Screening Andean Diversity Panel Dry Bean Lines for Resistance to Bacterial Brown Spot Disease Under Field Conditions in South Africa.

Bacterial brown spot (BBS) disease caused by Pseudomonas syringae pv. syringae is an important disease of dry bean (Phaseolus vulgaris L.), with grain yield losses of 55% reported in South Africa. This study aimed to identify BBS disease-resistant genotypes from 415 Andean Diversity Panel (ADP) dry bean lines and 5 check cultivars under field conditions across three sites in South Africa: Warden and Middelburg under natural infestation and Potchefstroom under artificial inoculation. Plants at Potchefstroom were inoculated with P. syringae pv. syringae using three isolates at 21, 28, and 36 days after planting, and disease scoring was done at 7, 14, and 21 days after inoculation following a modified 1 to 9 International Centre for Tropical Agriculture (CIAT) scale. The BBS severity percentage and the area under the disease progress curve (AUDPC) were applied to quantify the reaction of bean genotypes to BBS disease. The study identified 17.2% of evaluated germplasm as resistant and 45.3% as moderately resistant. Genotypes ADP-0592, ADP-0790, ADP-0120, and ADP-0008 were selected for both resistance and high seed yield across the three environments. Genotypes ADP-0546, ADP-0630, ADP-0120, and ADP-0279 were selected for both high yield and resistance at Warden, whereas ADP-0038, ADP-0721, and ADP-0790 were selected for both traits at Middelburg, and lastly, ADP-0120 and ADP-0079 were selected for both traits at Potchefstroom. The best genotypes selected for both high yield and BBS resistance had grain yield >1.45 t ha-1 across sites and >1.85 t ha-1 at individual sites, and they out yielded the best-performing check cultivar (1.13 t ha-1) and the grand mean yield (0.87 t ha-1) across sites. The AUDPC had a strong negative correlation (r = -0.55, P < 0.001) with grain yield at Potchefstroom. Medium-seeded genotypes showed a lower AUDPC than the large-seeded genotypes, and indeterminate genotypes showed a lower AUDPC than determinate genotypes. The genotypes selected for resistance and yield can be utilized in future dry bean improvement efforts for the South African bean market.

Analyses of African common bean (Phaseolus vulgaris L.) germplasm using a SNP fingerprinting platform: diversity, quality control and molecular breeding.

Common bean (Phaseolus vulgaris L.) is an important staple crop for smallholder farmers, particularly in Eastern and Southern Africa. To support common bean breeding and seed dissemination, a high throughput SNP genotyping platform with 1500 established SNP assays has been developed at a genotyping service provider which allows breeders without their own genotyping infrastructure to outsource such service. A set of 708 genotypes mainly composed of germplasm from African breeders and CIAT breeding program were assembled and genotyped with over 800 SNPs. Diversity analysis revealed that both Mesoamerican and Andean gene pools are in use, with an emphasis on large seeded Andean genotypes, which represents the known regional preferences. The analysis of genetic similarities among germplasm entries revealed duplicated lines with different names as well as distinct SNP patterns in identically named samples. Overall, a worrying number of inconsistencies was identified in this data set of very diverse origins. This exemplifies the necessity to develop and use a cost-effective fingerprinting platform to ensure germplasm purity for research, sharing and seed dissemination. The genetic data also allows to visualize introgressions, to identify heterozygous regions to evaluate hybridization success and to employ marker-assisted selection. This study presents a new resource for the common bean community, a SNP genotyping platform, a large SNP data set and a number of applications on how to utilize this information to improve the efficiency and quality of seed handling activities, breeding, and seed dissemination through molecular tools.

Genome-Wide Linkage and Association Mapping of Halo Blight Resistance in Common Bean to Race 6 of the Globally Important Bacterial Pathogen.

Pseudomonas syringae pv. phaseolicola (Psph) Race 6 is a globally prevalent and broadly virulent bacterial pathogen with devastating impact causing halo blight of common bean (Phaseolus vulgaris L.). Common bean lines PI 150414 and CAL 143 are known sources of resistance against this pathogen. We constructed high-resolution linkage maps for three recombinant inbred populations to map resistance to Psph Race 6 derived from the two common bean lines. This was complemented with a genome-wide association study (GWAS) of Race 6 resistance in an Andean Diversity Panel of common bean. Race 6 resistance from PI 150414 maps to a single major-effect quantitative trait locus (QTL; HB4.2) on chromosome Pv04 and confers broad-spectrum resistance to eight other races of the pathogen. Resistance segregating in a Rojo × CAL 143 population maps to five chromosome arms and includes HB4.2. GWAS detected one QTL (HB5.1) on chromosome Pv05 for resistance to Race 6 with significant influence on seed yield. The same HB5.1 QTL, found in both Canadian Wonder × PI 150414 and Rojo × CAL 143 populations, was effective against Race 6 but lacks broad resistance. This study provides evidence for marker-assisted breeding for more durable halo blight control in common bean by combining alleles of race-nonspecific resistance (HB4.2 from PI 150414) and race-specific resistance (HB5.1 from cv. Rojo).

Development of candidate gene markers associated to common bacterial blight resistance in common bean.

Common bacterial blight (CBB), caused by Xanthomonas axonopodis pv. phaseoli (Xap), is a major yield-limiting factor of common bean (Phaseolus vulgaris L.) production around the world. Two major CBB-resistant quantitative trait loci (QTL), linked to the sequence characterized amplified region markers BC420 and SU91, are located at chromosomes 6 and 8, respectively. Using map-based cloning approach, four bacterial artificial chromosome (BAC) clones from the BC420-QTL locus and one BAC clone containing SU91 were sequenced by Roche 454 technique and subsequently assembled using merged assemblies from three different programs. Based on the quality of the assembly, only the sequences of BAC 32H6 and 4K7 were used for candidate gene marker (CGM) development and candidate gene (CG) selection. For the BC420-QTL locus, 21 novel genes were predicted in silico by FGENESH using Medicago gene model, whereas 16 genes were identified in the SU91-QTL locus. For each putative gene, one or more primer pairs were designed and tested in the contrasting near isogenic lines. Overall, six and nine polymorphic markers were found in the SU91- and BC420-QTL loci, respectively. Afterwards, association mapping was conducted in a breeding population of 395 dry bean lines to discover marker-trait associations. Two CGMs per each locus showed better association with CBB resistance than the BC420 and SU91 markers, which include BC420-CG10B and BC420-CG14 for BC420_QTL locus, and SU91-CG10 and SU91-CG11 for SU91_QTL locus. The strong associations between CBB resistance and the CGs 10 and 14 from BC420_QTL locus and the CGs 10 and 11 from SU91_QTL locus indicate that the genes 10 and 14 from the BC420 locus are potential CGs underlying the BC420_QTL locus, whereas the genes 10 and 11 from the SU91 locus are potential CGs underlying the SU91_QTL locus. The superiority of SU91-CG11 was further validated in a recombinant inbred line population Sanilac × OAC 09-3. Thus, co-dominant CGMs, BC420-CG14 and SU91-CG11, are recommended to replace BC420 and SU91 for marker-assisted selection of common bean with resistance to CBB.