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.Electronic supplementary materialThe online version of this article (10.1007/s10722-019-00746-0) contains supplementary material, which is available to authorized users.

Drought stress is becoming one of the most important abiotic factors limiting productivity of common bean (Phaseolus vulgaris L.) globally. The objective of this study was to conduct a quantitative trait loci (QTL) analysis of drought tolerance in a recombinant inbred line (RIL) mapping population genotyped using single nucleotide polymorphism (SNP) markers. The RIL population was developed by crossing Portillo × Red Hawk, two Andean bean genotypes contrasting in reaction to drought stress and evaluated at two locations in Uganda for two seasons under drought stress (DS) and non‐stress (NS) conditions. Eighteen significant QTL signals were identified for phenology, yield component and partitioning traits on chromosomes Pv01, Pv02, Pv03, Pv04, Pv06, and Pv11 under DS and NS conditions. Quantitative trait loci for seed yield per plant (SY) were detected on Pv01, Pv02, Pv03, Pv04, and Pv06 under DS conditions. Colocalized QTL signals for pod weight per plant and SY were identified under DS on Pv01 (45.15 Mb) and on Pv02 (0.12 Mb), for phenology and SY on Pv03 near marker ss715639424 (40.16 Mb), and for SY and harvest index on Pv06 (17.92 Mb). Two candidate genes related to flowering were identified within a 35‐kb region from the ss715639424 marker on Pv03. Gene Phvul.003G189100 (30.3 kb) encodes “AGAMOUS‐LIKE 65 (AGL65),” which is essential for pollen development, and gene Phvul.003G189300 (17.9 kb) encodes “CYCLING DOF FACTOR 3 (CDF3)” that regulates flowering time. The same SY QTL, SY3.3PR on Pv03, was previously detected in Mesoamerican germplasm and could be used through marker‐assisted breeding to improve SY of Andean beans grown under DS.

common bean variety choice by farmers in Uganda is driven by seed yield plus end-use quality traits like market class and cooking time. Limited genotype by environment information is available for traits valued by consumers. this research evaluated yield, seed size, hydration properties, and cooking time of 15 common bean genotypes within market classes recognized by consumers along with three farmers' checks at nine on-farm locations in Uganda for two seasons. Yield ranged from 71 to 3,216 kg ha −1 and was largely controlled by location (21.5% of Total Sums of Squares [TSS]), plus the interaction between location and season (48.6% of TSS). Cooking time varied from 19 to 271 minutes with the genotypes Cebo Cela and Ervilha consistently cooking fastest in 24 and 27 minutes respectively. Comparatively, the local checks (NABE-4, NABE-15, and Masindi yellow) took 35 to 45 minutes to cook. Cooking time was largely controlled by genotype (40.6% of TSS). A GGE biplot analysis uncovered the presence of two mega-environments for yield and one mega-environment for cooking time. Identification of mega-environments for these traits will help expedite common bean breeding, evaluation, and variety selection through reduction of number of test environments needed for phenotype evaluations. the high yielding and fast cooking genotypes from this study can be targeted as parental materials to improve existing common bean germplasm for these important traits.

Common bean (Phaseolus vulgaris L.) is an important legume crop worldwide. The International Centre for Tropical Agriculture (CIAT) and its national partners in Africa aim to overcome production constraints of common bean and address the food, nutrition needs and market demands through development of multitrait bean varieties. Breeding is guided by principles of market‐driven approaches to develop client‐demanded varieties. Germplasm accessions from especially two sister species, P. coccineus and P. acutifolius, have been utilized as sources of resistance to major production constraints and interspecific lines deployed. Elucidation of plant mechanisms governing pest and disease resistance, abiotic stress tolerance and grain nutritional quality guides the selection methods used by the breeders. Molecular markers are used to select for resistance to key diseases and insect pests. Efforts have been made to utilize modern genomic tools to increase scale, efficiency, accuracy and speed of breeding. Through gender‐responsive participatory variety selection, market‐demanded varieties have been released in several African countries. These new bean varieties are a key component of sustainable food systems in the tropics.

SUMMARYRoot rots are one of the main biotic constraints to common bean (Phaseolus vulgaris L.) production, causing losses estimated at 221 000 metric tons a year in sub-Saharan Africa. Until recently, root rots in Ugandan common bean agroecologies were mostly caused by Pythium and Fusarium spp., especially in high altitude areas. But now, severe root rots are observed in low and medium altitude agroecologies characterized by dry and warm conditions. The objective of our study was therefore to ascertain the current prevalence and incidence of common bean root rot diseases in Ugandan common bean agroecologies. Our results show that root rots were present in all seven agroecologies surveyed. Overall, the most rampant root rot was southern blight caused by Sclerotium rolfsii Sacc., followed by root rots caused by Fusarium spp., Pythium spp. and Rhizoctonia solani, respectively. Our study clearly showed the influence of environmental conditions on the prevalence and incidence of common bean root rots. While Fusarium and Pythium root rots are favoured under low air temperature and high air humidity in highland areas, high incidence of southern blight is favoured by warm and moist conditions of lowland areas. The prevalence and incidence of common bean root rots was mapped, providing a reliable baseline for future studies. Similarly, hotspots identified for common bean root rots will be a very useful resource for evaluation of germplasm and breeding lines for resistance to root rots.