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Marker-assisted breeding for multiple disease resistance in market-class French beans in Kenya, University of Embu


University of Embu, Embu, Kenya

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The Embu University team. Left to right: Mr Brian Wafula, Dr Esther Arunga, Ms Serah Njau, Ms Nancy Munubi and Ms Grace Wambui Watare.



French bean (or green bean) is one of the most valuable export commodities produced in Kenya; the crop is sold both as fresh produce or in canned form. Its cultivation represents a major source of income for small-holder farmers. Several pathogens compromise the crop’s productivity: the viruses bean common mosaic virus (BCMV) and bean common mosaic necrosis virus (BCMNV); and the fungi Pseudocercospora griseola (responsible for angular leaf spot; ALS), Uromyces appendiculatus (rust) and Colletotrichum lindemuthianum (anthracnose; ANT). Chemical control of these diseases is not economically viable for small-scale farmers, while it also presents a hazard to both human health and the environment.


  1. To combine resistances to BCMV and BCMNV into advanced breeding lines through marker-assisted selection.

  2. To conduct yield trials of French bean lines with multiple disease resistances.

  3. To characterise the bean rust resistance genes in the MU#13 French bean breeding line.

  4. To identify molecular markers linked to rust resistance genes in MU#13 French bean breeding line.

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French beans growing in the Embu greenhouse.

Progress to date

  1. Sixteen advanced breeding lines were derived from a cross combining four bean varieties: Amy (the "recipient" variety to be improved), MU#13 (a rust resistant French bean variety), G2333 (a dry bean variety resistant to anthracnose) and Mex 54 (also a dry bean variety, resistant to angular leaf spot). These  lines were tested over two seasons (13 lines in 2021 and 16 lines in 2022) alongside the four parents and  commercial checks (Serengeti, Source, Seagull, Tausi and Vanilla in 2021, and Source and Seagull in 2022) in two field sites (Embu and Kutus) to establish their agronomic performance.

  2. The lines tested showed significant differences (P < 0.05) for % marketable pods in the two sites and for pod weight in Kutus. The commercial cultivars generally outperformed the breeding lines in pod length and % marketable pods. One breeding line yielded better that the best commercial check (Serengeti). However, Serengeti was susceptible to ALS whereas most of the breeding lines were resistant. All the genotypes that were tested were susceptible to BCMNV.

  3. The breeding program successfully developed lines with multiple disease resistance with the French bean plant stature. However, most breeding lines have slightly poor pod quality and yield as compared with the commercial cultivars. Therefore, the material is being improved further before release through an additional backcross to a commercial variety to improve pod quality and by introgressing resistance to BCMNV/BCMV.

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G2333  Mex 54

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Some of the French beans selected for improvement (i); dry bean donor varieties for disease resistance (G2333 for anthracnose and Mex 54 for angular leaf spot; ii); the Embu team doing field evaluations (iii); advanced French bean breeding lines (iv); 2022 field trials of advanced breeding lines; French bean data collection of pod traits (vi and vii).


Project team

Dr Esther Arunga

Principal Investigator, University of Embu.

Senior Lecturer at the Agricultural Resource Management, Dr Arunga, has led the KT French bean breeding project at Embu University College, Kenya, since 2013. A Kirkhouse Trust MSc and PhD scholar, she completed her doctoral degree in 2012. The title of her thesis was ‘French bean breeding for rust resistance in Kenya: pathogen diversity and host resistance’.

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Ms Serah Njau

PhD student, University of Embu

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Ms Grace Wambui Watare

Laboratory technician

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Mr Brian Weseka Wafula

MSc student, University of Embu

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Ms Nancy Munubi

MSc student, University of Embu

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Mr Anthony Kimani

Past member.         MSc student, graduated 2021 University of Embu


Combining ability and genetic mapping of pod quality and yield traits in locally adapted French beans (Phaseolus vulgaris) in Kenya

Ms Serah Njau

PhD in Plant Breeding and Genetics, University of Embu, 2018-2022.

Supervisors: Dr Esther Arunga, University of Embu, Professor Paul Gepts, University of California, Davis, USA, Dr Reuben Otsyula, Kenya Agricultural & Livestock Research Organization (KALRO).


Project objectives


  1. To document variation for the pod quality attributes pod wall fibre and suture string among a set of French bean varieties grown in Kenya.

