Bean Disease and Pest Resistance in Kenya

1. New Pythium species identified

Number of Pythium isolates characterized rose to 480.  Samples were collected from main bean growing areas in Uganda, Kenya and Rwanda. Characterization based on cultural and molecular (RFLPs and sequencing) techniques grouped the isolates into 27 species. These included known and previously unknown bean pathogenic species, putative new species and potential biological control agents. Of significance were the findings that isolates belonging to seven Pythium species (P. salpingophorum, P. nodosum, P. spinosum and P. tulorosum, P. vexans, P. graminicola and P. paroecandrum) were shown for the first time to be pathogenic to beans and possibly contributing to the root rot problem of beans in the region. 

Species distribution maps (Figures 1 - 3) were developed for Uganda, Kenya and Rwanda.  Results showed that P. ultimum var ultimum is the most prevalent species, followed closely by P. salpingophorum, P. torulosum and P. vexans. We are now screening germplasm using the pathogenic species identified.  Characterized species will also be the basis for developing fast detection techniques for Pythium spp occurring in the region. In addition, some identified Pythium species (e.g. Pythium oligandrum) are known to have antagonistic effects against pathogenic species of Pythium and these can potentially be used as biocontrol agents to manage Pythium root rots. 

2.  Characterization of the angular leaf spot pathogen, P. griseola:

Studies on prevalence and distribution of P. griseola races in Uganda, Rwanda and Kenya identified 35 pathotypes among 69 isolates. Race 31-39 was the most prevalent and was detected with high frequency in all countries. Several races were detected in only one country underscoring the importance of testing resistance genes in multiple sites. Some of the seven locus-specific microsatellite markers for ALS pathogen were used successfully to characterize isolates from Uganda and Rwanda. These markers will make it faster, cheaper and more accurate to categorize major pathogen groups of P. griseola and facilitate selective and targeted characterization through virulence.

 3. New sources with broader resistance to Pythium identified

We used 8 isolates representing 7 Pythium species to evaluate selected potential parents and sources of resistance. Seven lines  (RWR 719, AND 1056, MLB-49-89A, MLB 40-89A, SCAM-80CM/15, DFA 52 and AND 1055) were resistant to the different Pythium species), revealing the broad resistance carried by these genotypes. This increased our confidence in using these sources as parents to improve Pythium root rot resistant.

4. Better sources of resistance to angular leafspot found

Several common bean genotypes showed high levels of resistance to a wide spectrum of Andean and Mesoamerican P. griseola pathotypes from Africa, including the most aggressive and virulent pathotype 63-63, in multiple sites under field and greenhouse conditions.  Resistance to angular leaf spot was identified or confirmed in the following genotypes: Mexico 54, MAR 1, G5686, G10909, G4691, G 10613, G 19833 and G10474. In addition, fourteen recombinant inbred lines (RILs) derived from Andean (G19833) x Mesoamerican (DOR 364) cross, combined resistance to Andean and Mesoamerican lineages of P. griseola.

5. Genes governing resistance to angular leaf spot identified

Studies of 15 potential sources of resistance to angular leaf spot (including P. griseola differentials used globally) showed that the pattern of inheritance is complex. Five modes of inheritance were identified:

• Two dominant genes control resistance in Cornell 49242, Flor de Mayo, G10909.

• In PAN 72, G10474, Timoteo, Mex 54 and MAR 1, a single dominant gene controls resistance.

• In G2858, Amendoin and G10431, two recessive genes determine resistance.

• A single recessive gene controls resistance in G20743.

• Resistance in Montcalm and G5686 governed by two additive or partially recessive genes.

Mex 54, an important source of resistance (to a majority of races) in Africa, appears to have more (recessive and dominant) than one resistant gene. The results implied that more than one gene may be required to confer more durable resistance to seemingly wide range of races of P. griseola in Africa. Combining genes derived from Mesoamerican and Andean gene pools would be a better strategy in combating this disease.

 6. Inheritance of resistance to Pythium root rot determined

 There are extremely few sources of resistant to Pythium root rot with most of the commercial varieties being susceptible. The most affected genotypes are the large seeded of the Andean gene pool.  Success in managing the disease depends on the transfer of resistance into a wide range of commercial and non-commercial market class backgrounds. In studies to determine inheritance of resistance we demonstrated for the first time that, resistance to Pythium root rot in 5 genotypes (RWR 719, MLB-49-89A, SCAM80-CM/15, AND 1055 & AND 1062) was simply inherited, and conditioned by single dominant genes. The resistance genes identified have broader activities as demonstrated by the resistance reactions of the five genotypes across major Pythium species occurring in the region. Populations have been developed that will be used to identify markers that are linked to the resistance genes.

