Brigitte Uwimana IITA Uganda To develop molecular tools for selection in banana breeding through QTL analysis for Fusarium wilt R1 and SR4 Burrowing nematodes Radopholus similis Burrowing weevils ID: 755622
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Slide1
Work Package 3Progress at 2.5 years
Brigitte UwimanaIITA UgandaSlide2
To develop molecular tools for selection in banana breeding through:QTL analysis for:
Fusarium wilt (R1 and SR4) Burrowing nematodes (Radopholus
similis
)Burrowing weevilsDevelopment of predictive models for Genomic Selection for: Yield Other agronomic traits
Primary outcomeSlide3
Develop populations:Mapping populations (QTL analysis)
Training population (phase 1 for GS)Phenotype
Mapping populations
Training populationGenotypePhenotypic + genotypic dataLinkage maps and QTL mapping
Development of predictive models
Molecular tools: step by step
Year 1 and 2
Year 2, 3 and 4
Year 4
Year 4 and 5Slide4
Progress with Phenotyping
Population
Target number of genotypes
Foc
R1
Site
Parents
Phenotyped
/being
phenotyped
Phenotyping to be completed by
Kasaska
x Borneo
200KawandaTxT
62%
March 2018
Monyet
x Kokopo
180
Kawanda
TxS
71%
Nov 2017
Calcutta 4 x Calcutta 4
200
Kawanda
TxT
55%
Feb 2018
Paliama
x Borneo
200
Arusha
?
10%
?
Malaccensis
x
Malaccensis
(UQ)
200
Arusha
?
?
Slide5
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
Progress with PhenotypingSlide6
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%
March 2018Slide7
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
Sendusu
RxS
65%
Nov 2017Slide8
Progress with Phenotyping
Site
Training population (since 2013)
Cycle 1
Cycle 2
Cycle 3
Flowering
Harvest
Flowering
Harvest
Flowering
Harvest
Sendusu: low input
100%
98%
93%
87%
72%
65%
Sendusu: optimum input
100%
96%
96%
93%
82%
72%
Mbarara
78%
68%
54%
22%
11%
1%
Sendudu
: EET lines (200)
10%
-
-
-
-
-Slide9
Develop populations:Mapping populations (QTL analysis)
Training population (phase 1 for GS)Phenotype
Mapping populations
Training populationGenotypePhenotypic + genotypic dataLinkage maps and QTL mapping
Development of predictive models
Molecular tools: step by step
Year 1 and 2
Year 2, 3 and 4
Year 4
Year 4 and 5Slide10
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 populationBorneo is the only known parentThe population is a mixture of BC1 (backcrossed to Borneo) and F1 x F
1
Mapping to be done without a linkage mapGenotyping with 20 ISSR and 1 IRAP from UM (Monyet x Kokopo)
Dense SNP markers to be provided this year (Chip)
Progress with GenotypingSlide11
Training population for GS:307 lines:
2x (11%), 3x (85%), and 4
x
(4%) Genotyped using GBS10,807 SNPs scored bi-allelically5,579 SNPs scored per ploidy level Predictive models using data from 2 fields for 2 cycles
Prediction power ranging from 20% to 68%
Progress with Genotyping
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. Slide12
4 PhD students:SLU
UM
SU
IEB 3 MSc students:KU Leuven
Makerere
University
Capacity buildingSlide13
Mapping populations with pollination mistakesMore than one population per trait
Screening for Foc in Arusha: pathogen is silent Communication
ChallengesSlide14
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
Way forward