Brazil is the largest consumer and third highest producer of common beans (Phaseolus vulgaris L.) worldwide. Since the 1980s, the commercial Carioca variety has been the most consumed in Brazil, followed by Black and Special beans. The present study evaluates genetic diversity and population structure of 185 Brazilian common bean cultivars using 2827 high-quality single-nucleotide polymorphisms (SNPs). The Andean allelic introgression in the Mesoamerican accessions was investigated, and a Carioca panel was tested using an association mapping approach. The results distinguish the Mesoamerican from the Andean accessions, with a prevalence of Mesoamerican accessions (94.6%). When considering the commercial classes, low levels of genetic differentiation were seen, and the Carioca group showed the lowest genetic diversity. However, gain in gene diversity and allelic richness was seen for the modern Carioca cultivars. A set of 1060 ‘diagnostic SNPs’ that show alternative alleles between the pure Mesoamerican and Andean accessions were identified, which allowed the identification of Andean allelic introgression events and shows that there are putative introgression segments in regions enriched with resistance genes. Finally, genome-wide association studies revealed SNPs significantly associated with flowering time, pod maturation, and growth habit, showing that the Carioca Association Panel represents a powerful tool for crop improvements.

The common bean is characterized by high sensitivity to drought and low productivity. Breeding for drought resistance in this species involves genes of different genetic groups. In this work, we used a SEA 5 x AND 277 cross to map quantitative trait loci associated with drought tolerance in order to assess the factors that determine the magnitude of drought response in common beans. A total of 438 polymorphic markers were used to genotype the F8 mapping population. Phenotyping was done in two greenhouses, one used to simulate drought and the other to simulate irrigated conditions. Fourteen traits associated with drought tolerance were measured to identify the quantitative trait loci (QTLs). The map was constructed with 331 markers that covered all 11 chromosomes and had a total length of 1515 cM. Twenty-two QTLs were discovered for chlorophyll, leaf and stem fresh biomass, leaf biomass dry weight, leaf temperature, number of pods per plant, number of seeds per plant, seed weight, days to flowering, dry pod weight and total yield under well-watered and drought (stress) conditions. All the QTLs detected under drought conditions showed positive effects of the SEA 5 allele. This study provides a better understanding of the genetic inheritance of drought tolerance in common bean.

Fusarium wilt (Fusarium oxysporum f. sp. phaseoli, Fop) is one of the main fungal soil diseases in common bean. The aim of the present study was to identify genomic regions associated with Fop resistance through genome-wide association studies (GWAS) in a Mesoamerican Diversity Panel (MDP) and to identify potential common bean sources of Fop’s resistance. The MDP was genotyped with BARCBean6K_3BeadChip and evaluated for Fop resistance with two different monosporic strains using the root-dip method. Disease severity rating (DSR) and the area under the disease progress curve (AUDPC), at 21 days after inoculation (DAI), were used for GWAS performed with FarmCPU model. The p-value of each SNP was determined by resampling method and Bonferroni test. For UFV01 strain, two significant single nucleotide polymorphisms (SNPs) were mapped on the Pv05 and Pv11 for AUDPC, and the same SNP (ss715648096) on Pv11 was associated with AUDPC and DSR. Another SNP, mapped on Pv03, showed significance for DSR. Regarding IAC18001 strain, significant SNPs on Pv03, Pv04, Pv05, Pv07 and on Pv01, Pv05, and Pv10 were observed. Putative candidate genes related to nucleotide-binding sites and carboxy-terminal leucine-rich repeats were identified. The markers may be important future tools for genomic selection to Fop disease resistance in beans.

Common bean (Phaseolus vulgaris L.) is one of the most widely grown legumes in the world. Although the crop has high yield potential, average yields in Brazil are low due to several diseases. Angular leaf spot (ALS), caused by Pseudocercospora griseola, is among the most important diseases. A set of 81 accessions from the Instituto Agronômico (IAC, Campinas, SP) germplasm bank were evaluated for ALS resistance and genotyped by 12 microsatellites previously associated with ALS QTL resistance. Allele frequencies, number of alleles per locus, expected heterozygosity (He), and Shannon's Information Index (I) were calculated. The average Ho was 0.12, and the He was 0.54. The STRUCTURE analysis and UPGMA clustering based on Nei's genetic distance indicated a moderate degree of genetic diversity, with 4 and 5 main groups, respectively. Evaluation of the severity of ALS showed that 17% of the accessions had resistance. Cultivars were recommended for breeding crosses aimed at gaining in genetic diversity and resistance to ALS.

Fusarium oxysporum f. sp. phaseoli (Fop) J.B. Kendrich & W.C. Snyder is the causal agent of Fusarium wilt of common bean (Phaseolus vulgaris L.). The objective of this study was to develop microsatellite markers (SSRs) to characterize the genetic diversity of Fop. Two libraries enriched with SSRs were developed and a total of 40 pairs of SSRs were characterized. Out of these, 15 SSRs were polymorphic for 42 Fop isolates. The number of alleles varied from two to ten, with an average of four alleles per locus and an average PIC (Polymorphic Information Content) of 0.38. The genetic diversity assessed by microsatellites for Fop was low, as expected for an asexual fungus, and not associated with geographic origin, but they were able to detect enough genetic variability among isolates in order to differentiate them. Microsatellites are a robust tool widely used for genetic fingerprinting and population structure analyses. SSRs for Fop may be an efficient tool for a better understanding of the ecology, epidemiology and evolution of this pathogen.