  2. To quantify both the general and the specific combining ability with respect to a range of agronomic traits in French bean.

  3. To understand the genetic basis of variation in pod quality and yield.

  4. To develop molecular markers linked to genes responsible for variation in pod quality and yield.

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Ms Njau during her study visit at Professor Paul Gepts' lab at UC, Davis, spring 2022.

Progress to date


  1. A panel of French bean varieties has been characterised with respect to the key producer traits: time to flowering; pod length; percentage of extra fine pods and pod shape.

  2. A full diallele analysis has been conducted involving five French bean varieties (Serengeti, Vanilla, Amy, Seagull and Moonstone) and two dry bean varieties (G2333 and MCM5001). The resulting 49 lines are being subjected to both phenotypic and genotypic characterisation.There was a significant effect (P <0.001) of genotypes for all morpho-agronomic traits evaluated, and also a significant effect for environment for the traits apart from pod suture and plant height. Vanilla and Moonstone performed better than the other French beans in regards to pods per plant, pod weight per plant and pod length.

  3. A set of three mapping populations has been developed, bred from the crosses Serengeti x Mexico 54, Amy × G2333, and Vanilla × MCM5001. Each population has been generated via single seed descent resulting in sets of F2-derived F5 recombinant inbred lines.

  4. There are PvIND sequence differences between the stringy and non-stringy accessions of common bean. Stringy accessions have a single copy of PvIND sequence while non-stringy accessions have tandem duplication of PvIND, with a retrotransposon inserted at the beginning of the duplicated region. These sequence features may cause the PvIND overexpression associated with loss of pod strings.

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Green beans at the podding stage (i); Ms Njau during evaluation of pod wall fiber of French bean (ii); Royal Sluis ruler for measuring pod length and pod diameter for French bean (iii); Ms Njau in the screenhouse (iv).

Marker-assisted selection for resistance to bean common mosaic necrosis virus (BCMNV) in French bean cultivars in Kenya

Ms Grace Wambui Watare

MSc in Plant Breeding and Biotechnology, University of Embu.

Supervisors: Drs Esther Arunga and Bernard Gichimu, University of Embu.

Project objectives

  1. To document the variation for host resistance to BCMNV present in a panel of French bean cultivars. 

  2. To identify the genetic basis of BCMNV resistance present in French bean germplasm with the aid of molecular markers. 

  3. To introgress the gene bc-3 responsible for BCMNV resistance from a dry bean donor line into selected French bean cultivars.

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Ms Grace Wambui Watare

Progress to date

  1. Testing the set of Kenyan French bean cultivars in both the field (natural infection) and greenhouse (artificial inoculation) confirmed the absence of any genes conditioning resistance to BCMNV.

  2. A panel of 32 entries, comprising nine French bean and 23 dry bean varieties was subjected to genotyping using markers linked to a number of genes conditioning resistance to BCMV/BCMNV. Of interest to French bean improvement are the SCAR marker SBD5 (linked to bc-1-2) and the Elf4e gene (linked to bc-3).

  3. In order to render the French bean cultivars Amy, Vanilla and Serengeti resistant to BCM(N)V, each was crossed to MCM5001, MCM2001 and MCM1015. The materials, having reached the BC3F2 generation, are currently being genotyped using SBD5 and Elf4e.

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BCMNV symptoms on leaves (i); French bean breeding lines in the greenhouse (ii); field trials in KALRO Kakamega 2019 (iii).


Prevalence and host resistance of French beans to common bean rust in Western and Central Kenya

Mr Brian Weseka Wafula

MSc in Plant Breeding and Biotechnology, University of Embu.

Supervisors: Dr Esther Arunga and Dr Felix Rotich, University of Embu.

Project objectives

  1. To determine the prevalence of rust on French beans grown in Western and Central Kenya.

  2. To evaluate, under greenhouse conditions, a panel of common bean cultivars for their ability to resist infection by the rust pathogen.

  3. To map the rust resistance gene in the French bean breeding line MU#13.

  4. To identify molecular markers linked to the gene(s) conditioning rust resistance carried by MU#13.

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Mr Brian Weseka Wafula

Progress to date

  1. Rust infected French bean samples have been collected from Western (Bungoma, Kakamega and Uasin Gishu counties) and Central Kenya (Kirinyaga and Embu counties). Disease severity was evaluated using a 1-9 scale, and the effect of management practices assessed. Rust severity and incidence was found to be dependent on the choice of cultivar, indicating the presence of differential host resistance to rust.

