International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Cassava Biofortification: An Overview of IITA Harvest Plus Cassava Breeding Activities PA Kulakow, EY Parkes, NG Maroya, B Maziya-Dixon, H Ceballos, SK Friedrich, E Alamu, P Iluebbey, M Bakare, P Ilona, C Egesi, AGO Dixon 19 June 2012

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Biofortification Our goal is increase the nutritional quality of cassava to help reduce micronutrient deficiencies especially for women and young children Biofortification should a an economic and sustainable way to address hidden hunger Harvest Plus Phase 1 and Phase 2 has supported this work since 2004 Target countries – Nigeria and DR Congo

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Outline of presentation Stages of the cassava breeding program First release of ProVitamin A cassava varieties in Nigeria Next genotypes in the pipeline Early breeding stages High throughput screening tools - iCheck™ Carotene to complement other methods The future – new breeding methods

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Goal of IITA Biofortified Cassava Breeding Yellow cassava with a target concentration of 15 μg/g fresh wt. of β-carotene Roots with high dry matter to produce high quality biofortified foods from yellow cassava – garri, fufu, boiled roots Disease and pest resistance High yield Plant types preferred by farmers

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Typical Cassava Breeding Cycle Seedling nursery (SN) (no replication) Multi-location Uniform yield trial (UYT) (4 replications) Clonal evaluation (CE) (no replication) Preliminary yield trial (PYT) (2 replications) Advanced yield trial (AYT) (4 replications) Crossing Blocks – Source Populations National Variety Testing and On-Farm Trials Year 1 Year 2 Year 3 Year 4 Years 5 & 6 Multiplication and Release NARS Years 7 & 8 Rapid Multiplication One-cycle of recombination in 8 years.

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Cassava Agroecosystems in West Africa

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Performance of released ProVitamin A Varieties Clone Virus Disease Severity Fresh Tuber YieldDry matterTotal carotene scoret/ha%μg/g frwt 01/ / / (chk) Performance of 3 First Release Candidate Varieties in Ibadan Nigeria during 2009/10. Clone Virus Disease Severity Fresh Tuber Yield Dry matter Total carotene scoret/ha%μg/g frwt TMS I TMS I TMS I TMS I30572 (chk)

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – ProVitamin A Cassava Variety IITA TMS I011371

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – CRP 4: Biofortification Released pVAC varieties Parents Clonefemale x male IITA TMS 01/136894/0561 X 94/0263 IITA TMS 01/137194/0561 X 94/0263 IITA TMS 01/141295/0971 X 94/0561

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Historical Development of 01/1368, 01/1371, and 01/1412 YearActivity Parent’s seed produced Parent’s cloned 1999Parent clones hybridized 2000Seedling nursery in Ibadan 2001Genotypes cloned in Ibadan 2002Preliminary Yield Trial 2003Advanced Yield Trial Multi-location Yield Trials National Variety Release Trials – NRCRI On-farm trials 2011Variety Release Decisions and release

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Effect of Planting Date and Time of Harvest on Pro Vitamin A content in 3 yellow Cassava Varieties Locations : Ibadan, Umudike, Ubiaja Varieties: 01/1368, 01/1371 and 01/1412 Design: Split-split plot in Randomized Complete Block Design Main plot: Planting date Sub-plot: Harvesting age Sub-sub plot: Varieties

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Breeder's Seed Multiplication Established 2010 and cut in 2011 Ratooned in July-Aug 2011 Candidate VarietyArea (m 2 )Plant # IITA TMS I IITA TMS I IITA TMS I Combined 1368 and Total Multiplication ratio Foundation Seed ha established

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Breeder's Seed Multiplication available for planting in 2012 VarietyArea (m2)ha First Wave IITA TMS I IITA TMS I IITA TMS I Second Wave Candidates IITA TMS I IITA TMS I IITA TMS I

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Outline of presentation Stages of the cassava breeding program First release of ProVitamin A cassava varieties in Nigeria Next genotypes in the pipeline Early breeding stages High throughput screening tools - iCheck™ Carotene to complement other methods The future – new breeding methods

