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“IITA - the appliance of science”
       Harnessing interdisciplinary approaches for
                germplasm development




Sarah Hearne
                   International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
The bottom line
Development of varieties that are:

High yield potential
High yielding under farmer
conditions
Pest and disease resistant
Resistant to abiotic stress
Effective use of nutrients
Market preferred characteristics
Nutritious
Desired duration




                        International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Physiology
Pathology
Weed science
                   Breeding
Entomology
                  Agronomy
Nematology
                          IPM
Biotechnology
Biometrics
Bioinformatics


                 International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Tools to                 Phenotyping
accelerate /              Methodologies
better target /           Benchmark sites
improve
efficiency of            Molecular tools -markers
germplasm
improvement              Statistical methodologies

                         Breeding and selection
                         methodologies

                         Data management, analysis and
                         decision support tools

                  International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
How these tools        Rapid targeted selection of segregants
                        Molecular breeding
support
                        Rapid integrated data analysis
breeders?
                       Selection of parents
                        Heterotic grouping
                        Diversity assessment – allelic / general
                        Predictive breeding
                       Variety production and seed systems
                        DUS (distinct, uniform, stable)& VCU (value for cultivation and use)
                        Seed purity
                        Impact assessment
                       Stress interactions / host-pest interactions
                        Target breeding for specific stress
                        complexes / pest genotypes

                  International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Three years-           Maize molecular breeding
outputs and                   projects, methodologies
outcomes                      applications

Maize                  Maize genetic diversity
Cowpea                        global diversity
Cassava                Striga
Musa
                                         distribution, diversity
Striga
                                         pathogenicity

                       Resource development and use
Some highlights
                              cowpea, cassava and musa


                       Plans for the future

                  International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
DTMA




  Interdisciplinary team with many talents working
  across centers!
                  International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
DTMA   Multiple interconnected themes within the initiative

       Genomics
       Breeding
       Seed systems
       Impact assessment

       Drought
       Polygenic with high degree of epistasis

       GxE issues

       Phenotyping complexity – precision issues

       Can’t apply markers across populations for MAS
         International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Phenotyping   Increase throughput
              Enhance precision

              Benchmark sites with precision irrigation
              -Nigeria, Kenya, Zimbabwe, Zambia, Mexico




              International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Phenotyping                    Biomass/ senescence
                               Spectroradiometry – NDVI – rapid biomass
                               assessment
New tools
implemented

Collaboration with
breeders and
physiologists                  Transpiration
                                                               Leaf / canopy temperature
                               Water use
                               efficiency /                       NIRS & ash content
                               effectiveness


                     International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Molecular        DTMA- largest public sector molecular breeding
                 project for maize in the world
breeding
                 Monitor and coordinate phenotyping, genotyping,
                 data analysis and breeding turnaround across
                 projects

                 Work with physiologists on phenotyping methods
                 and site characterization

                 Work with molecular team on genotyping
                 technologies and bottlenecks

                 Work with biometricians on issues of pop size
                 and marker number and on simulations of new
                 approaches using real data

                 Work with bioinformaticians on issues of data
                 handling and processing
            International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Molecular        What strategy to use for molecular
                 breeding?
breeding
                 What markers to use?

                 How to do the genotyping?

                 What traits to look at using markers?:
                       Make adapted materials more
                       drought tolerant
                       Make drought tolerant materials
                       more disease tolerant




            International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Molecular        What strategy to use for molecular
                 breeding?
breeding
                    Classic QTL
                    ABQTL
                    MARS
                    GWS

                 What markers to use?
                   For breeding - SNP

                 How to do the genotyping?

                 What traits to look at using markers?:
                       Both drought and disease
                       -list of diseases and populations

            International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Molecular        Molecular breeding training course 2008
breeding         DTMA scientists
                 NARS and private sector partners
                 Side meetings
                 Breeding strategy?
                 Evaluated our own QTL data and looked at
                 necessary population sizes and marker
                 numbers – NO classic QTL

                 Private sector present advising
                 ABQTL and MARS breeding strategies
                 Defined a template for population planning
                 and molecular breeding implementation
                 Worked with breeders to define possible
                 populations – 35 potentials
            International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Marker assisted recurrent selection: MARS
                          -new lines
   Select                                                                    Genotype populations
   parents                                                                 Using 200-300 polymorphic
                 Make                                                             SNP markers
               populations
                                  Phenotype test cross
                                      populations
                                     in 3 or more
    Genotype parents               multilocation trials                                Find marker trait
Using ~1500 SNP markers                                                                associations for
                                                                                       drought tolerance




