Genetic improvement of common bean in Zambia for multiple diseases resistance using marker-assisted and conventional breeding

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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 in Zambia is mainly grown in the highlands of Northern and Muchinga provinces, which stretch into the Mbeya region of southern Tanzania. Despite the economic and nutritional importance of common bean in Zambia, its yield remains low due to biotic and abiotic stresses. The UNZA research team led by Dr Kamfwa is breeding common bean varieties expressing resistance to each of the diseases common bacterial blight, anthracnose and bean common mosaic virus.

Objectives

  1. Add the QTL conferring resistance to common bean bacterial blight (CBB), marked by SA5 and SU91, to lines of Kabulangeti previously improved by the introduction of Co-5 (conferring resistance to anthracnose- ANT), and bc-3 and I (providing resistance to bean common mosaic virus, BCMV).

  2. Understand the genetic basis of the resistance shown by the variety OAC Inferno to both anthracnose and common bacterial blight.

  3. Train two students in MSc plant breeding at the University of Zambia.

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Optimising the screening protocol for common bacterial blight in the greenhouse. Left: USWK-CBB-15 (resistant variety) and right: ADP 355 (susceptible variety).

Progress to date

  1. Near Isogenic Lines (NILs) have been developed for ANTH (Co-4 & Co-5) , CBB (SAP6) & BCMV (I, bc-3). NILs from crosses between Kabulangeti or Kijivu (ADP33) and G2333 (anthracnose resistance, Co-42) have been developed. ADP33 has Kabulangeti seed type but is superior in productivity than the Zambian Kabulangeti landrace. The offspring from these parents were backcrossed to BC5F1/BC5F2. Seed shape, size and colour have been recovered. The NILs developed for ANT will be used for fine-mapping the Co-4 locus to derive a better molecular marker for breeding resistance into susceptible cultivars.

  2. Introgression of SU91& SAP6 QTLs into Kabulangeti and ADP33 (aka Kijivu, a line with superior agronomic characteristics including early maturity) using USWK-CBB-17 (ADP 665) and Werna (ADP 118) as donor parents, both resistant to CBB. Over 110 BC6F2 families were screened for the presence of SAP6 to  maximise the chances of recovering the preferred seed size and colour in addition to disease resistance. The BC2F2 generation is currently under development. Since the target landrace for improvement (Kabulangeti) is not very productive, the pedigree method is being used to develop varieties with improved yield and agronomic traits. Improved lines are then screened with markers to identify those carrying the disease resistance loci.

  3. Research is ongoing to understand the genetic basis of ANT and CBB resistance in common bean variety OAC-Inferno. 200 recombinant inbred lines (RILs) have been created for these studies. These have initially been screened for resistance to a virulent race of anthracnose. Field trials were conducted in Malashi, Mpika in the 2021-22 season.

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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

 
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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.

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Mr Mwiinga Mulube

PhD Student, University of Zambia

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Ms Maria Mazala

Technician

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Mr Chikoti Mukuma  Pathologist, Zambia Agricultural Research Institute

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Ms Swivia Hamabwe MSc student, University of Nairobi

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Ms Miyoba Sansala

MSc student, University of Zambia

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Mr Kuwabo Kuwabo MSc student, University of Zambia

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Mr Lawrence Chanda MSc Student, University of Zambia

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Mr Mukuni Nkandela MSc Student, University of Zambia

STUDENT PROJECTS

Genetic dissection of common bacterial blight resistance in the Andean gene pool of common bean

Mr Mwiinga Mulube

PhD in Plant Breeding and Seed Systems, University of Zambia, 2022

Supervisors: Dr Kelvin Kamfwa and Dr Paul Gepts.

 

Project objectives

  1. To determine the incidence and severity of Common Bacterial Blight (CBB) in major bean growing areas of Zambia.

  2. To identify genomic regions and candidate genes associated with CBB resistance in the Andean Diversity Panel of common bean.

  3. To Map Quantitative Trait Loci (QTLs) for CBB resistance in an Andean population derived from a cross of the bean varieties Inferno (ADP 631) and Kabulangeti.

  4. To determine the effectiveness of the CBB major-effect QTLs SU91 and SAP6 against CBB strains in Zambia.

  5. To evaluate the yield stability and genotype × environment interaction (G×E) of CBB resistant elite lines.

Progress to date

  1. A diagnostic survey of CBB incidence and severity was carried out on the main bean growing areas in Zambia (ten districts which account for over 70% of production were targeted). Preliminary results showed a wide distribution of CBB ( 90.6 %) in the production area compared to anthracnose (60%). The level of damage caused by CBB (60.3 %) was also higher than for ANT (38. 8%). Farmers were asked about their source of seed (CBB is mainly transmitted through seed): 73.3 of the farmers interviewed obtained their seed from agro-dealers, and the remainder reused saved seed.

  2. A study was undertaken to identify genomic regions and candidate genes associated with CBB resistance in the Andean Diversity Panel (ADP, a potential source of resistance). 400 ADP lines were screened for CBB resistance in greenhouse conditions and scored using the CIAT severity scale (1-9).GWAS was conducted on 6 strains (Xa3353, Xa484, ZM4, Chito, UNZA and LSK). QTLs on pv3, pv7, pv9 & pv 11 were identified as very important in conditioning resistance against the Zambian strains.

