Development of higher yielding, faster cooking and disease resistant varieties of common bean for Zambia

University of Zambia (UNZA) Lusaka, Zambia

The UNZA Bean Breeding and Genetics team, 2022. Furthest left: Dr Kelvin Kwanfa (PI). Back row, left to right: Albertina Kalenga (intern), Rebecca Thole (MSc student), Bethel Njobvu (technician), Miyoba Sansala, Joseph Botha (intern), Peter Daka (greenhouse assistant). Middle row, left to right: Muwinga Mulube (PhD student), Isabel Mugovu (MSc student), Lushomo Mukakanga, Swivia Hamabwe (MSc student), Lawrence Chanda (MSc student), Kuwabo Kuwabo (MSc student). Front row, left to right: Mukuni Nkandela (MSc student), Modreen Chinji (MSc student), Lomanzi Chikani (intern), Dorcas Nalwamba (intern).

PROJECT OVERVIEW

Background

Common bean is mainly grown in the highlands of Northern and Muchinga provinces of Zambia. It is a source of food and nutritional security as well as income for small-holder farmers. Despite its nutritional and economic importance in the country, the average yield for common bean yield remains low due to biotic and abiotic stresses.

The overall programme led by Dr Kamfwa at the University of Zambia aims to develop bean varieties that are resistant to diseases that impact production in the country. These crop diseases include common bacterial blight (CBB), anthracnose (ANT) and bean common mosaic virus (BCMV).

Common bean field trials of eight elite breeding lines resistant to ANTH, CBB and BCMV in the kabulangeti seed colour. Malashi Research Station, Zambia, Feb 2025. Photograph taken with a drone.

In earlier phases of the programme, two improved bean varieties (Zerengeti and Kundalila) were developed to replace the popular landraces Kabulangeti and Lusaka, respectively. Zerengeti retains the same seed type as Kabulangeti but offers a 25% higher yield and is resistant to ANT. Kundalila mirrors Lusaka’s yellow seed colour, but it cooks faster, 30% higher yielding, and nutritionally superior due to its enhanced iron bioavailability. Both varieties were distributed to 620 farmers in Zambia for on-farm trials and cooking time tests with a  GCRF AgriFood Africa Innovation Award.

Research to understand the genetic basis of ANT and CBB resistance in common bean variety OAC-Inferno has been advanced. Two populations of RILs have been developed from crosses of OAC-Inferno with Kijivu and Lusaka (Zambian landraces), respectively. These were tested for resistance to ANT in the greenhouse and for resistance to ANT and CBB in the field. The genotypic analysis for these is ongoing.

The programme also identified 27 unique races of Colletotrichium lindemuthianum (the causative agent of the ANT disease) in Zambia.

Objectives

To identify faster cooking genotypes with high seed yield in the Kabulangeti, red-mottled (aka Calima) and yellow market classes of Andean beans.
To introgress ANTH and CBB resistance in selected high yielding and faster cooking genotypes in Kabulangeti, red-mottled and yellow market classes of Andean beans using MAS.
To map the genomic regions for cooking time, ANTH and CBB resistance in population of RILs derived from a cross of Kundalila (faster cooking) and ADP527 (a high yielding variety resistant to ANTH and CBB).
To evaluate the agronomic performance of breeding lines resistant to ANTH, CBB and BCMNV developed from the previous KT-funded projects.

Achievements

Three F₃ populations derived from crosses between Kundalila and bean varieties from the Kabulangeti, red-mottled, and yellow market classes have been developed and are currently being advanced to the F₄ generation.
Resistance to ANT and CBB has been successfully introgressed into faster-cooking market class varieties, including Mbereshi and Kundalila. BC₂ seeds have been harvested and are scheduled for genotyping.
To map genomic regions associated with cooking time, a cross between Kundalila and ADP527 has been made and is under evaluation.
Breeding lines resistant to ANT, CBB, and BCMV developed during previous programme phases are now undergoing agronomic performance evaluation. Eight elite lines, all in the Kabulangeti seed colour, were planted at the Malashi Research Station in Mpika and harvested in May 2025. The next phase will involve planting these lines in four on-station multi-location trials and one on-farm trial to assess performance across environments.