 Recombine the best materials
 using marker data to stack or                      Isolate new lines                                Use lines to
  pyramid favorable markers                          and phenotype                                   create new
    for two or more cycles                            under drought                                drought tolerant
       (no phenotyping)                                                                                varieties
Seed based DNA extraction
                        International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Y1
Molecular
breeding

Power of MARS                                                                                                           Y2


                                                                  Sel C0

                                                              Breeder lines
                                                                                                                        Y3
                                                                      MARS C2S1 lines
                                                          mid p
            If you have 20 regions under selection, freq of optimum
            genotype goes from 1 per trillion in cycle 0 to 1 in 5 in
            cycle 3

                    International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Marker assisted recurrent selection: MARS
                          -new lines
   Select                                                                    Genotype populations
   parents                                                                 Using 200-300 polymorphic
                 Make                                                             SNP markers
               populations
                                  Phenotype test cross
                                      populations
                                     in 3 or more
    Genotype parents               multilocation trials                                Find marker trait
Using ~1500 SNP markers                                                                associations for
                                                                                       drought tolerance




 Recombine the best materials
 using marker data to stack or                      Isolate new lines                                Use lines to
  pyramid favorable markers                          and phenotype                                   create new
    for two or more cycles                            under drought                                drought tolerant
       (no phenotyping)                                                                                varieties
Seed based DNA extraction
                        International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Molecular        Annual meeting 2008
breeding         Scheduling of phenotyping and genotyping
                 and cost of genotyping

                 Some seasons ~6500 individuals to
                 genotype

                 3 weeks to extract DNA and genotype

                 Genotyping option
                 Illumina golden gate – 1536 SNP markers




            International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Illumina golden gate – 1536 SNP markers

Molecular
breeding




            International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Molecular        Workshop Feb 2009
breeding         SNPlex no longer an option

                 BeadXpress

                 Illumina system 384 markers
                 Single plex assays – KBiosciences

                 DTMA – buy BeadXpress
                 Analysis of throughput and cost
                 Discussion with private sector
                 Visit to KBioscience

                 Presented data at 2009 DTMA annual
                 meeting in Zim - use KBiosciences
            International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Molecular        DTMA – 20 molecular breeding projects. 18
                 MARS/GWS (explained in next slide), 2 ABQTL (line
breeding         conversion) – WA had 5 MARS/GWS populations

                 Two genotyping platforms-

                 Illumina golden gate-
                      One diverse 1536 illumina OPA, 1330 good
                      SNP

                 KASPar – single plex primer extension based
                 assays designed for 1111 SNP

                 Will be using new 60k infinium assay in 2010

                 Genotyping by sequencing under evaluation



            International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Building on MARS        Some of the hit list:-
populations

We have high            MSV
breeding value
segregating             Striga hermonthica
populations
We have                 GLS
genotype data
                        Nematodes
What other high
value traits we
can phenotype
for…
                   International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Molecular          Tolerance to MSV
breeding
                   Breeder, Virologist, Biometrician
                   and Mol Geneticist
                   Abebe + – populations, field phenotyping
                   Lava – Screenhouse phenotyping and indexing,
                   field phenotyping
                   Sarah – Candidate marker identification,
                   population genotyping, tracking, data curation
                   Guy – Data handling and manipulation
                   Sarah and Jose – Data analysis and marker
                   identification
                   Contribute knowledge and markers for simple
                   traits to incorporate into breeding work


            International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Molecular          Resistance and tolerance to Striga
breeding
                   Breeders, Physiologist, Biometrician
                   and Mol Geneticist
                   Abebe and Baffour – populations, field
                   phenotyping
                   Sarah – Screenhouse phenotyping
                   Sarah – Candidate marker identification,
                   population genotyping, tracking, data
                   curation
                   Sarah and Jose – Data analysis and
                   marker identification
                   Contribute knowledge and markers for
                   identified traits to incorporate into breeding
                   work
            International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
GLS        Field phenotyping issues - Reliability

           Not a simple trait – or a single species (Lava)

           Development of improved phenotyping
           e.g. HTP detached leaf assay for GLS
           evaluations with pathologist - Ranajit

           Enable controlled infestation with different
           genotypes of pathogen (pathotypes / species
           with agroecological niches)




      International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
CML 488 maize inbred line
Nematodes

Pratylenchus
Meloidogyne                     Black
                                Lesions
                                 Reduced root
                                 mass

                             “Root galling”




     Un-infected                                                          Meloidogyne infested

                     International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Nematodes                Nematode and drought interaction