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Mr Mwiinga Mulube

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Mr Mulube collecting diseased samples during a CBB diagnostic survey (i); CBB symptoms on leaves (ii) and in a severely affected field (iii); screening for CBB resistance in the greenhouse using artificial inoculation with CBB isolates (iv and v).

Quantitative trait loci mapping for drought tolerance in an Andean recombinant inbred population of common bean (Phaseolus vulgaris)

 

Ms Swivia Hamabwe

MSc, Plant Physiology and Biochemistry, University of Nairobi, Kenya, 2020

Supervisors: Dr Nicholas A. Otieno, University of Nairobi, and Dr Kelvin Kamfwa, University of Zambia.

Project objectives

Drought is an increasingly important constraint to production and can result in the complete loss of a harvest. Most widely used sources of drought tolerance are from the Meso-American gene pool. Andean bean genotypes tolerant to drought have been identified. This projects aims to establish phenotypic correlations between various drought-related traits and their genetic basis using a set of 158 Recombinant Inbred Lines (RILs) bred from a cross between Bukoba amd Kijivu. Experiments include two pot trials and two seasons of field trials.

Progress to date

  1. A 12K(12000) single nucleotide polymorphisms (SNP) chip was used to screen the parents for polymorphisms (genetic diversity).

  2. 1840 markers were used to build the linkage map on the 11 common bean chromosomes.

  3. Two field trials and one pot trial have been completed.

 
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Ms Swivia Hamabwe

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Parental lines for the genetic mapping population: Kijivu (i) and Bukoba (ii); Ms Swivia measuring leaf temperature of different bean varieties under water stressed conditions and non stressed conditions (control; iii); results of the leaf temperature measurements (iv); pot trials (v) and field trials (vi).

Race characterization of Colletotrichum lindemuthianum in Zambia and identification of new sources of resistance to anthracnose in common beans

Ms Miyoba Sansala and Mr Chikoti Mukuma

 

Project objectives

Anthracnose (causative agent the fungus Colletotricum lindemuthianum) is present in 76% of the districts surveyed in Zambia. The objectives of this project were:

  1. To determine the genetic variability of C. lindemuthianum in Zambia.

  2. To identify new sources of resistance from the Andean Diversity Panel (ADP) using selected races of C. lindemuthianum from the major bean growing areas of Zambia.

Progress to date

  1. Samples of anthracnose-infected plants were collected from the major bean growing areas of Zambia, and characterised using a set of 12 differential cultivars planted on Styrofoam trays. 27 unique races were identified.

  2. The Andean Diversity Panel (made of 450 genotypes) was artifically inoculated with anthracnose, and a set of 150 Recombinant Inbred Lines 50 RILs was bred from a cross between a susceptible and a resistant parent to identify: i) the Andean genotypes resistant to larger number of races; ii) the genomic regions providing resistance to a larger number of races.

  3. OAC Inferno, a light red kidney variety, was identified as resistant to most races, and has been incorporated in breeding programmes as a donor parent for anthracnose resistant. Genome-wide Association Study (GWAS) and Quantitative Trait Loci (QTL) mapping using the ADP and RILs have revealed one genomic region on chromosome Pv02 and a second on Pv04 as responsible for resistance to most of the 27 races of the pathogen identified.

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Ms Miyoba Sansala infecting differential cultivars for the characterisation of ANT isolates.

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Mr Chikoti Mukuma

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The lesion interphase of infected beans (i) collected during field surveys are cut into small pieces, surface sterilised and base plated (ii). The plates are incubated until sporulation (iii). A single spore is excised and plated to obtain a pure isolate (iv), which was characterised using a set of differentials to identify resistant genotypes (v).

Genome-wide association analysis for anthracnose resistance in the Yellow Common Bean Collection

Mr Kuwabo Kuwabo

MSc, Plant Breeding & Seed Systems, the University of Zambia, 2020

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

 

Project objectives

The Yellow Bean Collection (YBC) comprises 300 entries developed by various breeding programmes, assembled by Dr. Karen Cichy at Michigan State University, USA.

The project objectives are to identify: i) genomic regions associated with resistance to anthracnose in the YBC, and ii) candidate genes for resistance to anthracnose. 

Progress to date

  1. The YBC has been screened in the greenhouse for resistance to selected races of anthracnose (5, 19, 39, 183, 1050 & 1105).

  2. 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.

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Mr Kuwabo Kuwabo loading a gel.

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Screening for anthracnose resistance in the greenhouse (i); only resistant plants are not killed after artificial infection with ANT isolates; GWAS for Resistance to Races 19, 51, 183 in the YBC showing a major Effect QTL on Pv04 (R2=21.4%; iii).

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.

 

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:

 

  1. Screen 25 advanced breeding lines developed by the project for CBB resistance.

  2. 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

  1.  The YBC has been screened in the greenhouse for resistance to selected races of           anthracnose (5, 19, 39, 183, 1050 & 1105).

  2.  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.

  3. 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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Mr Lawrence Chanda

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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

  • 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

 
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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

Location of UNZA's field trial sites.