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Mean CMD Severity Fresh yield Dry matter Total carotene Genotype t/ha%ug/g frwt TMS I TMS I TMS I TMS I TMS I TMS I TMS I Second Wave Candidate Varieties: Top genotypes from UYT Yellow Root 6 grown in ten environments

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – TMS I shows stable high TC across ten environments TMS I070593

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Promising Clone IITA TMS I Highest in TC over 5 locations (11.4 ug/g frwt) CMD Resistant Poundable Relatively high dry matter Good plant architecture Above average yield

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – National Performance Testing for Second Wave ProVitamin A Cassava Varieties National Coordinated Research Program – 9 locations Yellow Roots White roots IITA TMS I IITA TMS I IITA TMS I IITA TMS I IITA TMS I IITA TMS I NR 07/0167CIAT CR 36-2 NR 07/0220NR 04/0053 NR 04/0071 NR 04/0328

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Outline of presentation Stages of the cassava breeding program First release of ProVitamin A cassava varieties in Nigeria Next genotypes in the pipeline Early breeding stages High throughput screening tools - iCheck™ Carotene to complement other methods The future – new breeding methods

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Cassava Breeding Cycle Seedling nursery (SN) 43,845 Multi-location Uniform yield trial (UYT) multilocational Clonal evaluation (CE) 1,625 Preliminary yield trial (PYT) mapping popn Advanced yield trial (AYT) multilocational Crossing Blocks – 652,192 HS 50,470 S1, FS National Variety Testing 14 Year 1 Year 2 Year 3 Year 4 Years 5 & 6 Multiplication 9.5 ha and Release NARS Years 7 & 8 Rapid Multiplication Additional Trials: Local Germplasm Genetic Gain Mapping Populations Special Studies

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – New sources of variation for total carotenoids Production of elite x elite crosses Need to increase the genetic base of yellow root germplasm to avoid crossing only closely related parents Sources –Latin America – CIAT Botanic seeds Tissue culture plantlets –Yellow root African landraces –Potential new sources from inbreeding

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – CIAT Seedling Nursery CIAT HS Pedigree Genotype Number Total Carotene (µg/g fr. wt.) GM SM GM GM GM SM SM Parameter Total Carotene Means7.25 N81 Min3.2 Max13.9

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Botanic Seed Groups and Seedling nurseries Location Family No. No. surviving Ibadan (planting 1)* ,250 Ibadan (planting 2) Ikenne* 52110,551 Ubiaja33515,310 Zaria Total 43,845 Hybridization Group Elite Yellow Root X Elite Yellow Root Elite Yellow Root X Multiple Pest Resistance Elite Yellow Root X Poundable Elite Yellow Root X Yellow Root Other YR and WR X Poundable Yellow Root and CMD Resistance X CIAT Seedlings Elite Yellow Root Selfed Lines Other Selfed Lines Yellow Root and White Roots X CBSD Tolerant Lines Polyploid Parents Elite and other Yellow Root Half Sib Families *harvested Botanic Seed is available for distribution to partners throughout Africa

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Promising Parents: Ikenne Seedling Nursery – obsparentN iCheck (n) % samples mean iCheckSEminmax 1I I I I GM (11.3) I I I I GM I I

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Outline of presentation Stages of the cassava breeding program First release of ProVitamin A cassava varieties in Nigeria Next genotypes in the pipeline Early breeding stages High throughput screening tools - iCheck™ Carotene to complement other methods The future – new breeding methods

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – iCheck TM Carotene Portable Device to Estimate ProVitamin A in Cassava Samples Validated in comparison to spectrophotometer and also HPLc Rapid processing produces results in one day Field durable

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Comparison of HPLC, Spectrophotometer, NIRS and iCheck™ Carotene – Chopped root samples Trait Reference Values Range a Mean a SD a b-cryptoxanthin0.04 – cis BC0.11 – trans BC0.20 – cis BC0.10 – Total BC0.41 – Total Carotenoids (Spectrophotometer) 0.46 – Total Carotenoids (iCheck™ Carotene) 0.79 –

