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Positioning CIAT as leader in next generation breeding for roots, tubers and bananas
 

Positioning CIAT as leader in next generation breeding for roots, tubers and bananas

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Positioning CIAT as leader in next generation breeding for roots, tubers and bananas.

Positioning CIAT as leader in next generation breeding for roots, tubers and bananas.

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    Positioning CIAT as leader in next generation breeding for roots, tubers and bananas Positioning CIAT as leader in next generation breeding for roots, tubers and bananas Presentation Transcript

    • “Positioning CIAT as Leader in Next-Generation Breeding for Roots, Tubers and Bananas” Becerra Lopez-Lavalle L.A., CIAT’s Senior Scientist and CGIAR-RTB Leader for Variety Development CIAT Seminar Series – Cali 10 February 2014
    • Core - Team: 2009 - 2010 Tissue Culture Mol. Biology Breeding Molecular Markers Technology efective but time-consuming 06 Collaborators 02 Researchers 02 Agronomist
    • Core - Team: 2011 - 2014 Tissue Culture Mol. Biology WhiteFly Res. VIGS Bioinformatic & Data Management 06 Collaborators 10 Researchers 02 Agronomist 02 Support Staff Post Harvest Breeding
    • Core - Team: 2011 - 2014 Tissue Culture Mol. Biology WhiteFly Res. VIGS Bioinformatic & Data Management 06 Collaborators 10 Researchers 02 Agronomist 02 Support Staff Post Harvest Breeding
    • Staff Professional Deveploment Tissue Culture Mol. Biology WhiteFly Res. VIGS Bioinformatic & Data Management 03 Supervisors 3 Master Students Post Harvest Breeding
    • THANK YOU!!!!!!! Tissue Culture Mol. Biology WhiteFly Res. VIGS Bioinformatic & Data Management 06 Collaborators 10 Researchers 02 Agronomist 02 Support Staff Post Harvest Breeding
    • Current Research Carotenoid Synthase Pathway Whitefly control: a durable solution to cassava-disease pandemics (Africa and Asia) Enhancing Cassava productivity through more targeted use of global genetic diversity Whitefly resistance Functional Genetic for high quality cassava: pVA and Starch synthase pathways Next-generation sequencing A 25 µg Total Carotenoid Content B β-OHase Zeaxanthin LCYB LCYB + LCYE ZDS + CRTISO PDS + Z-ISO β-carotene Lycopene CMC-40 ζ-carotene Phytoene GGPP C Lutein PSY 15µg D β+ε-OHase α-carotene MEcu 72 Chromoplast 99 75% Amylopectin A Bemisia tabaci biotypeA KF059958 CIAT 99 30 New World Bemisia tabaci AY521259 Aleurolobus marlatti JQ340188 Asia Siphoninus philyreae JQ340199 Aleurocanthus inceratus HM150621 Aleurocanthus spiniferus JQ340176 45 Asia Crenidorsum micheliae JQ340190 97 C Aleurotrachelus trachoides KF059957 CIAT 98 Aleurothrachelus socialis KF059953 CIAT 89 88 New World D Aleurothrixus floccosus KF059956 CIAT Aleuroclava sp JQ340187 ADP 93 Asia Dialeurodes hongkongensis JQ340195 E New World Trialeurodes variabilis KF059962 CIAT Trialeurodes vaporiariorum KF192508 CIAT 99 G-IV Dialeurodes citri JQ340193 98 G-III Dialeuropora JQ340197 73 New World G-V 68 ADPG B G-II 99 Aleyrodinae ATP PPi F 100 Trialeurodes vaporariorum AY521265 GBSSI Aleuronudus melzeri KF059955 CIAT Aleurodicinae 25% Amylose G Aleurodicus dugessi AY521251 46 99 Lecanoideus floccissimus KF059960 CIAT H Aleurodicus dispersus KF059954 CIAT 95 99 Aleurodicus dispersus EU581838 I 75 Aleurodicus dispersus EU581837 Amyloplast Drosophila melanogaster ADW61439 100 Drosophila melanogaster ADW61333 Drosophila melanogaster AGE13862 0.20 0.15 0.10 0.05 0.00 G-VI G1P Asia / Asia-Minor Bemisia tabaci biotypeB KF059959 CIAT 96 DE SBEII SBEI SSIII SSII SSI Bemisia tabaci JN410741 Bemisia tabaci JN410738 81 100 G-I Starch Synthase Pathway Whitefly molecular identification Asia Metabolomic profiling
    • pVA and Starch: Why Functional Genetic for high quality cassava: pVA and Starch synthase pathways Challenge: Carotenoid Synthase Pathway 25 µg Total Carotenoid Content β-OHase Zeaxanthin LCYB LCYB + LCYE ZDS + CRTISO PDS + Z-ISO β-carotene Lycopene ζ-carotene Phytoene GGPP Lutein PSY 15µg β+ε-OHase α-carotene Chromoplast Starch Synthase Pathway 75% Amylopectin DE SBEII SBEI SSIII SSII SSI ATP PPi G1P ADPG ADP GBSSI 25% Amylose Amyloplast Malnutrition – Secure Source of Income for poor small-holder farmers
    • pVA and Starch: Hypothesis Functional Genetic for high quality cassava: pVA and Starch synthase pathways Amyloplast vs. Chromoplast Carotenoid Synthase Pathway 75% Amylopectin 25 µg Total Carotenoid Content SBEIIDE SBEI SSIII SSII SSI β-OHase Zeaxanthin LCYB LCYB + LCYE ZDS + CRTISO PDS + Z-ISO ATP PPi ADPG G1P 75% Amylopectin 25 µg Total Carotenoid Content β-carotene β-OHase Lycopene Zeaxanthin 15µg Zeaxanthin LCYB LCYB + LCYE ZDS + CRTISO PDS + Z-ISO ADPG ADP 25 µg Total Carotenoid Content Amyloplast ATP PPi ADPG G1P ADP ADP ZDS + CRTISO PDS + Z-ISO Amyloplast 25% Amylose G1P G1P ADPG Amyloplast 15µg β-OHase Zeaxanthin β-carotene Lycopene ζ-carotene Phytoene GGPP Chromoplast Lutein PSY 15µg 25 µg Total Carotenoid Content β+ε-OHase α-carotene β-OHase Zeaxanthin Chromoplast LCYB LCYB + LCYE ZDS + CRTISO PDS + Z-ISO ADP 25 µg Total Carotenoid Content β-carotene β-OHase Lycopene Lutein ZDS + CRTISO PDS + Z-ISO 15µg β+ε-OHase 25% Amylose Chromoplast Zeaxanthin LCYB LCYB + LCYE ζ-carotene Phytoene GGPP GBSSI GBSSI 25% Amylose LCYB LCYB + LCYE ZDS + CRTISO PDS + Z-ISO Chromoplast β+ε-OHase α-carotene PSY β-carotene Lycopene ζ-carotene Phytoene GGPP α-carotene Lutein PSY 15µg β+ε-OHase β-carotene ADPG G1P ADPG G1P ADP ZDS + CRTISO PDS + Z-ISO G1P ZDS + CRTISO PDS + Z-ISO ζ-carotene Phytoene GGPP PSY G1P ADP 25% Amylose Amyloplast Amyloplast β+ε-OHase α-carotene Chromoplast Starch Synthase Pathway 75% Amylopectin DE SBEII SBEI SSIII SSII SSI ATP PPi ADPG ADP GBSSI 25% Amylose Amyloplast β-carotene ZDS + CRTISO PDS + Z-ISO Lycopene PSY Lutein PSY β+ε-OHase α-carotene β+ε-OHase α-carotene Chromoplast Zeaxanthin LCYB LCYB + LCYE ZDS + CRTISO PDS + Z-ISO 25 µg Total Carotenoid Content β-carotene β-OHase Lycopene