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.
Fluconazole is the drug of choice for cryptococcal meningitis (CM) monoprophylaxis in resource-limited settings such as Uganda. Emerging fluconazole resistance linked to mutations in the Cryptococcus neoformans ERG11 gene (CYP51) has been observed in clinical isolates. Currently, the single nucleotide polymorphisms [SNPs] in the Cryptococcus spp. ERG11 gene that could be responsible for fluconazole resistance are poorly characterized within Ugandan C. neoformans clinical isolates. If available, this information would be useful in the management of cryptococcosis among HIV patients. This cross-sectional study investigates the SNPs present in the coding region of the C. neoformans ERG11 gene to determine the relationship between the SNPs identified and fluconazole susceptibility of the clinical isolates. 310 C. neoformans isolates recovered from the Cerebrospinal Fluid (CSF) of patients with HIV and cryptococcal meningitis were examined. The fluconazole half-maximal inhibitory concentrations (IC50 range: 0.25–32 μg/mL) was determined using the microbroth dilution method. A total of 56.1% of the isolates had low IC50 values of <8 μg/mL while 43.9% had high IC50 values ≥ 8 μg/mL. We amplified and sequenced 600 bp of the ERG11 coding sequence from 40 of the clinical isolates. Novel synonymous and 2 missense mutations, S460T and A457V, were identified in the ERG11 gene. The identified SNPs were not associated with differences in fluconazole IC50 values in vitro (p = 0.179).
Root rots cause severe yield losses of up to >70% in common bean (Phaseolus vulgaris L.) in most parts of the world, with devastating effects on the major commercial bean cultivars in East and Central Africa. Increased intensity of droughts and rains, and higher temperatures influence the occurrence and distribution of root rots, resulting in increased epidemics. The causal pathogens tend to occur in a complex, and since most cultivars do not have broad resistance, adverse effects continue to occur. The objective of this study was to evaluate the levels of dual resistance of new breeding lines (BL) developed for root rot resistance, as well as Andean (ADP) genotypes, for resistance to Fusarium (FRR) and Pythium root rots (PRR). Altogether, 316 new BL developed for root rot resistance and 295 ADP bean genotypes were evaluated at Kawanda in Uganda. There were significant differences (P<0.05) among genotypes for both root rots and yield. Thirty and 1.9 percent of the BL and ADP genotypes expressed resistance to both root rots. In addition, more than 80% of ADP genotypes showed susceptibility to both root rots. Yield was generally poor with means of 458 kg ha-1 for ADP, and ranging from 949 to 1075 kg ha-1 for the BL groups. Nonetheless, the 0.3 and 2.4% of the ADP and BL that yielded >2000 kg ha-1 expressed high yield potential, considering that majority of the genotypes yielded below 1000 kg ha-1.
Common bean (Phaseolus vulgaris L.) provides dietary protein, energy, fiber and micronutrients especially, iron and zinc to over 800 million people in Africa and Latin America. The crop has various seed types, but white beans are very popular in the processing industry. This study aimed to investigate agronomic and canning quality, cooking time and the response of white beans to root rots and angular leaf spot (ALS) that cause significant yield losses in bean production eastern Africa. Small and large seeded beans improved for drought tolerance were evaluated from 2013 to 2018. Significant (P<0.001) differences existed among the 151 genotypes for response to three pathogens (Fusarium cuneirostrum, Pythium ultimum and Pseudocercospora griseola), cooking time and canning quality traits. It was possible to select for single, dual and triple disease resistance. Resistance to each of the pathogens was expressed in 24-75% of the genotypes; while dual resistance to any two pairs of the pathogens occurred in 10-44% of the genotypes. The four genotypes; ICNBunsixSxB405/4C-1C-1C-88, RAZ-11, ETSNAP18 and ETSNAP3 that expressed resistance to three pathogens were cooked in 46-56 minutes, and are recommended as sources of resistance for breeding, but could be further improved for fast cooking and canning quality since a general below average canning quality was exhibited. Sixty-eight genotypes were cooked in <50 minutes while 24 expressed good to excellent visual canning quality. The genotypes like RAZ-120, RAZ36-Caballero, NavyLine-60, NavyLine-25, ZABR16573-25F22, ZABR16575-60F22, ETSNAP33, Bifortsmallseeded-15 and ZABR16574-37F22, that cooked in less than 45 minutes, exhibited good to excellent canning quality and resistant to intermediate response to the evaluated diseases were recommend for breeding purpose and for further evaluation for possible promotion.
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