 7. New markers tightly linked to angular leaf spot resistance genes

Tagging the genes and identifying molecular markers for use in MAS will facilitate the transfer of resistance to well-adapted market class type beans, and will allow pyramiding several genes into the same cultivar, a strategy that would make it difficult for a pathogen to breakdown this resistance. Ten AFLP markers, 1 SSR and 2 RAPD markers that are tightly linked to angular leaf spot resistance genes in 4 common bean genotypes (Mexico 54, G10909, MAR 1 and G10474) were identified.  Two of the AFLP markers (PF13-310.H2 in G 10909, and PF5-330.H2 in G 10474) were successfully converted to SCAR markers and the protocol for their use in marker assisted selection breeding was developed.

 8. Resistance genes transferred into principal market classes

 The ultimate goal is to develop varieties resistant or tolerant to different production constraints  (angular leaf spot disease and root rots, mainly Pythium and Fusarium pathogens), with the commercial grain quality and culinary properties desired by farmers. To achieve this goal, crosses were made to create several populations designed to transfer resistance of angular leaf spot, Pythium root rots, fusarium wilt or both into locally adapted commercial but susceptible cultivars. The focus was on preferred seed types in the region including both climbers and bush beans. A variety of crosses were designed primarily to transfer, combine and pyramid resistance to major diseases addressed by the project but not excluding other important diseases. Programs in Kenya and Uganda focused on improving bush red mottled, red kidney and small red beans while the focus in Rwanda were on climbing bean (assigned based on comparative advantage and complementarities). Recognizing that our priority diseases are part of a bigger problem, we are also constructing new gametes to combine best sources of resistance to angular leaf spot, Pythium root rots, drought, common bacterial blight and tolerance to low soil P, N and pH.

9. Partners create and share germplasm resources

More than 1029 lines and populations segregating primarily for angular leaf spot and Pythium root rots and other constraints (anthracnose, CBB, low N and P) were created and exchanged among project partners in Uganda, Kenya and Rwanda for evaluation in both screenhouse and under field conditions. These genotypes included both bush and climbing bean with a wide range of grain types, seed sizes, growth habits and adaptation to biotic and abiotic stress factors. They formed the basis of selection process by farmers and scientists under variable production environments.

 10. Farmers and scientists start participatory variety selection

Participatory breeding activities were successfully initiated in 2003 with planning meetings meant to identify germplasm, sites, site management, trial designs, evaluation procedures, and to assess training and capacity building needs of the partners. Participatory variety selection on both communal and (in some cases) individual plots in Kenya, Uganda and Rwanda was initiated at eight sites in the three countries, on F6 lines (from previously crosses) and other materials contributed by partners. Using this approach, 250 farmers were directly reached in a single season.  Efforts were expressly made to solicit feedback from women as well as male farmers, and at Kabale, researchers have also worked closely with bean seed/ grain traders—to try to get early feedback on market acceptability. Selection criteria included tolerance to root rots, vigor, pod load, time to maturity and yield. Through PVS farmers in the three countries made selections for further evaluations and seed multiplication. The approach used is meant to set up a system (in partner countries) that routinely integrate farmers’ criteria in varietal development and selection so as to increase the probability of acceptance and adoption and also to cut down the period of varietal development. 

11. Potential impact of Pythium resistant varieties

 In order to assess the potential of resistant varieties in an objective manner, an impact assessment of Pythium root rot resistant varieties (used under the project as parents in several crosses) that had previously been adopted in western Kenya districts of Kakamega and Vihiga was carried out. The study showed that between 35-80% of the households adopted at least one of the three root rot resistant varieties. This resulted in improved household food security and welfare in both districts for the vast majority of surveyed farmers (98% in Kakamega and 99% in Vihiga) mainly women. Farmers reported having more beans to eat and income gains due to the higher productivity of the resistant bean varieties. The results serve as a clear pointer to the potential benefits that are anticipated by developing varieties with popular commercial / preferred characteristics and which are also resistant to these diseases.