Zeaxanthin LCYB LCYB + LCYE ζ-carotene Phytoene GGPP Lutein PSY Lutein ZDS + CRTISO PDS + Z-ISO 15µg β+ε-OHase β+ε-OHase α-carotene PSY Lutein 15µg β+ε-OHase α-carotene Chromoplast Chromoplast Chromoplast Chromoplast β-OHase Zeaxanthin LCYB LCYB + LCYE ZDS + CRTISO PDS + Z-ISO Lutein β-carotene Lycopene ζ-carotene Phytoene GGPP α-carotene 25 µg Total Carotenoid Content Zeaxanthin β-carotene Lycopene ζ-carotene 15µg 25 µg Total Carotenoid Content β-carotene PSY 25 µg Total Carotenoid Content β-OHase Lycopene β-OHase Zeaxanthin LCYB LCYB + LCYE ζ-carotene Phytoene GGPP Lutein ZDS + CRTISO PDS + Z-ISO 15µg β+ε-OHase β+ε-OHase α-carotene α-carotene PSY Zeaxanthin LCYB LCYB + LCYE β-carotene ZDS + CRTISO PDS + Z-ISO Lycopene ζ-carotene Phytoene GGPP Lutein 15µg PSY Lutein 15µg β+ε-OHase α-carotene Chromoplast Chromoplast β-carotene Lycopene ζ-carotene Phytoene GGPP β+ε-OHase α-carotene Chromoplast Lutein 15µg 15µg β-OHase Zeaxanthin β-carotene Lycopene ζ-carotene 15µg Chromoplast β-carotene Lycopene ζ-carotene Phytoene GGPP ζ-carotene Phytoene GGPP 25 µg Total Carotenoid Content β-OHase PSY GBSSI 25% Amylose Lutein Zeaxanthin LCYB LCYB + LCYE Zeaxanthin β+ε-OHase α-carotene Chromoplast β-OHase PSY ADP Amyloplast β-OHase β-OHase LCYB LCYB + LCYE ZDS + CRTISO PDS + Z-ISO 15µg Chromoplast 25 µg Total Carotenoid Content LCYB LCYB + LCYE ZDS + CRTISO PDS + Z-ISO Phytoene GGPP β+ε-OHase α-carotene 25 µg Total Carotenoid Content LCYB LCYB + LCYE ZDS + CRTISO PDS + Z-ISO Phytoene GGPP ADPG Amyloplast 25 µg Total Carotenoid Content β-carotene Lycopene ζ-carotene Lutein PSY β+ε-OHase α-carotene Lutein 15µg Amyloplast Amyloplast 75% Amylopectin SBEIIDE SBEI SSIII SSII SSI ATP PPi G1P 25% Amylose ZDS + CRTISO PDS + Z-ISO Phytoene GGPP Lutein 15µg Zeaxanthin β-carotene Lycopene ζ-carotene Phytoene PSY GBSSI 25% Amylose 75% Amylopectin SBEIIDE SBEI SSIII SSII SSI PSY β-OHase ADP 25% Amylose 25% Amylose Amyloplast ADPG LCYB LCYB + LCYE β-carotene Lycopene ζ-carotene Phytoene GGPP β+ε-OHase α-carotene 25 µg Total Carotenoid Content LCYB LCYB + LCYE ZDS + CRTISO PDS + Z-ISO ADPG GGPP GBSSI ATP PPi ZDS + CRTISO PDS + Z-ISO Lutein 15µg Chromoplast Amyloplast 75% Amylopectin SBEIIDE SBEI SSIII SSII SSI ATP PPi ADPG ADP GBSSI GBSSI PSY GBSSI 25 µg Total Carotenoid Content Zeaxanthin Chromoplast ADPG GBSSI G1P LCYB LCYB + LCYE Lycopene ζ-carotene Phytoene GGPP ADP β-OHase Zeaxanthin 25% Amylose G1P ADP ZDS + CRTISO PDS + Z-ISO ADPG β+ε-OHase α-carotene ATP PPi G1P ATP PPi ADPG GBSSI 25% Amylose 25 µg Total Carotenoid Content β-OHase β-carotene Chromoplast 75% Amylopectin SBEIIDE SBEI SSIII SSII SSI SBEIIDE SBEI SSIII SSII SSI ATP PPi G1P ADP 15µg G1P 15µg Chromoplast Amyloplast 75% Amylopectin SBEIIDE SBEI SSIII SSII SSI ADPG Zeaxanthin ATP PPi Lutein PSY β+ε-OHase α-carotene GBSSI 25% Amylose Amyloplast 75% Amylopectin SBEIIDE SBEI SSIII SSII SSI ATP PPi G1P 25 µg Total Carotenoid Content β-OHase LCYB LCYB + LCYE ADP GBSSI 25% Amylose Amyloplast ζ-carotene ζ-carotene Phytoene GGPP Lutein 15µg ADPG SBEIIDE SBEI SSIII SSII SSI β-carotene Lycopene Chromoplast 25 µg Total Carotenoid Content Zeaxanthin LCYB LCYB + LCYE β-carotene Lycopene ATP PPi ADP GBSSI 25% Amylose 75% Amylopectin β-OHase Zeaxanthin LCYB LCYB + LCYE 75% Amylopectin SBEIIDE SBEI SSIII SSII SSI ATP PPi ADPG GBSSI 25% Amylose 25 µg Total Carotenoid Content β-OHase 75% Amylopectin SBEIIDE SBEI SSIII SSII SSI ATP PPi ADP α-carotene Chromoplast 25 µg Total Carotenoid Content 75% Amylopectin SBEIIDE SBEI SSIII SSII SSI ATP PPi G1P Lycopene Amyloplast Amyloplast 75% Amylopectin SBEIIDE SBEI SSIII SSII SSI ADP G1P Chromoplast 15µg ADPG ADP Amyloplast Amyloplast Phytoene PSY G1P ADPG GBSSI 25% Amylose 25 µg Total Carotenoid Content Lutein PSY β+ε-OHase ATP PPi ATP PPi G1P ADP GBSSI 25% Amylose β-carotene Lycopene ζ-carotene Phytoene GGPP β+ε-OHase α-carotene Lutein PSY Chromoplast Zeaxanthin 15µg α-carotene 75% Amylopectin SBEIIDE SBEI SSIII SSII SSI SBEIIDE SBEI SSIII SSII SSI ADPG ADP Lutein β+ε-OHase β-OHase LCYB LCYB + LCYE ZDS + CRTISO PDS + Z-ISO Lutein PSY β+ε-OHase α-carotene Phytoene GGPP Chromoplast 75% Amylopectin β-carotene Lycopene ζ-carotene Phytoene GGPP 15µg Lycopene ζ-carotene GBSSI 25% Amylose ATP PPi ATP PPi Zeaxanthin β-carotene α-carotene LCYB LCYB + LCYE ZDS + CRTISO PDS + Z-ISO Lutein PSY Zeaxanthin β-carotene 25 µg Total Carotenoid Content Zeaxanthin β-carotene Lycopene ζ-carotene Phytoene GGPP β-OHase LCYB LCYB + LCYE ZDS + CRTISO PDS + Z-ISO ADP SBEIIDE SBEI SSIII SSII SSI Amyloplast GGPP ZDS + CRTISO PDS + Z-ISO 25 µg Total Carotenoid Content Lutein β+ε-OHase α-carotene 75% Amylopectin β-OHase Lycopene ζ-carotene 15µg β-OHase Zeaxanthin LCYB LCYB + LCYE Amyloplast β-carotene Lycopene ζ-carotene 15µg Chromoplast ADPG Amyloplast 75% Amylopectin SBEIIDE SBEI SSIII SSII SSI 25 µg Total Carotenoid Content LCYB LCYB + LCYE ZDS + CRTISO PDS + Z-ISO Phytoene β-OHase Zeaxanthin PSY PSY 25 µg Total Carotenoid Content β-OHase LCYB LCYB + LCYE ZDS + CRTISO PDS + Z-ISO Phytoene GGPP β+ε-OHase α-carotene GGPP Chromoplast 25 µg Total Carotenoid Content 25% Amylose ATP PPi 75% Amylopectin ZDS + CRTISO PDS + Z-ISO β-carotene Lycopene ζ-carotene 15µg Chromoplast Lutein β+ε-OHase α-carotene Chromoplast 25 µg Total Carotenoid Content Lutein PSY α-carotene SBEIIDE SBEI SSIII SSII SSI GBSSI G1P ZDS + CRTISO PDS + Z-ISO Phytoene GGPP 15µg β+ε-OHase ADP Amyloplast Zeaxanthin LCYB LCYB + LCYE Lycopene ζ-carotene Lutein PSY 75% Amylopectin ADPG G1P GBSSI 25% Amylose Amyloplast Zeaxanthin β-carotene 15µg β+ε-OHase ADP β-OHase Zeaxanthin Phytoene GGPP ATP PPi GBSSI 25% Amylose β-OHase 25% Amylose 75% Amylopectin SBEIIDE SBEI SSIII SSII SSI ATP PPi ADPG G1P β-OHase Lycopene ζ-carotene 15µg Lutein PSY GBSSI Zeaxanthin β-carotene Chromoplast Zeaxanthin β-carotene Lycopene ζ-carotene Phytoene GGPP β+ε-OHase α-carotene 25 µg Total Carotenoid Content β-OHase LCYB LCYB + LCYE β-OHase ZDS + CRTISO PDS + Z-ISO 15µg ADPG Amyloplast 25 µg Total Carotenoid Content GBSSI PSY 25 µg Total Carotenoid Content LCYB LCYB + LCYE ζ-carotene Lutein PSY ATP PPi G1P ADPG Phytoene GGPP α-carotene 25% Amylose β-carotene Lycopene Phytoene GGPP SBEIIDE SBEI SSIII SSII SSI GBSSI ADP LCYB LCYB + LCYE ZDS + CRTISO PDS + Z-ISO ZDS + CRTISO PDS + Z-ISO 75% Amylopectin ADP Amyloplast 75% Amylopectin SBEIIDE SBEI SSIII SSII SSI 25 µg Total Carotenoid Content Lutein β+ε-OHase α-carotene Zeaxanthin ATP PPi G1P Amyloplast 75% Amylopectin β-carotene β-OHase LCYB LCYB + LCYE ADPG G1P GBSSI 25% Amylose SBEIIDE SBEI SSIII SSII SSI GBSSI 25% Amylose Chromoplast 25 µg Total Carotenoid Content Chromoplast ATP PPi 75% Amylopectin ADP SBEIIDE SBEI SSIII SSII SSI LCYB LCYB + LCYE ADP ADPG 15µg β+ε-OHase 75% Amylopectin SBEIIDE SBEI SSIII SSII SSI ADPG ATP PPi G1P GBSSI 25% Amylose Lycopene ζ-carotene Phytoene PSY 15µg α-carotene SBEIIDE SBEI SSIII SSII SSI ATP PPi G1P GGPP Lutein PSY 75% Amylopectin GBSSI 25% Amylose Amyloplast β-carotene Lycopene ζ-carotene Phytoene GGPP Chromoplast ADP 75% Amylopectin SBEIIDE SBEI SSIII SSII SSI ZDS + CRTISO PDS + Z-ISO β-OHase β+ε-OHase α-carotene ATP PPi G1P Amyloplast ADPG LCYB LCYB + LCYE 25 µg Total Carotenoid Content Lutein PSY SBEIIDE SBEI SSIII SSII SSI GBSSI 25% Amylose ζ-carotene Phytoene GGPP ADP 75% Amylopectin SBEIIDE SBEI SSIII SSII SSI ATP PPi G1P
    • pVA and Starch: Infrastructure Functional Genetic for high quality cassava: pVA and Starch synthase pathways Carotenoid Synthase Pathway 25 µg Total Carotenoid Content β-OHase Zeaxanthin LCYB LCYB + LCYE ZDS + CRTISO PDS + Z-ISO β-carotene Lycopene ζ-carotene Phytoene GGPP Lutein PSY 15µg β+ε-OHase α-carotene Chromoplast Starch Synthase Pathway 75% Amylopectin DE SBEII SBEI SSIII SSII SSI ATP PPi G1P ADPG ADP GBSSI 25% Amylose Amyloplast Equipment needed:
    • pVA and Starch: Plant materials Functional Genetic for high quality cassava: pVA and Starch synthase pathways Carotenoid Synthase Pathway 25 µg Total Carotenoid Content β-OHase Zeaxanthin LCYB LCYB + LCYE ZDS + CRTISO PDS + Z-ISO β-carotene Lycopene ζ-carotene Phytoene GGPP Lutein PSY 15µg β+ε-OHase α-carotene Chromoplast Starch Synthase Pathway 75% Amylopectin DE SBEII SBEI SSIII SSII SSI ATP PPi G1P ADPG ADP GBSSI 25% Amylose Amyloplast PEDIGREE:
    • pVA and Starch: Phenotyping Functional Genetic for high quality cassava: pVA and Starch synthase pathways Carotenoid Synthase Pathway 25 µg Total Carotenoid Content β-OHase Zeaxanthin LCYB LCYB + LCYE ZDS + CRTISO PDS + Z-ISO β-carotene Lycopene ζ-carotene Phytoene GGPP Lutein PSY 15µg β+ε-OHase α-carotene Chromoplast Starch Synthase Pathway 75% Amylopectin DE SBEII SBEI SSIII SSII SSI ATP PPi G1P ADPG ADP GBSSI 25% Amylose Amyloplast BIOCHEMICAL TEST:
    • pVA and Starch: Data consistency Functional Genetic for high quality cassava: pVA and Starch synthase pathways Three years evaluation 2011, 2012 and 2013 Total Carotenoid Content (HPLC method) Carotenoid Synthase Pathway 30 25 µg Total Carotenoid Content 25 β-OHase Zeaxanthin ZDS + CRTISO PDS + Z-ISO Lycopene ζ-carotene Phytoene PSY 15 10 Lutein 15µg y = 1.0007x + 1.7402 R² = 0.821 5 β+ε-OHase α-carotene 0 0 5 10 15 20 25 2011 Chromoplast Total Carotenoid Content (HPLC method) Linear (Total Carotenoid Content (HPLC method)) β-carotene content (HPLC method) 16 14 12 10 2012 GGPP 20 β-carotene 2012 LCYB LCYB + LCYE 8 6 y = 1.0899x - 0.0065 R² = 0.8194 4 2 0 0 2 4 6 8 10 12 2011 b-carotene content (HPLC method) Linear (b-carotene content (HPLC method)) 14
    • Carotenoid Synthase Pathway β-OHase Zeaxanthin ZDS + CRTISO PDS + Z-ISO GGPP PSY β-carotene Lycopene Phytoene 15µg α-carotene β+ε-OHase 45 Chromoplast 40 0 GM3732-28 GM3736-78 GM3736-84 GM3736-29 GM3732-19 GM3732-22 GM3736-75 GM3736-40 GM3736-56 GM3736-26 GM3736-45 GM3736-37 GM3736-34 GM3732-02 GM3732-05 GM3732-34 GM3736-17 GM3736-16 GM3732-17 GM905-57 GM3736-32 GM3736-15 GM3732-18 GM3736-58 GM3736-59 GM3732-11 GM3732-08 GM3736-77 GM3736-20 GM3736-69 GM905-60 GM3732-29 GM3732-30 GM3736-66 GM3736-38 GM3736-36 GM3732-01 GM3736-76 GM3732-21 GM3736-51 GM3736-43 GM3732-16 GM3736-18 GM3736-85 GM3736-12 GM3736-44 GM3732-37 GM3732-13 GM3736-13 GM3736-02 GM3736-06 GM3736-48 GM3736-53 GM3736-54 GM3736-74 GM3732-23 GM3732-36 GM3736-72 GM3732-31 GM3736-57 GM905-52 GM3736-52 GM3736-03 GM3736-08 GM3732-25 GM3736-19 GM3736-11 GM3732-27 GM3736-23 GM3736-80 GM3732-12 GM3732-35 GM3736-05 GM3736-79 GM3732-14 GM3732-04 GM3736-63 GM3732-20 GM3732-32 GM3732-09 GM3736-24 GM3736-25 GM3736-41 GM3732-33 GM3736-73 GM3732-03 GM3736-10 GM3732-06 GM3736-22 GM3736-61 GM3736-35 GM3736-47 GM3736-21 GM3736-30 GM3736-27 GM3736-70 GM3732-07 GM3736-39 GM3732-15 GM3736-49 GM3736-81 GM3732-10 GM3736-09 GM3736-33 GM3736-50 GM3732-24 GM3736-28 GM3736-71 GM3736-64 GM3736-14 GM3736-55 GM3736-82 GM3736-42 GM3736-46 GM3736-62 GM3736-67 GM3736-01 GM3736-83 LCYB LCYB + LCYE Carotenoid Potential Functional Genetic for high quality cassava: pVA and Starch synthase pathways Carotenoid Gained pVA and Starch: The potential Three years evaluation 2011, 2012 and 2013 IPP 25 µg Total Carotenoid Content Geranylgeranyl diphosphate Phytoene synthase Phytoene ζ-carotene Phytoene desaturase Lutein Lycopene ξ-carotene desaturase Lycopene-beta-cyclase  -carotene (vitamin A precursor) PTFN 2012 PTH 2012 TCH 2012 35 30 25 20 15 10 5
