Markers in blue are associated with ANT resistance and those in red are associated with ALS resistance. The SSR-IAC167, PvM95, and sacaffold00021_89379 markers (green) were associated with resistance to both diseases. The map was drawn with MapChart (Voorrips 2002), and marker positions are represented in Mb.

Fig 4. Example of two homologous gene structure predictions showing the marker location in the locus PvM93.