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Kabulangeti, the most popular bean variety in Zambia (i); a successful BC1 cross between Kabulangeti (recurrent parent) and G2333, donor for anthracnose resistance (ii); development of Near Isogenic Lines (NILs) resistant (R) and susceptible (s) to anthracnose (rp- recurrent parent; iii); field trials in 2021 (iv) and in 2022 with the participation of farmers in the selection of varieties (v).

PROJECT TEAM MEMBERS

Kelvin and team

Dr Kelvin Kamfwa

Principal Investigator, University of Zambia.

Dr Kamfwa has led the KT-funded bean improvement programme in Zambia since its inception in 2017. He holds a PhD in Plant Breeding, Genetics and Biotechnology from Michigan State University, USA, and an MSc in Crop Science from Makerere University, Uganda.

Ms Swivia Hamabwe Co-PI

Mr Mwiinga Mulube

PhD Student, University of Zambia

Ms Maria Mazala

Technician

Mr Lawrence Chanda MSc Student, University of Zambia

Mr Mukuni Nkandela MSc Student, University of Zambia

MSc STUDENT PROJECTS

Quantitative trait loci analysis and introgression of common bacterial blight resistance in Zambian preferred market classes of common bean

Mr Lawrence Chanda

MSc, Plant Breeding & Seed Systems, the University of Zambia, 2021

Supervisors: Dr Kelvin Kamfwa and Dr Paul Kachapulula, University of Zambia.

Lawrence

Mr Lawrence Chanda

Project objectives

Common bacterial blight (CBB) is a seedborne disease caused by Xanthomonas axonopodis pv. phaseoli and Xanthomonas fuscans. The disease is responsible for yield losses of 20-60% in susceptible cultivars. The project objectives are to:

Screen 25 advanced breeding lines developed by the project for CBB resistance.
Mapping quantitative trait loci (QTLs) associated to resistance to CBB in an Andean population derived from a cross between Solwezi (susceptible to CBB but an important market class) and AO-3A (resistant to CBB).

Progress to date

The YBC has been screened in the greenhouse for resistance to selected races of anthracnose (5, 19, 39, 183, 1050 & 1105).
A genome wide association study (GWAS) has shown that resistance to the anthracnose races tested is controlled by clusters of major genes mapping to chromosomes Pv01, Pv02 & Pv04.
150 F4:12 Recombinant inbred lines (genotyped with 6000 SNPs markers) derived from a cross between AO-3A x Solwezi and their parents were tested for their reaction to three CBB characterised isolates. The frequency distribution of recombinant inbred lines for severity scores against the isolates has been determined.

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Parent varieties: Solwezi leaves showing symptoms of CBB infection (i); Solwezi beans (ii); AO-3A plants are resistant to CBB (iii); AO-3A beans (iv); experimental set-up for testing the reaction of the RILs to CBB infection, Lusaka, 2022 (v).

PUBLICATIONS

Parker, T., Bolt, T., Williams, T., Penmetsa, R. V., Mulube, M., Celebioglu, B., ... & Gepts, P. (2024). Seed color patterns in domesticated common bean are regulated by MYB‐bHLH‐WD40 transcription factors and temperature. The Plant Journal, 119(6), 2765-2781.
Sansala, M., Kuwabo, K., Hamabwe, S. M., Kachapulula, P., Parker, T., Mukuma, C., & Kamfwa, K. (2024). Race structure and molecular diversity of Colletotrichum lindemuthianum of common bean in Zambia. Plant Disease, 108(4), 857-865.