    • Carotenoid Synthase Pathway β-OHase Zeaxanthin ZDS + CRTISO PDS + Z-ISO GGPP PSY Lycopene β-carotene Phytoene 15µg α-carotene β+ε-OHase 45 Chromoplast 40 0 GM3732-28 GM3736-78 GM3736-84 GM3736-29 GM3732-19 GM3732-22 GM3736-75 GM3736-40 GM3736-56 GM3736-26 GM3736-45 GM3736-37 GM3736-34 GM3732-02 GM3732-05 GM3732-34 GM3736-17 GM3736-16 GM3732-17 GM905-57 GM3736-32 GM3736-15 GM3732-18 GM3736-58 GM3736-59 GM3732-11 GM3732-08 GM3736-77 GM3736-20 GM3736-69 GM905-60 GM3732-29 GM3732-30 GM3736-66 GM3736-38 GM3736-36 GM3732-01 GM3736-76 GM3732-21 GM3736-51 GM3736-43 GM3732-16 GM3736-18 GM3736-85 GM3736-12 GM3736-44 GM3732-37 GM3732-13 GM3736-13 GM3736-02 GM3736-06 GM3736-48 GM3736-53 GM3736-54 GM3736-74 GM3732-23 GM3732-36 GM3736-72 GM3732-31 GM3736-57 GM905-52 GM3736-52 GM3736-03 GM3736-08 GM3732-25 GM3736-19 GM3736-11 GM3732-27 GM3736-23 GM3736-80 GM3732-12 GM3732-35 GM3736-05 GM3736-79 GM3732-14 GM3732-04 GM3736-63 GM3732-20 GM3732-32 GM3732-09 GM3736-24 GM3736-25 GM3736-41 GM3732-33 GM3736-73 GM3732-03 GM3736-10 GM3732-06 GM3736-22 GM3736-61 GM3736-35 GM3736-47 GM3736-21 GM3736-30 GM3736-27 GM3736-70 GM3732-07 GM3736-39 GM3732-15 GM3736-49 GM3736-81 GM3732-10 GM3736-09 GM3736-33 GM3736-50 GM3732-24 GM3736-28 GM3736-71 GM3736-64 GM3736-14 GM3736-55 GM3736-82 GM3736-42 GM3736-46 GM3736-62 GM3736-67 GM3736-01 GM3736-83 LCYB LCYB + LCYE Carotenoid Potential Functional Genetic for high quality cassava: pVA and Starch synthase pathways Carotenoid Gained pVA and Starch: No Lycopene Three years evaluation 2011, 2012 and 2013 IPP 25 µg Total Carotenoid Content Geranylgeranyl diphosphate Phytoene synthase Phytoene ζ-carotene Phytoene desaturase Lutein Lycopene ξ-carotene desaturase  -carotene (vitamin A precursor)    Lycopene-beta-cyclase PTFN 2012 PTH 2012 TCH 2012 35 30 25 20 15 10 5
    • Carotenoid Synthase Pathway β-OHase Zeaxanthin ZDS + CRTISO PDS + Z-ISO GGPP PSY β-carotene Lycopene Phytoene 15µg α-carotene β+ε-OHase 45 Chromoplast 40 15 0 GM3732-28 GM3736-78 GM3736-84 GM3736-29 GM3732-19 GM3732-22 GM3736-75 GM3736-40 GM3736-56 GM3736-26 GM3736-45 GM3736-37 GM3736-34 GM3732-02 GM3732-05 GM3732-34 GM3736-17 GM3736-16 GM3732-17 GM905-57 GM3736-32 GM3736-15 GM3732-18 GM3736-58 GM3736-59 GM3732-11 GM3732-08 GM3736-77 GM3736-20 GM3736-69 GM905-60 GM3732-29 GM3732-30 GM3736-66 GM3736-38 GM3736-36 GM3732-01 GM3736-76 GM3732-21 GM3736-51 GM3736-43 GM3732-16 GM3736-18 GM3736-85 GM3736-12 GM3736-44 GM3732-37 GM3732-13 GM3736-13 GM3736-02 GM3736-06 GM3736-48 GM3736-53 GM3736-54 GM3736-74 GM3732-23 GM3732-36 GM3736-72 GM3732-31 GM3736-57 GM905-52 GM3736-52 GM3736-03 GM3736-08 GM3732-25 GM3736-19 GM3736-11 GM3732-27 GM3736-23 GM3736-80 GM3732-12 GM3732-35 GM3736-05 GM3736-79 GM3732-14 GM3732-04 GM3736-63 GM3732-20 GM3732-32 GM3732-09 GM3736-24 GM3736-25 GM3736-41 GM3732-33 GM3736-73 GM3732-03 GM3736-10 GM3732-06 GM3736-22 GM3736-61 GM3736-35 GM3736-47 GM3736-21 GM3736-30 GM3736-27 GM3736-70 GM3732-07 GM3736-39 GM3732-15 GM3736-49 GM3736-81 GM3732-10 GM3736-09 GM3736-33 GM3736-50 GM3732-24 GM3736-28 GM3736-71 GM3736-64 GM3736-14 GM3736-55 GM3736-82 GM3736-42 GM3736-46 GM3736-62 GM3736-67 GM3736-01 GM3736-83 LCYB LCYB + LCYE Carotenoid Potential Functional Genetic for high quality cassava: pVA and Starch synthase pathways Carotenoid Gained pVA and Starch: Unknown carotenoids Three years evaluation 2011, 2012 and 2013 IPP 25 µg Total Carotenoid Content Geranylgeranyl diphosphate Phytoene synthase Phytoene ζ-carotene Phytoene desaturase Lutein Lycopene ξ-carotene desaturase Lycopene-beta-cyclase  -carotene (vitamin A precursor) PTFN 2012 PTH 2012 TCH 2012 35 30 25 20 Unknown Carotenoids 10 5
    • Carotenoid Synthase Pathway β-OHase Zeaxanthin ZDS + CRTISO PDS + Z-ISO GGPP PSY β-carotene Lycopene Phytoene 15µg α-carotene β+ε-OHase Chromoplast 25 0 GM3732-28 GM3736-78 GM3736-84 GM3736-29 GM3732-19 GM3732-22 GM3736-75 GM3736-40 GM3736-56 GM3736-26 GM3736-45 GM3736-37 GM3736-34 GM3732-02 GM3732-05 GM3732-34 GM3736-17 GM3736-16 GM3732-17 GM905-57 GM3736-32 GM3736-15 GM3732-18 GM3736-58 GM3736-59 GM3732-11 GM3732-08 GM3736-77 GM3736-20 GM3736-69 GM905-60 GM3732-29 GM3732-30 GM3736-66 GM3736-38 GM3736-36 GM3732-01 GM3736-76 GM3732-21 GM3736-51 GM3736-43 GM3732-16 GM3736-18 GM3736-85 GM3736-12 GM3736-44 GM3732-37 GM3732-13 GM3736-13 GM3736-02 GM3736-06 GM3736-48 GM3736-53 GM3736-54 GM3736-74 GM3732-23 GM3732-36 GM3736-72 GM3732-31 GM3736-57 GM905-52 GM3736-52 GM3736-03 GM3736-08 GM3732-25 GM3736-19 GM3736-11 GM3732-27 GM3736-23 GM3736-80 GM3732-12 GM3732-35 GM3736-05 GM3736-79 GM3732-14 GM3732-04 GM3736-63 GM3732-20 GM3732-32 GM3732-09 GM3736-24 GM3736-25 GM3736-41 GM3732-33 GM3736-73 GM3732-03 GM3736-10 GM3732-06 GM3736-22 GM3736-61 GM3736-35 GM3736-47 GM3736-21 GM3736-30 GM3736-27 GM3736-70 GM3732-07 GM3736-39 GM3732-15 GM3736-49 GM3736-81 GM3732-10 GM3736-09 GM3736-33 GM3736-50 GM3732-24 GM3736-28 GM3736-71 GM3736-64 GM3736-14 GM3736-55 GM3736-82 GM3736-42 GM3736-46 GM3736-62 GM3736-67 GM3736-01 GM3736-83 LCYB LCYB + LCYE Carotenoid Potential Functional Genetic for high quality cassava: pVA and Starch synthase pathways Carotenoid Gained pVA and Starch: DMC do not matter Carotenoids vs Dry Matter Content (DMC) IPP Geranylgeranyl diphosphate Gains from 2010/12 to 2013 From 25ug to 29ug in TCC From 15ug to 22ug in TBC 25 µg Total Carotenoid Content Phytoene synthase Phytoene ζ-carotene Phytoene desaturase Lutein Lycopene ξ-carotene desaturase Lycopene-beta-cyclase (vitamin A precursor) Dry Matter Content (2012)  -carotene 50 45 40 35 30 20 High β-carotene has no penalty on DMC 15 10 5
    • pVA and Starch: During 2014 Functional Genetic for high quality cassava: pVA and Starch synthase pathways Carotenoid Synthase Pathway 25 µg Total Carotenoid Content β-OHase Zeaxanthin LCYB LCYB + LCYE ZDS + CRTISO PDS + Z-ISO β-carotene Lycopene ζ-carotene Phytoene GGPP PSY Lutein 15µg β+ε-OHase α-carotene Chromoplast SSR and SNPs
    • pVA and Starch: Which Molecular Markers Functional Genetic for high quality cassava: pVA and Starch synthase pathways Carotenoid Synthase Pathway Unraveling the genetics of high pVA 61003 Mapping Pop. A10-Chr10 0.0 2.9 A12-Chr12 CIR0003 RGA-8A-1c BNL4059 CIR0272b 0.0 6.3 25 µg Total Carotenoid Content β-OHase Lutein 15µg β+ε-OHase BNL0598a BNL3537c CIR0166a A1110 377.3 BNL2960 61003 Mapping Pop. D10-Chr20 0.0 D13-Chr18 158.7 CIR0277 qF5-VBS BNL2652b BNL1079 BNL3479 BNL3280b qF4-VBS 61.9 75.1 87.1 95.8 qF4-VBS qF3-VBS qF3-FGAW5 qF3-FGAW6 qF3-FGAW4 qF3-VBS qF3-FGAW3 qF3-FGAW6 qF3-FGAW5 CIR0166b qF3-FGAW4 149.8 qF3-FGAW3 CIR0121 BNL3838 BNL3948 CIR0171b BNL0946 BNL3993 CIR0171d BNL0169 Unig22B10b Gate1AC11a BNL0193 BNL2544 qF3-W3 0.0 12.3 15.0 20.5 BNL1145 48.7 49.3 63.4 77.9 88.8 93.9 104.2 128.7 qF3-VBS BNL1161 338.0 349.4 qF3-VBSb BNL1045b BNL2495 CIR0085b 315.1 qF3-FGAW6 BNL3537b 310.4 326.3 330.8 qF3-FGAW5 CIR0272a 274.7 qF3-FGAW6b 248.9 CIR0171c qF5-VBS BNL1160 qF4-VBS 250.8 qF5-VBS Chromoplast BNL0256 272.4 α-carotene 232.8 qF4-VBS PSY CIR0148 BNL1045a CIR0293 BNL3537a BNL0598b 215.1 218.0 ζ-carotene BNL1673 140.5 146.9 160.2 172.8 188.4 qF5-VBS 110.9 Lycopene Phytoene GGPP CIR0199a BNL1693 qF3-VBSa ZDS + CRTISO PDS + Z-ISO β-carotene CIR0009 86.4 99.8 qF3-FGAW6a 66.6 Zeaxanthin LCYB LCYB + LCYE
