Work Package 3 Progress at 2.5 years Brigitte Uwimana IITA Uganda

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

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

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)

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

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%

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%

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% -

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

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)

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.  

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

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

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