Mwense, B. P., Hamabwe, S. M., Kuwabo, K., Mataa, M., Miklas, P. N., Mukuma, C., & Kamfwa, K. (2024). Evaluation of Pinto Genotypes of Common Bean for Resistance to Anthracnose. Legume Science, 6(2), e228.

Kelvin, K., Pimpa, S., Hamabwe, S., Kuwabo, K., & Bangotse, M. (2024). Genetic variability for tolerance against aluminium toxicity of selected common bean genotypes.

Kamfwa, K. (2024). Evaluation of yellow common bean (Phaseolus vulgaris L.) genotypes for resistance to anthracnose. Journal of Plant Breeding and Crop Science, 16(2), 27-35.

Hamabwe, S. M., Otieno, N. A., Odhiambo, J. A., Parker, T., & Kamfwa, K. (2024). Agronomic and morpho‐physiological response of Andean genotypes of common bean to terminal drought. Crop Science, 64(6), 3521-3532.

Hamabwe, S.M., Otieno, N.A., Soler-Garzón, A., Miklas, P.N., Parker, T., Kramer, D.M., Chattopadhyay, A., Cheelo, P., Kuwabo, K. and Kamfwa, K., 2023. Identification of quantitative trait loci for drought tolerance in Bukoba/Kijivu Andean mapping population of common bean. Theoretical and Applied Genetics, 136(11), pp.1-17.

Sansala, M., Kuwabo, K., Hamabwe, S., Kachapulula, P., Parker, T., Mukuma, C. and Kamfwa, K., 2023. Race Structure and Molecular Diversity of Colletotrichum lindemuthianum of Common Bean in Zambia. Plant Disease, (ja).

Siamasonta, F., J. Njobvu, S. Hamabwe, K. Munyinda, J.D. Kelly, and K. Kamfwa. 2021. Genome‐wide association analysis of resistance to aluminum toxicity in the roots of common bean seedlings. Crop Science. https://doi.org/10.1002/csc2.20454

Bassett, A., K. Kamfwa, D. Ambachew, and K. Cichy. 2021. Genetic variability and genome-wide association analysis of flavor and texture in cooked beans (Phaseolus vulgaris L.). Theoretical and Applied Genetics 134: 959–978. doi: 10.1007/s00122-020-03745-3

Nalupya, Z., C. Mukuma, S. Hamabwe, D. Lungu, P. Gepts, and K. Kamfwa. 2021. Characterization of Colletotrichum lindemuthianum Races in Zambia and evaluation of the CIAT Phaseolus core collection for resistance to anthracnose. Plant Disease. https://doi.org/10.1094/PDIS-02-21-0363-RE

Binagwa, P., S. M. Traore, M. Egnin, G.C. Bernard, I. Ritte, D. Mortley, K. Kamfwa, G. He, and C.C. Bonsi. 2021. Genome-wide identification of powdery mildew resistance in common bean. Frontiers in Genetics. doi: 10.3389/fgene.2021.673069

Mungalu, H., Sansala, M., Hamabwe, S., Mukuma, C., Gepts, P., Kelly, J.D. and Kamfwa, K., 2020. Identification of race‐specific quantitative trait loci for resistance to Colletotrichum lindemuthianum in an Andean population of common bean. Crop Science, 60(6), pp.2843-2856. doi: 10.1002/csc2.20191

Njobvu, J., S. Hamabwe, K. Munyinda, J.D. Kelly, and K. Kamfwa. 2020. Quantitative trait loci mapping of resistance to aluminum toxicity in common bean. Crop Science 40: 1294-1302. https://doi.org/10.1002/csc2.20043

Publications

The Kirkhouse Trust team visits Dr Kelvin Kamfwa's research group, UNZA, Zambia, 2017. Left to right: Dr Kamfwa; Mr Antony Bowes; Dr Robert Koebner; Professor Paul Gepts and Professor Sir Ed Southern.

PROJECT LOCATIONS

Interactive Map

Location of UNZA's field trial sites.