    • pVA and Starch: Novel starches Functional Genetic for high quality cassava: pVA and Starch synthase pathways Waxy and small-granule cassava Easy hydrolysis good for bioethanol and bioplastic production 75% Amylopectin DE SBEII SBEI SSIII SSII SSI X Starch Synthase Pathway ATP PPi 75% Amylopectin G1P DE SBEII SBEI SSIII SSII SSI ADPG ADP ATP PPi G1P GBSSI ADPG 25% Amylose ADP GBSSI 25% Amylose Amyloplast Amyloplast
    • pVA and Starch: Novel starches Functional Genetic for high quality cassava: pVA and Starch synthase pathways Waxy and small-granule cassava 75% Amylopectin DE SBEII SBEI SSIII SSII SSI Starch Synthase Pathway ATP PPi 75% Amylopectin G1P DE SBEII SBEI SSIII SSII SSI ADPG ADP XGBSSI ATP PPi G1P 100% amylopectin ADPG 25% Amylose ADP GBSSI 25% Amylose Amyloplast Amyloplast
    • pVA and Starch: Novel starches Functional Genetic for high quality cassava: pVA and Starch synthase pathways Waxy and small-granule cassava Important to bear in mind: Type and quality of the amylopectin is control by the starch-synthase pathway 75% Amylopectin DE SBEII SBEI SSIII SSII SSI Starch Synthase Pathway ATP PPi 75% Amylopectin G1P DE SBEII SBEI SSIII SSII SSI ADPG ADP XGBSSI ATP PPi G1P ADPG 25% Amylose ADP GBSSI 25% Amylose Amyloplast Amyloplast
    • pVA and Starch: Novel starches Functional Genetic for high quality cassava: pVA and Starch synthase pathways Starch Synthase Pathway 75% Amylopectin DE SBEII SBEI SSIII SSII SSI ATP PPi G1P ADPG ADP GBSSI 25% Amylose Amyloplast Waxy and small-granule cassava
    • pVA and Starch: Novel starches WAXY Functional Genetic for high quality cassava: pVA and Starch synthase pathways GBSSI: Responsible for Waxy cassava Starch Synthase Pathway 75% Amylopectin DE SBEII SBEI SSIII SSII SSI ATP PPi G1P ADPG ADP GBSSI 25% Amylose Amyloplast • GBSSI in cassava is ~3400 bp • 2 to 4 allelic versions • Among 7 different sources of the mutation span 126 SNPs • 3 are diagnostic of the trait
    • pVA and Starch: Novel starches WAXY New-V 4Wx -1Ne w-V2 Wx 7-1N ew-V 1Wx 70 AC2 7-1 New CL -V3 4 2Wx 3N ew 77 CL A-V 4 15W 40 6N x ew CL 51 A-V 42 5W -3N x CL ew A-V 42 -3N 7W ew x ACU V4 AM B W 2 20 9 x 6- V3 AM 5N NW 20 ew x C 6-V L4 5N 4W 1ew 6N x -V ew 6W Ax V2 W x AC27 AC27-1 AC2 91 24 82 57 24 24 24 62 A-V2Wx CL44-2N ewA-V1 Wx CL44-2New CL41-6NewA-V7Wx CL41-6NewA-V3Wx 4N 6-2 31 3 SM 24 24 24 24 24 24 24 24 _0 24 AC 75 V7 1C AB 2 O 04 K958 639 C O TTO 49 55 33P N TT 14 O O CH PU IC LU N KP S VE EA N3 09 aV VE 3N N3 Wx 09a V2 VE NW N30 x 9aV 1NW CUB x 29-V GBS SJF 7089 6NWx 48N Wx CUB23 -V4N Wx VEN309 bV2NW x XP 24 24 46 99 24 66 99 87 24 24 24 26 26 24 24 CUB23-V 3NWx TME-3NewV1PSg NWx 24 24 18 18 25 24 66 24 36 24 24 24 27 21 99 73 24 81 22 VE N2 NC AU 72 VE XB4 9-V 1 N2 9-60 9N 9- V4NW W V4 NWx x VE NW x N2 9-V x CU 3N B2 W VE C -V1 x N3U 0Bb NW 9 2V -V4 1N NW x Wx x TMS30555V1r AM 50 evPSgNWx CUB 6-5NW 2-V3 x NW CUB x 2-V6 NWx CU VEN2B2-V5NWx 9-V2NW x IcD All non-waxy landraces carried the non-waxy allele(s), but waxy types also carried non-waxy alleles C4revV2PSgNWx VEN29-V1NWx GB SS 96 95 85 26 34 34 81 18 49 39 84 Amyloplast x W x V5 Wx 1W x AV4 W-xV 3W ew A8A ew A-V 6N ew A-V w 2- 6N -24N ew 6 L4 41- 6Ne -24N x C 31 6 1W CL SL43 331 M1 A-V C SM ew -3N 42 Wx CL 2N 3-V 5NWx B2 75 CU B23-V NWxWx 99 -V a CU 58096 V4N 28 B CU N3 VE 99 99 2PSgNWx TME-3NewV x V2NW CUB27NWx CUB2-VV1PSgNWx C4rev 2 24 5 GBSSI 25% Amylose 91 26 82 51 24 ADP 24 62 90 90 89 54 55 29 21 19 ADPG VEN29-V7NWx CL41-1NewAV3W x AM206-5 New-V1Wx CUB29V5NW 24 x CUB29 24 -V CL4 2-3N 7NWx ewA CL4 -V3W 2 x CL4 -3NewA 82 -V6 2-6 Wx New CL 42A-V 6N CL 4W 53 ew 42 x A-V CL 75 2W SM4 6New x 11 A-V SM 33-1 N 1W e 33 6-3 wA x 16 2N V4 CL e W -3 2N wA- x CL 41V3 ew 42 6N W A-6 ew x V4 Ne AW V6 wA x -V Wx 3W x 24 24 24 G1P PAN139-V6NWx 24 8 ATP PPi 24 24 11 DE SBEII SBEI SSIII SSII SSI CUB29-V2NWx VEN29-V6NWx 8NWx VEN29-V x -V1NW x W PAN139PSgN 5V2rev 2Wx 3055 wA-V TMS Wx 2N e -V1 316-3 ewA SM3 -32N x 316 S 5NWY SM3 9-V NE A N13 M 0 PA416 7 Wx IX 6N SS 3-V NWx GB B2 1 CU 23-V NWx 4 x B CU 58-V NW x B V5 W CU 29- 4N Wx N -V N VE 139 10 N -V PA N29 VE x CUB58-V3NW 24 24 47 75% Amylopectin 24 24 CUB58-V1NWx Starch Synthase Pathway x W V1 x A3W ew -V x W wA V2 1 Ne x A-5 33 w 5 4W Ne 31 -V SM 5 3 A 5ew S M 33 1 x -5N 2W 15 SM -V 33 x wA SM 1W Ne A-V 2-3 86 4 w Wx Ne CL -V5 1-6 ew L4 C -5N x 94 206 V1W 71 AM wA Ne 1-1 CL4 Wx 2N 58-V x CUB 1NW 29-V 2Wx CUB ew-V 6-5N AM20 Wx 9-V2N PAN13 36 24 3NWx 76 PAN139-V 5N 5- 24 A-V ew All waxy types carried the waxy allele(s) 67 AC J1 1 x 3W w-V x Ne -V2W 6-5 ewAx 20 4N49W -2 AM 316 089 x SM3SJ-F7 NW S58 V5 GBB 6Wx wA-V CU -2Ne 3Wx CL44 2NewA-V x CL44wA-V5W 44-2Ne CL AV2Wx CL41-1New CL44-2NewA-V4Wx Waxy and small-granule cassava x 4W Functional Genetic for high quality cassava: pVA and Starch synthase pathways
