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

Abstract

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).

Dissection of Resistance Genes to Pseudomonas syringae pv. phaseolicola in UI3 Common Bean Cultivar

“…The Pse-2 gene, conferring resistance to races 2, 3, 4, 5, 7, 8 and 9, was previously linked in repulsion to the Pse-1 gene for resistance to races 1, 5, 7 and 9 [ 6 ], but the linkage distance between Pse-1 and Pse-2 has not yet been discerned. Recently, Tock et al [ 47 ] mapped a major-effect QTL for the races 2, 7, 8, and 9 on LG10 that overlaps the one reported here (3.411–3.457 Mb), and concluded that it corresponds to race-specific loci Pse-2 . This may indicate that UI3 contains an alternative race-specific resistance allele to the one mapped by Tock et al [ 47 ] and that is tightly linked but is functionally distinct from the race-specific Pse-2 gen.…”

“…Recently, Tock et al [ 47 ] mapped a major-effect QTL for the races 2, 7, 8, and 9 on LG10 that overlaps the one reported here (3.411–3.457 Mb), and concluded that it corresponds to race-specific loci Pse-2 . This may indicate that UI3 contains an alternative race-specific resistance allele to the one mapped by Tock et al [ 47 ] and that is tightly linked but is functionally distinct from the race-specific Pse-2 gen. The Pse-1 gene was completely linked to the SCARs markers SH11.800 and ST8.1350 [ 5 ], but the localization of these markers based on their sequence homology with the reference genome ( ; ) is very distant, 11.18 and 40.99 Mb, respectively.…”

“…Two populations of ~500 F 2 lines from two crosses of the differential resistant cultivar Red Mexican UI3 (R P 1 ) by the differential susceptible cultivars Tendergreen (S P 2 , T) and A52 (S P 2 ) [ 4 , 47 ], were evaluated for resistance to P. syringae pv. phaseolicola .…”

“…The 76 QTLs for pod, primary and trifoliate leaf, and stem resistance to the nine halo blight races were positioned on the eleven common bean LGs [ 46 ]. The QTL mapping in three Recombinant Inbred (RI) populations and an association mapping in an Andean Diversity Panel of common bean identified one major QTL on LG04 conferring resistance to multiple races and several minor race-specific resistance QTLs on LGs 05, 06, 08, 09 and 10 [ 47 ]. However, despite the fact that organ specificity has been shown recently in common bean- Psp interaction [ 46 ], the molecular basis of organ specificity is little characterized, and it is poorly understood why the pathogen preferentially infects only some organs and not the entire plant.…”

Winged bean (Psophocarpus tetragonolobus (L.) DC.) for food and nutritional security: synthesis of past research and future direction

“…Renewed efforts could mirror, to an extent, what the dedicated international centre did back during the 70 s and 80 s, by creating a panel of common accessions for phenotypic screening, and for development of populations with shared molecular information. Such steps are critical also in the development of mapping populations, linkage mapping, and Genome Wide Association Studies (GWAS) for trait discovery, as shown in soybean (Li et al 2018), chickpea (Bajaj et al 2016;Saeed and Darvishzadeh 2017), mung bean (Noble et al 2018), and common bean (Tock et al 2017). This would allow us also to combine phenotypic and genetic data across different environments and assess the degree of adaptability and plasticity of winged bean.…”