Genetic Improvement in Uganda’s Andean Bean Breeding Program · Feed the Future Innovation Lab...

Feed the Future Innovation Lab for Collaborative

Research on Grain Legumes

Genetic Improvement in Uganda’s Andean Bean Breeding Program

Highlights

Stanley T. Nkalubo, Blessing A.Odogwu, Boris M.E. Alladassi, Evarist Basil, Isaac Dramadri, Dennis Katuramu, Gabriel Luyima,

Karen Cichy, Carols Urrea, James Steadman and James Kelly

13 -18th August 2017; Ouagadougou, Burkina Faso

Feed the Future Innovation Lab for Collaborative Research on Grain Legumes

• Uganda’s Population (2014 census)- 34.5 million

– 2050 estimated to grow to 105 million

• Population growth- 3.3%

• Agriculture accounts for 22.9% GDP; generates 85%export earning (MAAIF-2016)

• Agriculture is the largest employer in Uganda with 72%workforce in the sector (World Bank, 2016)

• Women account for 3/4 of agricultural labor force and 9out of 10 food producing labor in Uganda.

• Beans occupy over 12% of the total cultivated area andare grown by more than 85% of farmers (MAAIF, 2016)

• Contribute about 2.3% of the GDP (MAAIF 2016)

Introduction


A Case for Common Dry Bean in Uganda • The common dry bean (Phaseolus vulgaris) is the most

important legume grown and consumed in Uganda

• Per capita bean consumption is about 29kg annually, (SPIA,2014) contributing, on average, 40% of total human dietaryprotein and about 4% of total calorie intake (FAOSTAT, 2016).

• Play a significant role in ensuring food /nutrition security andincomes for rural smallholder especially the women andchildren .

• Greater than 80% of bean famers grow beans of Andeanorigin and are prone to multiple biotic and abiotic stressesthat occur on farmers’ fields at the same time- has greatlyundermined their potential.

• Need to understand the status of nature and types ofpathogen within the country for effective interventions.

• Need for the introgression of multiple resistances within thesame genotype.


Major Constraints to Production and Productivity

Bean root rots

Angular leaf spot

Bean Common Mosaic Virus Bean rust

Common Bacterial Blight

Bean anthracnose

Bean stem Maggot (bean fly)

Bean Weevil (Bruchids)

DroughtLeaf beetle


• Improving Genetic Yield Potential of Andean Beans withIncreased Resistances to Drought and Major Foliar Diseases andEnhanced Biological Nitrogen Fixation (BNF)

– Integrate traditional and marker-assisted selection (MAS) approachesto combine resistances to economically important foliar diseases,drought and improved biological nitrogen fixation (BNF) and assessacceptability of fast cooking, high mineral content in a range of large-seeded, high-yielding Andean Ugandan bean germplasm.

– Characterize pathogenic and genetic variability of isolates of foliarpathogens collected and identify sources of resistance to ALS, ANT,CBB, BCMV and bean rust

– Use single nucleotide polymorphism, SNP-based genome-wideassociation mapping to uncover regions associated with droughttolerance, disease resistance, cooking time and BNF to identify QTLsfor use in MAS to improve Andean germplasm.

– Develop phenometric approaches to improving the efficiencies ofbreeding for abiotic stress tolerance, especially drought.

– Institutional/Human Capacity Building

LIL interventions and achievements on genetic improvement


Germplasm assembly and characterization

• Total 758 accessions assembled and characterized

• Adaptability to Uganda environments - 94.5% (716)

• 34 (4.8%) had preferred traits and characteristicsand with potentially competitive yield

⁻ Undergoing field evaluation trails and two tofour may be released as new varieties inUganda

• Lines with preferred traits (e.g. resistance to foliardiseases) but poorly adapted

⁻ Utilized in crosses to improve Ugandan elitelines for desirable traits (e.g. fast cooking,resistance to diseases and pests: Rust, CBB,BCMV, anthracnose, ALS root rots, bruchids,stem maggot and drought tolerance)