    • pVA and Starch: Novel starches WAXY New-V 4Wx -1Ne w-V2 Wx 7-1N ew-V 1Wx 70 AC2 7-1 New CL -V3 4 2Wx 3N ew 77 CL A-V 4 15W 40 6N x ew CL 51 A-V 42 5W -3N x CL ew A-V 42 -3N 7W ew x ACU V4 AM B W 2 20 9 x 6- V3 AM 5N NW 20 ew x C 6-V L4 5N 4W 1ew 6N x -V ew 6W Ax V2 W x AC27 AC27-1 AC2 91 24 82 57 24 24 24 62 A-V2Wx CL44-2N ewA-V1 Wx CL44-2New CL41-6NewA-V7Wx CL41-6NewA-V3Wx 4N 6-2 31 3 SM 24 24 24 24 24 24 24 24 _0 24 AC 75 V7 1C AB 2 O 04 K958 639 C O TTO 49 55 33P N TT 14 O O CH PU IC LU N KP S VE EA N3 09 aV VE 3N N3 Wx 09a V2 VE NW N30 x 9aV 1NW CUB x 29-V GBS SJF 7089 6NWx 48N Wx CUB23 -V4N Wx VEN309 bV2NW x XP 24 24 46 99 99 87 26 26 24 24 24 66 24 36 24 24 24 27 21 99 73 24 81 22 VE N2 NC AU 72 VE XB4 9-V 1 N2 9-60 9N 9- V4NW W V4 NWx x VE NW x N2 9-V x CU 3N B2 W VE C -V1 x N3U 0Bb NW 9 2V -V4 1N NW x Wx x TMS30555V1r AM 50 evPSgNWx CUB 6-5NW 2-V3 x NW CUB x 2-V6 NWx CU VEN2B2-V5NWx 9-V2NW x All non-waxy landraces carried the non-waxy allele(s), but waxy types also carried non-waxy alleles C4revV2PSgNWx VEN29-V1NWx GB SS x W x V5 Wx 1W x AV4 W-xV 3W ew A8A ew A-V 6N ew A-V w 2- 6N -24N ew 6 L4 41- 6Ne -24N x C 31 6 1W CL SL43 331 M1 A-V C SM ew -3N 42 Wx CL 2N 3-V 5NWx B2 75 CU B23-V NWxWx 99 -V a CU 58096 V4N 28 B CU N3 VE 99 99 2PSgNWx TME-3NewV x V2NW CUB27NWx CUB2-VV1PSgNWx C4rev 96 95 85 26 34 34 81 18 49 39 IcD 91 26 82 51 84 Amyloplast 24 62 2 24 5 GBSSI 25% Amylose VEN29-V7NWx CL41-1NewAV3W x AM206-5 New-V1Wx CUB29V5NW 24 x CUB29 24 -V CL4 2-3N 7NWx ewA CL4 -V3W 2 x CL4 -3NewA 82 -V6 2-6 Wx New CL 42A-V 6N CL 4W 53 ew 42 x A-V CL 75 2W SM4 6New x 11 A-V SM 33-1 N 1W e 33 6-3 wA x 16 2N V4 CL e W -3 2N wA- x CL 41V3 ew 42 6N W A-6 ew x V4 Ne AW V6 wA x -V Wx 3W x 24 24 24 ADP PAN139-V6NWx 24 90 90 89 54 55 29 21 19 ADPG x CUB58-V3NW 24 24 24 G1P CUB29-V2NWx VEN29-V6NWx 8NWx VEN29-V x -V1NW x W PAN139PSgN 5V2rev 2Wx 3055 wA-V TMS Wx 2N e -V1 316-3 ewA SM3 -32N x 316 S 5NWY SM3 9-V NE A N13 M 0 PA416 7 Wx IX 6N SS 3-V NWx GB B2 1 CU 23-V NWx 4 x B CU 58-V NW x B V5 W CU 29- 4N Wx N -V N VE 139 10 N -V PA N29 VE 24 8 ATP PPi 24 11 DE SBEII SBEI SSIII SSII SSI 24 24 47 75% Amylopectin 24 24 18 18 25 24 Starch Synthase Pathway Is cassava really diploid (2X)? 24 24 CUB58-V1NWx 24 66 CUB23-V 3NWx TME-3NewV1PSg NWx x W V1 x A3W ew -V x W wA V2 1 Ne x A-5 33 w 5 4W Ne 31 -V SM 5 3 A 5ew S M 33 1 x -5N 2W 15 SM -V 33 x wA SM 1W Ne A-V 2-3 86 4 w Wx Ne CL -V5 1-6 ew L4 C -5N x 94 206 V1W 71 AM wA Ne 1-1 CL4 Wx 2N 58-V x CUB 1NW 29-V 2Wx CUB ew-V 6-5N AM20 Wx 9-V2N PAN13 36 24 3NWx 76 PAN139-V 5N 5- 24 A-V ew All waxy types carried the waxy allele(s) 67 AC J1 1 x 3W w-V x Ne -V2W 6-5 ewAx 20 4N49W -2 AM 316 089 x SM3SJ-F7 NW S58 V5 GBB 6Wx wA-V CU -2Ne 3Wx CL44 2NewA-V x CL44wA-V5W 44-2Ne CL AV2Wx CL41-1New CL44-2NewA-V4Wx Waxy and small-granule cassava x 4W Functional Genetic for high quality cassava: pVA and Starch synthase pathways
    • Whitefly research: WHY Whitefly control: a durable solution to cassava-disease pandemics (Africa and Asia) Whiteflies have been called Whitefly resistance A B CMC-40 “The pest of 21st Century” Tomato C Citrus D MEcu 72 Whitefly molecular identification Bemisia tabaci JN410741 Asia / Asia-Minor Bemisia tabaci JN410738 Bemisia tabaci biotypeB KF059959 CIAT 100 A Bemisia tabaci biotypeA KF059958 CIAT 96 99 30 New World G-I 99 81 Bemisia tabaci AY521259 Aleurolobus marlatti JQ340188 Asia Siphoninus philyreae JQ340199 Aleurocanthus inceratus HM150621 45 B Asia Crenidorsum micheliae JQ340190 97 C Aleurotrachelus trachoides KF059957 CIAT 98 Aleurothrachelus socialis KF059953 CIAT 89 88 New World G-II Aleurocanthus spiniferus JQ340176 D Aleurothrixus floccosus KF059956 CIAT Aleuroclava sp JQ340187 Dialeurodes citri JQ340193 98 93 G-III Dialeuropora JQ340197 73 Asia Dialeurodes hongkongensis JQ340195 E New World Trialeurodes variabilis KF059962 CIAT Trialeurodes vaporiariorum KF192508 CIAT 99 G-IV 68 New World G-V Aleyrodinae 99 F 100 Trialeurodes vaporariorum AY521265 Aleurodicinae Aleuronudus melzeri KF059955 CIAT G Aleurodicus dugessi AY521251 46 99 Lecanoideus floccissimus KF059960 CIAT H Aleurodicus dispersus KF059954 CIAT 95 99 Aleurodicus dispersus EU581838 I 75 Aleurodicus dispersus EU581837 100 Drosophila melanogaster ADW61333 Drosophila melanogaster AGE13862 0.20 0.15 0.10 0.05 0.00 G-VI Drosophila melanogaster ADW61439 Asia Cotton Zucchini Palm
    • Whitefly research Whitefly control: a durable solution to cassava-disease pandemics (Africa and Asia) Whitefly Pest response Bio-assay Whitefly resistance A A B B CMC-40 C D C MEcu 72 Whitefly molecular identification Bemisia tabaci JN410741 Asia / Asia-Minor Bemisia tabaci JN410738 Bemisia tabaci biotypeB KF059959 CIAT A Bemisia tabaci biotypeA KF059958 CIAT 96 99 30 New World G-I 99 81 100 Bemisia tabaci AY521259 Aleurolobus marlatti JQ340188 Asia Siphoninus philyreae JQ340199 Aleurocanthus inceratus HM150621 45 B Asia Crenidorsum micheliae JQ340190 97 C Aleurotrachelus trachoides KF059957 CIAT 98 Aleurothrachelus socialis KF059953 CIAT 89 88 New World G-II Aleurocanthus spiniferus JQ340176 D Aleurothrixus floccosus KF059956 CIAT Aleuroclava sp JQ340187 Dialeurodes citri JQ340193 98 93 G-III Dialeuropora JQ340197 73 Asia Dialeurodes hongkongensis JQ340195 E New World Trialeurodes variabilis KF059962 CIAT Trialeurodes vaporiariorum KF192508 CIAT 99 G-IV 68 New World G-V Aleyrodinae 99 F 100 Trialeurodes vaporariorum AY521265 Aleurodicinae Aleuronudus melzeri KF059955 CIAT G Aleurodicus dugessi AY521251 46 99 Lecanoideus floccissimus KF059960 CIAT H Aleurodicus dispersus KF059954 CIAT 95 99 Aleurodicus dispersus EU581838 I 75 Aleurodicus dispersus EU581837 100 Drosophila melanogaster ADW61333 Drosophila melanogaster AGE13862 0.20 0.15 0.10 0.05 0.00 G-VI Drosophila melanogaster ADW61439 Asia
    • Whitefly research Whitefly control: a durable solution to cassava-disease pandemics (Africa and Asia) Whitefly resistance A B CMC-40 C D MEcu 72 Whitefly molecular identification Bemisia tabaci JN410741 Asia / Asia-Minor Bemisia tabaci JN410738 Bemisia tabaci biotypeB KF059959 CIAT A Bemisia tabaci biotypeA KF059958 CIAT 96 99 30 New World G-I 99 81 100 Bemisia tabaci AY521259 Aleurolobus marlatti JQ340188 Asia Siphoninus philyreae JQ340199 Aleurocanthus inceratus HM150621 45 B Asia Crenidorsum micheliae JQ340190 97 C Aleurotrachelus trachoides KF059957 CIAT 98 Aleurothrachelus socialis KF059953 CIAT 89 88 New World G-II Aleurocanthus spiniferus JQ340176 D Aleurothrixus floccosus KF059956 CIAT Aleuroclava sp JQ340187 Dialeurodes citri JQ340193 98 93 G-III Dialeuropora JQ340197 73 Asia Dialeurodes hongkongensis JQ340195 E New World Trialeurodes variabilis KF059962 CIAT Trialeurodes vaporiariorum KF192508 CIAT 99 G-IV 68 New World G-V Aleyrodinae 99 F 100 Trialeurodes vaporariorum AY521265 Aleurodicinae Aleuronudus melzeri KF059955 CIAT G Aleurodicus dugessi AY521251 46 99 Lecanoideus floccissimus KF059960 CIAT H Aleurodicus dispersus KF059954 CIAT 95 99 Aleurodicus dispersus EU581838 I 75 Aleurodicus dispersus EU581837 100 Drosophila melanogaster ADW61333 Drosophila melanogaster AGE13862 0.20 0.15 0.10 0.05 0.00 G-VI Drosophila melanogaster ADW61439 Asia Whitefly SSR and AFLP genetic map SNP markers are underway
