Thrid Annual Meeting of Bio-Cassava Plus, Kampala, April 19-21, 2008

1. Improving Delayed Post-Harvest Physiological Deterioration (PPD) in Cassava : A Molecular Breeding Approach C. Cuambe; A.Rosero; C.Egesi, Barrera E., Gutierrez J., Ospina C., Morante N., Moreno M., Alzate A., Sanchez T., Marin J., J. Tohme; Ceballos H., Fregene M., Thrid Annual Meeting of Bio-Cassava Plus, Kampala, April 19-21, 2008

2. Outline • Antecedents • Genetic Mapping of Delayed PPD • Development of BC2 populations • Molecular Breeding of Delayed PPD in Cassava Gene pools • Conclusions and perspectives • Acknowledgement

3. Delayed Post-Harvest Physiological Deterioration (PPD) in F1 inter-specific hybrid of M.Walkerae CW429-1

4. Development and Evaluation of BC1 Mapping Population (B1PD289)

5. Development and Evaluation of BC1 Mapping Populations (B1PD280)

6. SSR Marker Genotyping of BC1 Delayed PPD Mapping Populations • 530 SSR markers evaluated in parental genotypes • 150 polymorphic markers evaluated in 3 BC1 families • Construction of linkage groups for each of the families • QTL analysis (single marker and interval mapping Marker SSRY45

7. SSR Markers Associated with Delayed PPD in Cassava

8. Development of BC2 Populations for Delayed PPD and Resistance to CMD • Based on Phenotypic and QTLs for delayed PPD about 20 BC1 progenies were selected for generation of BC2 breeding populations • Genetic crosses were made to CMD resistant parents and 1400 sexual seeds generated • Delayed PPD+CMD resistant families were established in vitro from embryo axes

9. BC2 Populations for Delayed PPD

10. Shipment of Back Cross Derivates of CW429-1 to Partners • Ohio State University; Twenty nine BC1 progenies with delayed PPD were shipped in July 2007 (R.Sayre) • BC2 progenies with delayed PPD will be shipped in June, 2008 to: • NaCRRI, Namulonge (A. Bua) • NRCRI, Umudike (C.Egesi) • CRI, Kumasi (E.Okai) • KARI, Katumani (J.Kamau) • ARI, Naliendele (G. Mkamilo) • IITA, Ibadan (M.Gedil)

11. Molecular Breeding of Delayed PPD in African Cassava Gene Pools • Validation of QTLs for delayed PPD, and resistance to CMD in the BC2 progenies • Genome-wide fingerprint of BC2 progenies to select those with minimum amount of M. walkerae genome • Selection of BC2 progenies for use as parents in making genetic crosses • Generation of 40 families across collaborating institutions • Marker-assisted selection (MAS) of BC3 genotypes that combine delayed PPD, CMD resistance, and other end-users preferred traits • One year on-station and two year on-farm trials

12. M.Walkerae (Wae 001) SM909-25 X Three cycles of evaluation of delayed PPD confirmed transfer of the trait from the wild parent SM909-25 MTAI8 F1 CW429-1 X CMD Resistant Parental Lines …C4, AR30-3, C33, C14A-1… Evaluation, genotyping and QTL mapping of delayed PPD to develop markers for MAS BC1 3 families X Shipment of BC2 families to NARs partners and selection of best lines for crosses to elite line for variety development BC2 24 families CIAT and NARs Elite Lines X Evaluation of BC3 families at NARs and CIAT and selection of best lines that combine delayed PPD, resistance to CMD, and other end-user preferred traits BC3 40 families Molecular Breeding of Delayed PPD in African Cassava Gene Pools

13. 2005-’06 2007- ‘09 2009-’10 2011 • Product Development • Development of breeding populations • QTL Analysis • Second cycle of genetic crosses and analysis • US$450,000 for 3 years • Product Deployment • Evaluation on-farm and with farmers • Multiplication of breeders seed • US$300,000 for 2 years • Product Commercialization • Commercial scale multiplication • Large scale production and processing • Post-ante impact assessment US$3-4M • Trait Discovery • Identification of parents • Preliminary QTL analysis • US$150,000 Time-line and Cost estimates on the MAB Project for Delayed PPD Time

14. Sources of Funding • Trait Discovery phase funded exclusively by Bio-cassava Plus • Product Development Phase is being funded by Bio-cassava Plus and GCP but we still have a shortfall of US$300,000 • We still don’t have funding for the product deployment and commercialization phases • We have received tremendous encouragement and support in our search for funds from Professor Eugene Terry

15. 100% 80% 60% 40% 20% 10% 0% Standard Operating Procedure (SOP) For Evaluating PPD

16. High Throughput SNP Markers Genotyping Platform at CIAT • 2356 SNPs from sequence of 19208 full length cDNA clones (10879 genes)based on a panel of 3 genotypes • Primer design complete for single base extension • Intial testing of parents using the Luminex bead SNP detection system • Another set of SNPs based on a physical map being developed at UM Current CIAT Luminex SNP detection Capacity: 96 genotypes x 50 SNP X 5 runs per day =25,000 data points per day

17. Laboratory Information Management Systems (LIMS) • Institutional Efforts at CIAT since 2004 • For Quality control from field to lab and back • Storing and tracking information

18. Acknowledgements CIAT ARIs • Constantino Cuambe • Amparo Rosero • Chiedozie Egesi • Emmanuel Okogbenin • Adriana Nunez • Luis Guillermo Santos • Nelson Morante • Joe Tohme • Hernan Ceballos • IITA • Melaku Gedil • Alfred Dixon • Barbara Schaal (Wash. U.) • Ken Olson (Wash. U.) • Robert Bertram (USAID) NARS • Anthony Pariyo (NaCRRI) • Elizabeth Okai (CRI) • Chiedozie Egesi (NRCRI) • Geoffery Mkamilo (ARI) • Joe Kamau (KARI) SAC of Bio-cassava Plus • Professor Eugene Terry With support from Biocassava Plus and CIAT

19. Acknowledgement • Emmanuel Okogbenin • Janeth Gutierrez • Paula Hurtado • Jaime Marin • Cesar Ospina • Edgar Barrera • Manabu Ishitani • Hernan Ceballos • Joe Tohme • Martin Fregene CIAT NRCRI IITA • Chiedozie Egesi • Kenneth Nwosu • Francis Ogbe • Suleiman Kahya • Kemi Ogundapo • Satoru Muranaka • Christian Fatokun • Ousmane Boukar • Dong-Jin K. • Alfred Dixon • Melaku Gedil ARIs GCP • Carmen deVicente • Humberto Gomez • Brigitte Mangin • Pablo Rabinowicz

20. Thank You