⁻ >350 different crosses have bean generated asa way of improving Ugandan elite lines


Fusarium root rot

Pythium root rot

Incidences and severities for the different bean pathogens determined and mapped

Sclerotium root rot

Bean Rust incidence

Regions & Status ALS RRs Anth Rust BCMV CBBSouth western Region

Incidence 88-95 75-88 50-67 20-34 25-40 40-60

Severity 81-96 45-55 28-35 10-17 10-30 35-50Central RegionIncidence 85-94 80-94 57-64 56-68 5-10 60-85

Severity 85-100 60-66 34-45 22-40 1-5 50-64Southern RegionIncidence 93-100 75-89 40-58 34-53 15-30 58-90

Severity 90-100 50-62 30-45 23-36 5-10 36-77Eastern Region

Incidence 82-96 60-79 33-39 18-36 5-10 23-48

Severity 77-80 35-44 12-28 10-28 1-5 15-35Northern Region

Incidence 80-98 65-70 45-58 34-55 10-25 26-45

Severity 70-83 28-40 35-42 24-35 5-10 10-35


Isolation and characterization of bean foliar and rot pathogens

• Pure cultures prepared and morphological characterization completed for• 45 ALS Isolates• 6 Rust pathotypes (2-0, 4-0, 50-0, 5-1, 4-33, and 63-19. )• 27 Anthracnose pathotypes• 220 Fusarium spp. Isolates• 47 Pythium spp. Isolates• 400 Sclerotium rolfsii Isolates

Sample collection Pathogen isolation Single spore isolates

Morphological Characterization: Fibrous mycelia and few sclerotia, and B. Compact mycelia with several sclerotia

Genotyping: Agarose gels showing fingerprints of different Sclerotium rolfsii isolates generated using RAMS 6 marker.


Identification of resistant/tolerance sources

• Rust: Identified Seven (7) resistant lines that include; Mexico 309,CNC, P1181996, Mexico 235, Redland pioneer, Oura Negro andAurora.

– Identified 15 SNP markers associated with rust resistance anddesigned nine (9) KASP markers that will need to be validated.

• Common bacterial blight (CBB): Identified resistant four (4) lineswith both leaf and pod resistance; NE2-14-8, NE17-14-29, NE14-09-78 and VAX3.

• Bean common Mosaic Virus (BCMV): Identified three(3)resistant lines to BCMV including; SCR 48, SCN 9 and SCN 6.

• Sclerotium rolfsii root rot: Identified four (4) lines with relativelygood resistance including; ALB 155, ALB 171, KWP 17 and KWP 9

• Drought: Identified 7 lines with tolerance to drought including;ADP-102, ADP-41, ADP-47, ADP-61, ADP-617, ADP-660 and ADP-678.

– These have been crossed with Uganda market class bean lines andprogenies undergoing evaluations.


Evaluation of lines with superior foliar diseaseresistance, drought tolerance and shorter cooking timeand high mineral bioavailability

• 23 ADP lines that were evaluated for shorter cooking time,adaptability, and consumer and market preference

– Nine (9) farmer groups composed of 326 farmers (96 men and230 women) in three agroecologies in Uganda.

– Seven (7) lines namely ADP 0512, ADP 0009, ADP 0001, ADP0468, ADP 0521, ADP 0098, and ADP 0522 have been selected byfarmers through PVS trial as most preferred.

– These will be advance for further evaluation and also crossedwith other Andean Uganda market class varieties

• Drought trials: Promising drought tolerant lines SCR 26, SEN 98, SCN11 and SCN 1 have been sent for DUS/NPT and possible release.- byend of year 2017.


• In the aspect of capacity building, four postgraduate studentshave been engaged and trained under the project. Thestudents are at different levels of their researches;

• Ms. Blessing Odogw; is a PhD student at Makerere Universityundertaking studies under the research topic “Resistance tocommon bean (Phaseolus vulgaris L.) rust (Uromycesappendiculatus (Pers. Pers.) Unger.) in Uganda”

Identified hotspots for rust disease in Uganda.