    • Whitefly research Whitefly control: a durable solution to cassava-disease pandemics (Africa and Asia) Whitefly resistance A B CMC-40 C D MEcu 72 Whitefly molecular identification Bemisia tabaci JN410741 Asia / Asia-Minor Bemisia tabaci JN410738 Bemisia tabaci biotypeB KF059959 CIAT A Bemisia tabaci biotypeA KF059958 CIAT 96 99 30 New World G-I 99 81 100 Bemisia tabaci AY521259 Aleurolobus marlatti JQ340188 Asia Siphoninus philyreae JQ340199 Aleurocanthus inceratus HM150621 45 B Asia Crenidorsum micheliae JQ340190 97 C Aleurotrachelus trachoides KF059957 CIAT 98 Aleurothrachelus socialis KF059953 CIAT 89 88 New World G-II Aleurocanthus spiniferus JQ340176 D Aleurothrixus floccosus KF059956 CIAT Aleuroclava sp JQ340187 Dialeurodes citri JQ340193 98 93 G-III Dialeuropora JQ340197 73 Asia Dialeurodes hongkongensis JQ340195 E New World Trialeurodes variabilis KF059962 CIAT Trialeurodes vaporiariorum KF192508 CIAT 99 G-IV 68 New World G-V Aleyrodinae 99 F 100 Trialeurodes vaporariorum AY521265 Aleurodicinae Aleuronudus melzeri KF059955 CIAT G Aleurodicus dugessi AY521251 46 99 Lecanoideus floccissimus KF059960 CIAT H Aleurodicus dispersus KF059954 CIAT 95 99 Aleurodicus dispersus EU581838 I 75 Aleurodicus dispersus EU581837 100 Drosophila melanogaster ADW61333 Drosophila melanogaster AGE13862 0.20 0.15 0.10 0.05 0.00 G-VI Drosophila melanogaster ADW61439 Asia Grant to be approved in 2014
    • Whitefly research Whitefly control: a durable solution to cassava-disease pandemics (Africa and Asia) Grant to be approved in 2014 Whitefly resistance A B CMC-40 C D MEcu 72 Whitefly molecular identification Bemisia tabaci JN410741 Asia / Asia-Minor Bemisia tabaci JN410738 Bemisia tabaci biotypeB KF059959 CIAT A Bemisia tabaci biotypeA KF059958 CIAT 96 99 30 New World G-I 99 81 100 Bemisia tabaci AY521259 Aleurolobus marlatti JQ340188 Asia Siphoninus philyreae JQ340199 Aleurocanthus inceratus HM150621 45 B Asia Crenidorsum micheliae JQ340190 97 C Aleurotrachelus trachoides KF059957 CIAT 98 Aleurothrachelus socialis KF059953 CIAT 89 88 New World G-II Aleurocanthus spiniferus JQ340176 D Aleurothrixus floccosus KF059956 CIAT Aleuroclava sp JQ340187 68 Dialeurodes citri JQ340193 98 93 G-III Dialeuropora JQ340197 73 Asia Dialeurodes hongkongensis JQ340195 E Trialeurodes variabilis KF059962 CIAT New World Trialeurodes vaporiariorum KF192508 CIAT 99 F G-IV Aleyrodinae 99 100 Trialeurodes vaporariorum AY521265 G Aleurodicus dugessi AY521251 46 99 Lecanoideus floccissimus KF059960 CIAT H Aleurodicus dispersus KF059954 CIAT 95 99 Aleurodicus dispersus EU581838 I 75 Aleurodicus dispersus EU581837 100 Drosophila melanogaster ADW61333 Drosophila melanogaster AGE13862 0.20 0.15 0.10 0.05 0.00 G-VI Drosophila melanogaster ADW61439 New World Asia G-V Aleurodicinae Aleuronudus melzeri KF059955 CIAT Dr. Adriana Bohorquez Post Doctoral Fellow
    • Lesson learned: Cassava genetic resource are critical to advance crop development. Understanding them fully is imperative A B CMC-40 C MEcu 72 D
    • Positioning CIAT as a Leader in RTB Improvement By 2012 Cassava Genetics / Molecular breeding working like Swiss clock Tissue Culture Mol. Biology WhiteFly Res. VIGS Bioinformatic & Data Management The Best Team Post Harvest Breeding
    • RTB Leader for Development of Varieties
    • Global Cassava Diversity: Cross-Cutting Enhancing Cassava productivity through more targeted use of global genetic diversity Next-generation sequencing Metabolomic profiling
    • Global Cassava Diversity: Strategy Enhancing Cassava productivity through more targeted use of global genetic diversity Next-generation sequencing Metabolomic profiling mGWAS and GWAS High pVA Waxy
    • Global Cassava Diversity: OMICS Enhancing Cassava productivity through more targeted use of global genetic diversity Data generation and analysis pipeline Next-generation sequencing Sampling • Selection of relevant breeding genotypes Metabolomic profiling • Geographic distribution RAD-SEQ Bioinformatic Pipeline Pop. GENOMICS Whole Genome Region/Window • Mapping to REF-GENOME • Pop. Structure • Adequate data filtering • Pop. diversity • Variant detection and genotyping (NGSEP) • Differential and random matting estimates • Nucleotide diversity • Tajima’s D • Kernell smoothed FSTs SNP-KIT Genotype validation/ Identification • Identification of highly informative SNPs to discriminate among cassava accessions
    • Global Cassava Diversity: OMICS Enhancing Cassava productivity through more targeted use of global genetic diversity Next-generation sequencing • Metabolomic profiling 1,900 Experimental nurseries • Nearly 15’000,000 data points
    • Global Cassava Diversity: OMICS Enhancing Cassava productivity through more targeted use of global genetic diversity • • Important genotypes: MCol22, MCol1505, MCol1684, MBra12. • Next-generation sequencing Identification of the 139 founders CIAT’s cassava breeding program Identification of 25 trait-specific genotypes to construct the Cassava-Basic Metabolome Profile Founder freq. Metabolomic profiling X Genotypes
    • Global Cassava Diversity: OMICS Enhancing Cassava productivity through more targeted use of global genetic diversity CIAT’s cassava collection compositions Next-generation sequencing Metabolomic profiling SAMPLING: • • • • • • Founders CIAT’s breeding program CIAT’s Core collection Other Landraces Wild Manihot species Improved Cassava Materials African materials 0139 0429 0163 0054 0170 0300 1255
    • Cassava Agro-biodiversity Enhancing Cassava productivity through more targeted use of global genetic diversity NextGen sequencing: RAD-seq Next-generation sequencing Metabolomic profiling 820 acc. 435 acc.
