1. Work Package 3 Progress at 2.5 years
Brigitte Uwimana
IITA Uganda

2. Primary outcome
To develop molecular tools for selection in banana breeding through:
QTL analysis for:
Fusarium wilt (R1 and SR4)
Burrowing nematodes (Radopholus similis)
Burrowing weevils
Development of predictive models for Genomic Selection for:
Yield
Other agronomic traits

3. Molecular tools: step by step
Develop populations:
Mapping populations (QTL analysis)
Training population (phase 1 for GS)
Phenotype
Mapping populations
Training population
Genotype
Phenotypic + genotypic data
Linkage maps and QTL mapping
Development of predictive models
Year 1 and 2
Year 2, 3 and 4
Year 4
Year 4 and 5

4. Progress with Phenotyping
Population
Target number of genotypes
Foc R1
Site
Parents
Phenotyped/being phenotyped
Phenotyping to be completed by
Kasaska x Borneo
200
Kawanda
TxT
62%
March 2018
Monyet x Kokopo
180
TxS
71%
Nov 2017
Calcutta 4 x Calcutta 4
55%
Feb 2018
Paliama x Borneo
Arusha ?
10%
Malaccensis x Malaccensis (UQ)

5. Progress with Phenotyping
Foc SR4: building on previous research
At the University of Queensland and University of Malaya
UQ:
Fine mapping of the resistance region: from 33 to 15 candidate genes
Testing resistance markers in other lines
Defining resistance in the Malaccensis x Malaccensis population and compare with resistance to R1 in the same population
UM: population was lost, crosses going on, availing genotypic and transcriptomic resources

6. Progress with Phenotyping
Population
Target number of genotypes
Weevil
Site
Parents
Phenotyped/being phenotyped
Phenotyping to be completed by
Kasaska x Borneo
200
Kawanda
SxR
62%
March 2018
Monyet x
Kokopo
180
Sendusu
RxS
23%

7. Progress with Phenotyping
Population
Target number of genotypes
Nematode
Site
Parents
Phenotyped/being phenotyped
Phenotyping to be completed by
Kasaska x
Borneo
200
Sendusu
RxS
95%
Nov 2017
Calcutta 4 x
Zebrina GF
180
65%

8. Progress with Phenotyping
Site
Training population (since 2013)
Cycle 1
Cycle 2
Cycle 3
Flowering
Harvest
Sendusu: low input
100%
98%
93%
87%
72%
65%
Sendusu: optimum input
96%
82%
Mbarara
78%
68%
54%
22%
11% 1%
Sendudu: EET lines (200)
10% -

9. Molecular tools: step by step
Develop populations:
Mapping populations (QTL analysis)
Training population (phase 1 for GS)
Phenotype
Mapping populations
Training population
Genotype
Phenotypic + genotypic data
Linkage maps and QTL mapping
Development of predictive models
Year 1 and 2
Year 2, 3 and 4
Year 4
Year 4 and 5

10. Progress with Genotyping
Mapping populations:
Genotyping going on with 19 SSR markers at IEB to check for pollination mistakes
Complete for Kasaska x Borneo:
Pollination errors
Kasaska available different from the Kasaska in the population
Borneo is the only known parent
The population is a mixture of BC1 (backcrossed to Borneo) and F1 x F1
Mapping to be done without a linkage map
Genotyping with 20 ISSR and 1 IRAP from UM (Monyet x Kokopo)
Dense SNP markers to be provided this year (Chip)

11. Progress with Genotyping
Training population for GS:
307 lines: 2x (11%), 3x (85%), and 4x (4%)
Genotyped using GBS
10,807 SNPs scored bi-allelically
5,579 SNPs scored per ploidy level
Predictive models using data from 2 fields for 2 cycles
Prediction power ranging from 20% to 68%
Nyine M., B. Uwimana, R. Swennen, M. Batte, A. Brown, P. Christelová, E. Hřibová, J. Lorenzen, J. Doležel (Submitted) Trait variation and genetic diversity in a banana genomic selection training population, PLOS ONE.
Nyine M., B. Uwimana, J. Lorenzen, R. Swennen, E. Hřibová, H. Vanrespaille, M. Batte, A. Brown, V. Akech, J. Doležel (in preparation) Genomic selection in a polyploid crop: the impact of genotype by environment interaction and allelic dosage on predictive ability of genomic selection models in banana, PLOS Genetics.

12. Capacity building 4 PhD students: 3 MSc students: SLU UM SU IEB
KU Leuven
Makerere University

13. Challenges Mapping populations with pollination mistakes
More than one population per trait
Screening for Foc in Arusha: pathogen is silent
Communication

14. Way forward Phenotyping to be completed by March 2018
Genotyping by June 2018
Preliminary QTL mapping by September 2018
Predictive models to be enriched with data from Mbarara and EET
Select genotypes for validation