Identified bean rust pathotypes in Uganda.

Identified exotic and indigenous sources of rustresistance.

Identified some SNP markers linked to rust resistance .

Blessing completed her studies and has submitted her thesisfor examination and has returned to teach at University of PortHarcourt, Nigeria.

Developing Human Capacity


• In an effort to improve precision in breeding for drought tolerance in common dry beans,

• Isaac Dramadri a PhD student at Michigan State Univ. isconducting research on the “Genomic and phenometricapproaches to dissect physiological responses associatedwith drought adaptation within the Andean common beangenepool”

Conducting a genome-wide association analysis for terminal drought tolerance in Andean common beans

Has deployed the use of MultispeQ in both green house and field high throughput phenotyping for drought tolerance

Evaluating ADP lines for drought stress under greenhouse and field conditions

Trained RA and Technicians on the use of photosynQ for field phenotyping

Drought nursery in the field at Namulonge

Developing Human Capacity- cont’d

Research Assistants getting hands on training in the use of photosynQ


• Mr. Alladassi Mahulé Elysé Boris, MSc. Student atMAK- University, Uganda. Conducted research on“Genetics of resistance to Common Bacterial Blightdisease of Common Bean (Phaseolus vulgaris L.) inUganda”. He was able to

Identify genotypes with resistance to both leaf and pod CBB

Determined the mode of inheritance of CBB resistance for leaf and pod among selected Ugandan Andean genotypes

Observed low correlation between leaf and pod reaction to CBB pathogen ( r = 0. 39; p < 0.001). i.e. all CBB screening procedure should focus on both leaf and pod inoculation for prudence

• Already graduated and he currently teaching post-University.

Developing Human Capacity- cont’d

Field and Screenhouse experiments for germplasm screening

Culture of Xanthomonasisolate Kawempe 1

Leaf inoculation using razorblade method


CBB symptoms on leaf of susceptible Vs Resistant Genotype

CBB symptoms on pod of susceptible Vs Resistant Genotype


• Mr. Basil Evarist Kavishe MSc. Student at MAK,Uganda who conducted research on “Resistanceto bean common mosaic potyviruses and itsinheritance in selected Ugandan beans”-Submitted his thesis for examination

Identified sources of resistance to BCMVand BCMNV in the selected exotic andcommercially released common bean linesin Uganda

Determine the mode of inheritance ofgenes for BCMV and BCMNV resistance inUganda Andean bean genotypes

Developing Human Capacity - cont’d

BCMNV-Symptom on Roba 1

Mosaic symptom on NABE 26 C

BCMNV vs BCMV


Developing Human Capacity - cont’d• The collaborative research has enabled us to build research capacity not

only in terms of graduate training but also in short courses for knowledgeand skills for Research Assistants, Technicians and farmers. Used mobile nursery for collection and identification of rust isolates

Drought and disease screening (isolation and inoculation) methods,data capture and management of bean foliar diseases in screenhouseand field.

Marker assisted breeding

• Farmers have also been equipped with information and skills on Identification and possible control of foliar bean diseases

Use of improve technologies for increased bean production andproductivity


Journal Publications1. Prevalence and variability of the common bean rust in Uganda. (2016). African Journal of Agricultural Research.

11(49), 4990- 4999. DOI:10.5897 /AJAR2016.11600 ISSN: 1991-637X. Authors: Odogwu, B.A.; Nkalubo, S.;Mukankusi, C.; McCoy, S.; Paparu, P.; Rubaihayo, P.; Kelly, J.D.and Steadman, J.

2. Phenotypic and genotypic screening of rust resistance in common bean germplasm in Uganda. (2017)Euphytica. 213:49. DOI 10.1007/s10681-016-1795-y. Authors: Blessing A. Odogwu; Stanley T. Nkalubo; ClareMukankusi; Thomas Odong; Halima E. Awale; Rubaihayo Patrick; James D. Kelly.