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Comparison of HPLC, Spectrophotometer, NIRS and iCheck™ Carotene – Mashed or blended root samples Trait Reference Values Range a Mean a SD a b-cryptoxanthin0.04 – cis BC0.11 – trans BC0.20 – cis BC0.10 – Total BC0.41 – Total Carotenoids (spectrophotometer)0.46 – Total Carotenoids (iCheck™ Carotene)0.79 –

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – genotypes sampled in four replications (from 4 trials) correlation 0.83 R2 0.69

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Outline of presentation Stages of the cassava breeding program First release of ProVitamin A cassava varieties in Nigeria Next genotypes in the pipeline Early breeding stages High throughput screening tools - iCheck™ Carotene to complement other methods The future – new breeding methods

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Next Generation Cassava Breeding: Genomic Selection Modify the breeding process using selection based on genotype information 1.Reduce the cassava breeding cycle to one year 2.Enhance early flowering and recombination 3.Share information – Cassavabase.org 4.Efficient use of genomic tools

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Typical Cassava Breeding Cycle Seedling nursery (SN) (no replication) Multi-location Uniform yield trial (UYT) (4 replications) Clonal evaluation (CE) (no replication) Preliminary yield trial (PYT) (2 replications) Advanced yield trial (AYT) (4 replications) Crossing Blocks – Source Populations National Variety Testing and On-Farm Trials Year 1 Year 2 Year 3 Year 4 Years 5 & 6 Multiplication and Release NARS Years 7 & 8 Rapid Multiplication One-cycle of recombination in 8 years.

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Cassava Breeding on a One-Year Cycle Potential to increase gain from selection per unit time. Faster multiplication and phenotyping of selected genotypes to evaluate proof of concept for genomic selection Rapid production of potential varieties for farmer evaluation Rapid variety release and impact Complements two-year and longer approaches

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Genomic Selection on an Annual Cycle MonthsObjective Activity 1Activity 2Activity 3Activity 4 Jun-DecFirst cycle Recombination Crossing block June Hybridization Aug-Oct Harvest early seeds Oct-Dec. Harvest late seeds Jan-MaySeedling nurserySeed germination CMD - screening Multiplication Mar- May GenotypingDNAGBSGS model Jun-JunField - Phenotyping GBS – genotype by sequencing, GS – apply genomic selection statistical model Jun-DecSecond cycle Recombination Crossing block June Hybridization Aug-Oct Harvest early seeds Oct-Dec. Harvest late seeds Jan-MaySeedling nurserySeed germination CMD - screening Multiplication Mar- May GenotypingDNAGBSGS model Jun-JunField - Phenotyping

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – CRP RTB: Next Generation Cassava Breeding –Genotype by Sequencing Elite Cassava Breeding lines –Assembly of historical phenotypic data in genetic gain trials and uniform yield trials –Association mapping –Assessement of genetic diversity to facilitate exploitation of heterosis 641 Elite Cassava Breeding Lines Relationships between yellow root genotypes based on 4000 SNP markers

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Actions to Achieve a One Year Breeding Cycle Efficient organization of all field activities –Planting, hybridization, seed harvest, DNA processing and data analysis Fast cassava technology –Reduce time to onset of flowering and increase prolificacy of flowers –Can 6-month buds be grafted to high flowering root stocks? Optimal nursery management –Irrigation and fertilization Selection for reduced seed dormancy, high flowering and high fertility

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Cassavabase.org Database for genomic and phenotypic data to support Next Generation Cassava Breeding Source of information on genotypes including images, fingerprints, characterization Genomic selection tools

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – CRP-RTB: Cassava Trait Ontology 120 traits defined for ICASS database with partners 60 default traits identified for IBP fieldbook – trans. to Spanish, French, Portuguese Utilized by Cassavabase.org and Agtrial.org Root Neck Length CO_334: Root Shape CO_334: Stem Color CO_334: Root Number CO_334: Outer Skin Color CO_334:

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – Acknowledgement Project Support from Harvest Plus through IFPRI and CIAT with funding from the Bill and Melinda Gates Foundation Harvest Plus I ( ) Harvest Plus II ( )

International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – A Bright Future for Cassava Breeding