Pathogen Distribution, Characterization and Identification of Resistance Markers associated with Root Rot Resistance in Common Beans

Lead Research Organisation: National Crops Resources Res Inst NaCRRI
Department Name: National Beans Programme


The common bean is an important legume crop in East and Central Africa, cultivated on smallholder farms, mainly by women, for food and income generation. In Ugandan, beans provide 45% of the total human dietary protein and play a significant role in ensuring food security. Beans provide a cheap source of protein to most vulnerable groups such as children below five years, pregnant mothers and AIDS patients.
Despite its importance, the production of common beans is hampered by abiotic stresses such as land shortages due to increasing population, reduced soil fertility and recurrent droughts; and biotic stresses such as diseases. Some of the economically important diseases of beans are the root rots. In sub-Saharan Africa, yield losses due to bean root rots is estimated at about 221,000 metric tons per year.
The National Bean Programmes in the countries of eastern and central Africa, together with Centro Internacional de Agricultura Tropical (CIAT) have invested a lot effort in bean root rot research. They have identified two types of root rots (Pythium and Fusarium root rots) that are particularly severe in highland areas associated with decreasing land size and agricultural intensification; and have developed resistant varieties that are now been grown by farmers in these areas. Efforts are also underway to introduce resistance into other commercial backgrounds. However, the root rot problem still remains a big challenge and the disease seems to be featuring in areas and environments where it was not observed before.
The proposed research therefore seeks to; 1) determine the current importance of Pythium spp. and of other root pathogens previously considered unimportant, particularly Sclerotium rolfsii, 2) conduct phenotypic and genotypic characterization of S. rolfsii, 3) screen improved lines and farmer varieties for resistance to Sclerotium root rot and 4) develop resistant markers that can be used in varietal improvement for resistance to Sclerotium root rot.
This research will benefit both farmers and bean researchers in eastern and central Africa where bean root rots are a major problem. By identifying resistant varieties that can be used directly or in bean improvement programmes, we will greatly contribute towards reducing losses due to root rots and ensuring food security for the farming communities of Uganda and other common bean growing countries in the region. The immediate benefit of the proposed research to the farmers is the reduction of yield losses due to bean root rots. This will result from farmers growing resistant or tolerant bean varieties identified during screening for Sclerotium root rot resistance. The Uganda national bean programme is a member of the Pan-Africa Bean Research Alliance which is an alliance of 28 countries in sub-Saharan Africa. CIAT facilitates this partnership. Results from this research will be shared and also benefit researchers and end-users of other PABRA members countries where root rots are a problem. The proposed research will also develop technologies that can be used by pathologists and breeders of common beans in eastern and central Africa.

Technical Summary

Common bean (Phaseolus vulgaris L.) root rots cause an estimated yield loss of 221,000 metric tons per year in sub-Saharan Africa (Wortmann et al. 1998). Pythium spp. and Fusarium solani f.sp. phaseoli are known to cause severe root rots in high altitude areas characterized by cool temperatures and high relative humidity. However, high incidences of bean root rots are now observed in low and medium altitude bean agro-ecologies characterized by dry and warm conditions. This may indicate that, either 1) other pathogens rather than Pythium spp. and FSP are responsible for the observed root rots, and/or 2) changing climatic conditions and intensified land use have led to changes in prevalence and distribution of Pythium spp. and FSP.

The objectives of the proposed research are to 1) collect S. rolfsii and Pythium spp. isolates and map their distribution in the different bean agro-ecologies in Uganda, 2) conduct phenotypic and genotypic characterization of S. rolfsii and Pythium spp. isolates, 3) develop molecular diagnostic tools for detection of S. rolfsii, 4) screen breeding lines and local germplasm for identification of Sclerotium root rot resistance sources and 5) identify molecular markers associated with Sclerotium root rot resistance genes.

We shall employ widely accepted methodologies such as surveys, AFLPs and KASPAR based genotyping to achieve our objectives.

The findings of our study will be useful to both pathologists and bean breeders. The mapped distribution and severity of bean root rots will provide a baseline for future studies on incidence and severity. Data on pathogen characterization will be very useful in identification of new species. Studies on diversity are particularly important for plant pathologists because of the changing climatic conditions in most agroecologies of the world. The resistance markers we identify will be applied widely by bean breeders in MAS breeding to quicken breeding for Sclerotium root rot resistant varieties.

Planned Impact

Bean root rots affect the food security of resource poor farmers by severely reducing yield of common beans. This in return impacts on their daily protein intake, since beans are a major protein source. In Uganda, beans account for 45% protein intake. By identifying resistant varieties that can be grown by farmers; and used in introgressing root rot resistance in market-class varieties, this research will greatly contribute towards ensuring food security for the farming communities of Uganda and other common bean growing countries in the region. The ultimate beneficiary of the proposed research is the bean farmer. However, the scientific community, especially the pathologists and breeders will greatly benefit from the knowledge generated by this study.

Some major immediate impact to the farming community will be improved yields from growing resistant or tolerant varieties recommended by this project. However, in the long term farmers will benefit from growing root rot resistant varieties developed with the aid of technologies generated under the proposed research.

Impacts to the research community will be accessibility to Pythium spp. and Sclerotium rolfsii
Isolates for use in future experiments. Mapping the distribution of the two root rot pathogens will enable breeders tailor their breeding programmes to meet the needs of farmers in the different bean agroecologies. Breeders will benefit from using S. rolfsii resistance markers in introgressing resistance genes into market-class varieties. Using the PABRA partnership mechanisms, results will be useful and have impact beyond Uganda. The use of resistance markers will shorten the breeding process significantly.

To ensure that impacts due to the proposed study are achieved, we shall use the following pathways to disseminate our findings. 1) Root rot pathogen distribution in the different bean agroecologies of Uganda will be published in a brochure availed to breeders and extension workers. 2) Resistant varieties derived from evaluation or improvement on the basis of characterized pathogens will be availed, evaluated and selected both on station and on-farm with the participation of farmers, extension services and breeders. On-farm demonstration plots will be established in root rot hotspots for farmer observations. Farmers will then choose varieties they would like to grow. 3) Information about root rot resistant or tolerant varieties will be published in a brochure. For additional benefits, the same brochure will also carry information about recommended root rot management options. Elite lines will be shared among PABRA partners. 4)Information about diagnostic tools and novel resistance markers will be widely published in international peer-reviewed journals, conference proceedings and other important scientific publications for wider accessibility by the agricultural research fraternity. This will be achieved at the end of the project.


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