  2. 77 common bean genotypes (14 landraces, 20 French bean cultivars, 28 dry bean cultivars, 3 breeding lines and 12 bean rust differential cultivars) were screened for resistance to bean rust on station during the 2021 long-rain cropping season using Randomized Complete Block Design with 3 replications.

  3. 10 single spore isolates obtained from the survey have been characterised using a set of 12 differential cultivars: 4 physiological races were identified. These races were used to screen 10 seeds of each genotype for resistance to rust in greenhouse conditions.

  4. Allelism tests performed for the bean rust resistance genes in the MU#13 French bean breeding line.

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Rust in bean single crop (i); screening for rust resistance in the greenhouse (ii); differential reaction of MU#13 and Amy to rust (iii).


Pyramiding of genes to confer multiple disease resistance into market class French bean varieties in Kenya

Ms Nancy Munubi

MSc in Plant Breeding and Biotechnology, University of Embu.

Supervisors: Dr Esther Arunga and Dr Felix Rotich, University of Embu.

Project objectives


1.To develop French bean breeding lines that combine resistance to multiple diseases through the stacking of disease resistance genes.

2.To evaluate the yield traits of French bean lines with pyramided genes for disease resistance.

3.To characterise the anthracnose resistance genes in the MU#13 French bean breeding line.

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Ms Nancy Munubi

Progress to date

  1. Coursework completed.

  2. An F1 population with multiple disease resistance has been developed. This will be followed by three backcrosses to the recurrent parents to improve pod quality.

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Development of the F1 population (i); successful crosses (ii and iii).


  • Parker, T.A., Cetz, J., de Sousa, L.L., Kuzay, S., Lo, S., de Oliveira Floriani, T., Njau, S., Arunga, E., Duitama, J., Jernstedt, J. and Myers, J.R., 2022. Loss of pod strings in common bean is associated with gene duplication, retrotransposon insertion, and overexpression of PvIND. New Phytologist. In press.


  • Kamiri, A.K., Arunga, E.E., Rotich, F. and Otsyula, R., 2021. Response of French bean genotypes to Colletotrichum lindemuthianum and evaluation of their resistance using SCAR markers. African Journal of Biotechnology 20: 51-65.

  • Arunga, E.E. and Odikara, O.S., 2020. Characterization of Kenyan French Bean genotypes into gene pool affiliations using allele specific markers. African Journal of Biotechnology 19: 653-660.

  • Kimno, S.K., Kiplagat, O.K., Arunga, E.E. and Chepkoech, E., 2016. Evaluation of selected French bean (Phaseolus vulgaris L.) genotypes for resistance to angular leaf spot (Pseudocercospora griseola) in Western Kenya. Journal of Experimental Agriculture International 13: 1-6.

  • Arunga, E.E., Ochuodho, J.O., Kinyua, M.G., Owuoche, J.O. and Chepkoech, E. 2015. Genetic diversity of determinate French beans grown in Kenya based on morpho-agronomic and simple sequence repeat variation. Journal of Plant Breeding and Crop Science. 7 :240-250.

  • Arunga, E.E., Ochuodho, J.O., Kinyua, M.G. and Owuoche, J.O., 2012. Characterization of Uromyces appendiculatus isolates collected from snap bean growing areas in Kenya. African Journal of Agricultural Research 7: 5685-5691.

  • Arunga E.E., Ochuodho J.O., Kinyua M.G., Owuoche J.O. 2012. Characterization of Uromyces appendiculatus isolates collected from snap bean growing areas in Kenya. African Journal of Agricultural Research 7: 5685-5691  doi: 10.5897/AJAR12.1826.

  • Arunga, E.E., Van Rheenen, H.A. and Owuoche, J.O., 2010. Diallel analysis of Snap bean (Phaseolus vulgaris L.) varieties for important traits. African Journal of Agricultural Research, 5: 1951-1957.

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Participants to the 2017 Annual African Bean Consortium (ABC) Meeting visit Dr Arunga's (far left) greenhouse at the University of Embu.


Interactive Map

Location of the University of Embu's field trial sites.

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