3. Inheritance of resistance to common bacterial blight in four selected common bean (Phaseolus vulgaris L.)genotypes (2017). Journal of Plant Breeding and Crop Science. 9(6), 71-78.DOI: 10.5897/JPBCS2017.0644Authors: Boris M. E. Alladassi, Stanley T. Nkalubo, Clare Mukankusi, Eric S.Mwale, Paul Gibson, Richard Edema,Carlos A. Urrea, James D. Kelly and Patrick R. Rubaihayo

4. Genetic analysis of resistance to common bean rust disease in Uganda. (2016) RUFORUM Working DocumentSeries (ISSN 1607-9345) No. 14 (1): 699-705. http://repository.ruforum.org. Authors: Odogwu, B.A., Nkalubo, S.and Rubaihayo, P.

5. Yield loss associated with common bean rust in Uganda. (2017). Manuscript under review in Field CropsJournal. Authors Odogwu, B.A; Nkalubo, S.T; and Rubaihayo, P.

6. SNP identification and marker assay development for high-throughput selection of bean rust resistance.Proposed Journal: PLOS ONE. (Yet to be submitted). Authors: Odogwu, B.A.; Yao, N.; Odeny, D.; Shorinola,ONjung’e, Nkalubo, S.T. and Rubaihayo, P.

7. Screening of common bean germplasm for combined leaf and pod resistance to common bacterial blightdisease in Uganda. (Yet to be submitted). Authors: Boris M. E. Alladassi, Stanley T. Nkalubo, Clare Mukankusi,Hellen N. Kayaga, Paul Gibson, Richard Edema, Carlos A. Urrea, James D. Kelly and Patrick R. Rubaihayo

http://repository.ruforum.org/


Conclusion• Research activities undertaken resulted in;• Acquisition of different nurseries comprising of 758 bean accessions• Identified several lines with good resistance to rust, CBB, root rots,

anthracnose, BCMV and drought tolerance.• Generated multiple crosses (>350) to introgress multiples resistances

into backgrounds of susceptible Ugandan germplasm and generatedprogenies that are being evaluated.

• Four Journal publications so far.• Seven fast cooking lines from ADP panel series and drought tolerant

lines being evaluated on-farm with farmers identifying superiorgenotypes with both market and consumption preference traits.

• Collection, isolation, characterization and determination of incidences,severities and understanding modes of inheritance to resistances of keyfoliar diseases.

• These outputs so far generated are envisaged to contribute to thedevelopment of varieties and germplasm with high yield potential,improved resistance to multiple foliar pathogens, and water useefficiency under limited soil water conditions, and contribute toimproved yield and on-farm profitability for especially the resourcepoor farmers in Uganda and within the region.


Project TeamJames KellyJames Steadman Carols UrreaKaren Cichy

Acknowledgements

Postgraduate StudentsBlessing A.OdogwuBoris M.E. AlladassiEvarist BasilIsaac DramadriDennis Katuramu

Other contributorsEunice KesiimePamela PaparuGabriel LuyimaBecACEDOFarmers


Thank you for your attention

Lets make beans more available to all households for improved livelihoods

Genetic Improvement in Uganda’s Andean Bean Breeding Program��HighlightsIntroductionA Case for Common Dry Bean in Uganda Major Constraints to Production and Productivity LIL interventions and achievements on genetic improvement Germplasm assembly and characterizationSlide Number 7Slide Number 8Identification of resistant/tolerance sourcesEvaluation of lines with superior foliar disease resistance, drought tolerance and shorter cooking time and high mineral bioavailabilitySlide Number 11Slide Number 12Slide Number 13Slide Number 14BCMNV vs BCMVSlide Number 16Journal PublicationsConclusionSlide Number 19Slide Number 20

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