    • Cassava Agro-biodiversity Enhancing Cassava productivity through more targeted use of global genetic diversity Next-generation sequencing Metabolomic profiling NextGen sequencing: Whole genome 11 acc. 06 acc.
    • Cassava Agro-biodiversity Enhancing Cassava productivity through more targeted use of global genetic diversity Next-generation sequencing NGSEP Metabolomic profiling
    • Cassava Agro-biodiversity Enhancing Cassava productivity through more targeted use of global genetic diversity Next-generation sequencing 1. Sequence Analysis using NGSEP on 346 cassava specimens • 292 Cassava accessions from LAC • 054 Wild Manihot species 2. Strong differentiation between wild and cultivated specimens Metabolomic profiling • 614,000 SNPs were used to trace for the closest wild relatives to cassava 3. Complex patterns of population structure within M. esculenta • 99,037 SNPs were used.
    • Cassava Agro-biodiversity FLA PER ALT FLA PER TST FLA CTH GUT AES ALT Wild Manihots WKE K1 Southern South America K2 Caribbean K3 Mesoamerican K4 Andean Cordillera (High lands) K5 Savanna K6 Amazon and Eastern Brazil
    • Cassava Agro-biodiversity Southern South America Caribbean Mesoamerica Savanna Andean Ranges Amazon & Eastern Brazil
    • Cassava Agro-biodiversity High level of genetic diversity found in Mesoamerican landraces 7% 70% K1 Southern South America K2 Caribbean K3 Mesoamerican K4 Andean Cordillera (High lands) K5 Savanna K6 Amazon and Eastern Brazil
    • Cassava Agro-biodiversity K2 K1 K3 K5 K4 Cassava has a geographical sub-population distribution that suggest northward southward movement. K6 K1 K1 Southern South America K2 Caribbean K3 Mesoamerican K4 Andean Cordillera (High lands) K5 Savanna K6 Amazon and Eastern Brazil
    • Cassava Agro-biodiversity High pVA Southern South America Caribbean WF resistance Mesoamerica Savanna Andean Ranges Amazon & Eastern Brazil
    • Signs of selection in cassava Cassava Wild Cassava Chromosomes much needed
    • Global Cassava Diversity: Genomics DEVELOPING A CORE SET OF SNPs FOR VALIDATION AND IDENTIFICATION OF CASSAVA ACCESSIONS High Quality SNPs Technical criteria for SNPtype™ Assays in Fluidigm. Highly Informative SNPs shared between WGS and RAD-seq No SNPs around 40bp SNP/Scaffold Filters: Repetitive regions and CNVs GC content from 40 to 65 Mínimum MAF 0.2 Quality Score: Higher than 40 More than 10 homozygous differences
    • Application: SNP-kit for variety ID This core set of 181 SNPs enabled: • Accurate identifications of CIAT’s Cassava materials, and • Allowed for the assessment of the diversity of uncharacterized cassava collected in Amazonian native communities A set of the most 181 informative SNPs discovered by RAD-seq were validated by Fluidigm SNP-type chip technology. 9,216 data points 96 SNPs 96 DNAs Unknown germplasm CIAT’s germplasm 48 SNPs 48 DNAs 2,304 data points HOM HET HOM
    • Global Cassava Diversity: Metabolomics Enhancing Cassava productivity through more targeted use of global genetic diversity Next-generation sequencing Metabolomic profiling Materials for Metabolomic profiling Genotype 1 BRA488 2 DOM2 3 COL2017 4 PAR36 5 MPER183 6 MCOL2436 7 MECU72 8 MCUB74 9 CUB23 10 PAN139 11 TMS604444 12 TME3 13 TMS305555 14 BRA1A 15 MCOL1505 16 MCOL1522 17 GUA35 18 CUB25 19 MVEN25 20 MCOL22 21 MGUA85 22 MVEN77 23 MCOL113 24 MCOL638 25 MCOL1684 Trait Clones High Cianide Content 6 High Dry Matter Content 6 High Sugar Content 6 High Amilose Content 6 High PPD Tolerance/Frog Skin disease/Low Carotene 6 High Carotene/Trips Susceptible 6 WF Resistance/Bacteriosis Susceptible 6 High Culinary Quality/Z06 adaptation 6 Waxi Potential 6 Trips Resistance 6 Transformacion 6 CMD 6 CMD 6 High carotene 6 Z01 nd Z04 adaptation 6 Z05 adaptation 6 Low Sugar Content 6 Low Amilose Content 6 Low Culinary Quality 6 PPD susceptible 6 Adaptation Z02 6 Drought tolerance 6 Adaptation Z06 6 Bacteriosis resistance 6 Z03 adaptation 6 150
    • Global RTB Diversity for breeding APPS Enhancing RTB productivity through more targeted use of global genetic diversity Next-generation sequencing Metabolomic profiling Why Metabolomics • It has been determined that there are approximately 31,000 genes in cassava, 37,000 in banana, and 39,000 in potato. For sweetpotato and yams is still unknown. • However how these gene interact with each or in other words how are they connected in networks is UNKNOWN. • The big challenge is: TO MEASURE HOW these genes interact in networks – METABOLOMICS is the best approach.
    • Global RTB Diversity for breeding APPS Enhancing RTB productivity through more targeted use of global genetic diversity Next-generation sequencing Metabolomic profiling Why Metabolomics • Genome-scale metabolic networks provide a comprehensive structural framework for qualitative and quantitative measure of genotype-phenotype relationships.
    • Breeding Applications: Statistical “omics” Enhancing RTB productivity through more targeted use of global genetic diversity Next-generation sequencing Non-target Profiling Making sense of the data Metabolomic profiling http://www.sciencedirect.com/science/article/pii/S0375960106006530#gr003
    • Breeding Applications: Statistical “omics” Enhancing RTB productivity through more targeted use of global genetic diversity Analytical Challenge Next-generation sequencing Metabolomic profiling System Biology Analysis for Breeding Regulome Regulomics http://www.genengnews.com/Media/images/Article/UnivVA_MetabolicNetwork7514635831.jpg
    • Breeding Applications: Statistical “omics” Enhancing RTB productivity through more targeted use of global genetic diversity Future of Genetic Gain?? Next-generation sequencing Regulome Metabolomic profiling http://www.embl.de/research/units/scb/patil/
    • Breeding Applications: Statistical “omics” Enhancing RTB productivity through more targeted use of global genetic diversity Future of Genetic Gain?? Next-generation sequencing Regulome Metabolomic profiling pVA carotenoid biosynthetic pathways http://www.embl.de/research/units/scb/patil/
    • Breeding Applications: Statistical “omics” Enhancing RTB productivity through more targeted use of global genetic diversity Next-generation sequencing Metabolomic profiling Metabolite clusters-traits Hoekenga Lab Pipeline: LC/MS Fingerprinting
    • Metabolomics: Team Enhancing RTB productivity through more targeted use of global genetic diversity Next-generation sequencing Post-Doctoral fellow and PhD candidate appointed Metabolomic profiling Elisabete Barros-Carvalho (PhD) Paul Fraser (PhD) Elliot Price (PhD candidate)
    • RTB Transformational Breeding Positioning CIAT as a Leader in RTB breeding in 2nd CRP Phase MWAS DNA RNA Genome Transcriptome eQTL Genotype Proteins Metabolites Phenotype Proteome Metabolome Phenome pQTL Molecular mQTL - mGWAS Trait QTL - GWAS & GS networks Phenotype System Biology Analysis for Breeding with high genetic gains
    • RTB Transformational Breeding Platform Positioning CIAT as a Leader in RTB breeding in 2nd CRP Phase Rich a consensus on GENETIC GAIN in RTBs RTB genetic gains means: On the one hand, increasing the frequency of favorable alleles and opposing their losses through drift. On the other, reducing the frequency of deleterious alleles, which can result in an excess of genetic load
    • Acknowledgment
    • AD1 – 800BC AD1 – 800BC THANK YOU AD800- 1000 AD630