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.

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We announce the genome sequence for Xanthomonas species strain Nyagatare, isolated from beans showing unusual disease symptoms in Rwanda. This strain represents the first sequenced genome belonging to an as-yet undescribed Xanthomonas species known as species-level clade 1. It has at least 100 kb of genomic sequence that shows little or no sequence similarity to other xanthomonads, including a unique lipopolysaccharide synthesis gene cluster. At least one genomic region appears to have been acquired from relatives of Agrobacterium or Rhizobium species. The genome encodes homologues of only three known type-three secretion system effectors: AvrBs2, XopF1 and AvrXv4. Availability of the genome sequence will facilitate development of molecular tools for detection and diagnostics for this newly discovered pathogen of beans and facilitate epidemiological investigations of a potential causal link between this pathogen and the disease outbreak.

Iron and zinc are essential micronutrients for normal human growth and development and are commonly deficient in diets of the most vulnerable. Common bean (Phaseolus vulgaris L.), one of the leading staple foods in East and Central Africa, is a valuable source of quality protein and micronutrients, specifically iron, zinc, and vitamins. Natural variation in micronutrient concentration exists among bean germplasm. Identification of varieties with high iron and zinc seed concentration (FESEED/ZNSEED) for promotion in food systems and utilisation in breeding programs is one strategy of addressing the problem of malnutrition in Africa. Three hundred and four lines sourced from the International Centre for Tropical Agriculture (CIAT) and its partners through the Pan Africa Bean Research Alliance (PABRA), were evaluated for agronomic traits, disease response, yield, FESEED, and ZNSEED. They were organized in four groups; PABRA fast track, Rwanda seeds of hope, HarvestPlus regional nutrition nursery and Uganda collection. Six checks were included; a universal high FESEED climbing bean (MIB465), low FESEED regional climbing bean (Decelaya), universal low FESEED bush bean (DOR500), regional high FESEED bush bean (RWR2154), and two yield checks (CAL96 and Vuninkingi for bush and climbing bean). The FESEED checks were selected based on their relative performance to other genotypes in several experiments by a community of bean breeders through the H+ program. Field trials were established at the National Agricultural Laboratories, Kawanda from 2011 to 2013. Days to maturity and flowering, vigor, yield, and reaction to diseases were evaluated. Micronutrient analysis was conducted using X-ray Fluorescence (XRF) and data confirmed using Inductively Coupled Plasma Atomic Emission Spectrometry (ICP-AES). Lines were significantly different (P≤0.05) in all the parameters assessed. FESEED and ZNSEED varied highly between seasons and among the entries ranging between 36-90 ppm and 24-47 ppm across the four nurseries. Twenty-six lines were selected as high iron beans (HIBs) based on XRF data; 12 of these were confirmed as HIB based on ICP data that is more accurate. Of these, two bush beans, Jesca (large purple speckled) and RW547 (medium grey) and two climbing beans, CAB2 (medium white seeded) and Ndimirakaguja (small cream) were the most superior in FESEED across seasons. With the exception of CAB2, these lines were relatively high yielding >2000 kgha -1 . There was no significant correlation of FESEED or ZNSEED to yield. Nonetheless, FESEED and ZNSEED positively (0.59) correlated indicating that selection for superiority in one variable would result in a high value in the other.