                         Breeders, Nematologist, Physiologist,
Interaction              Biometrician and Mol Geneticist
between drought          Abebe and Baffour – lines – parents of MARS
and nematode –           populations
flowering date           Danny – Screenhouse phenotyping-
and ASI                  nematodes
                         Sarah – Screenhouse phenotyping-
                         drought
                         Sarah and Jorge – Data analysis


                         Contribute knowledge and markers for
                         identified traits to incorporate into breeding
                         work
                  International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
What other             Selection of parents
applications to         Heterotic grouping
support                 Diversity assessment – allelic / general
                        Predictive breeding
breeders?
                       Genotyping of potential parents
                       Variety production and seed systems
                        DUS (distinct, uniform, stable)& VCU (value for cultivation and use)
                        Seed purity
                        Impact assessment
                       Testing the quality of outgrower produced
                       hybrid seed in Zimbabwe

                       Genotyping IITA released maize lines
                       using 60k SNP chip to facilitate tracking of
                       IITA germplasm for impact assessment
                  International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Numbers,           Molecular breeding is a balancing
numbers            act
everywhere…




                                                                $
                   How do we balance competing
                   demands for funds and optimize
                   genetic gain?
              International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
A                                          MD= 5 cM            B                                                MD= 5 cM
                                                                                                    0.70                                                                     0.50
                                                                                                                                                                                                           PVE=1%




                                                                                                                                        Standard error of estimated effect
                                                                                                    0.65                                                                     0.45                          PVE=2%
                                                                                                    0.60




                                                                         Estimated genetic effect
                                                                                                                                                                             0.40                          PVE=3%
                                                                                                    0.55
                                                                                                    0.50                                                                     0.35                          PVE=4%
                                                                                                    0.45                                                                     0.30                          PVE=5%
                                                                                                    0.40                                                                     0.25                          PVE=10%
                                                                                                    0.35                                                                     0.20                          PVE=20%
                                                                                                    0.30                                                                     0.15                          PVE=30%
                                                                                                    0.25

    Analysis of pop                                                                                 0.20
                                                                                                    0.15
                                                                                                    0.10
                                                                                                                                                                             0.10
                                                                                                                                                                             0.05
                                                                                                                                                                             0.00

    size and marker




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                                                                                                                    Population size                                                     Population size
                                                                         C                                          MD= 10 cM           D                                               MD= 10 cM
                                                                                                    0.70                                                                     0.50

    density on QTL                                                                                                                                                                                         PVE=1%




                                                                                                                                        Standard error of estimated effect
                                                                                                    0.65                                                                     0.45                          PVE=2%
                                                                                                    0.60




                                                                         Estimated genetic effect
                                                                                                                                                                             0.40                          PVE=3%
                                                                                                    0.55
                                                                                                                                                                             0.35                          PVE=4%
    detection                                                                                       0.50
                                                                                                    0.45
                                                                                                    0.40
                                                                                                                                                                             0.30
                                                                                                                                                                             0.25
                                                                                                                                                                                                           PVE=5%
                                                                                                                                                                                                           PVE=10%
                                                                                                    0.35                                                                     0.20                          PVE=20%
                                                                                                    0.30                                                                     0.15                          PVE=30%
                                                                                                    0.25
                                                                                                    0.20                                                                     0.10
                                                                                                    0.15                                                                     0.05
                                                                                                    0.10                                                                     0.00




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                                                                                                                    Population size                                                     Population size
               100                                                       E                                                              F
                                                                                                    0.70            MD= 20 cM                                                0.50       MD= 20 cM
                90                                                                                                                                                                                         PVE=1%




                                                                                                                                        Standard error of estimated effect
                                                                                                    0.65                                                                     0.45                         MD=5 cM
                                                                                                                                                                                                           PVE=2%
                                                                                                    0.60
                80

                                                                         Estimated genetic effect
                                                                                                                                                                             0.40                          PVE=3%
                                                                                                    0.55
                                                                                                                                                                             0.35                          PVE=4%
                70                                                                                  0.50
   Power (%)




                                                                                                    0.45                                                                     0.30                          PVE=5%
                60                                                                                  0.40                                                                     0.25                         MD=10 cM
                                                                                                                                                                                                           PVE=10%
                                                                                                    0.35                                                                     0.20                          PVE=20%
                50                                                                                  0.30                                                                     0.15                          PVE=30%
                                                                                                    0.25
                40                                                                                  0.20                                                                     0.10
                                                                                                                                                                                                          MD=20 cM
                                                                                                    0.15                                                                     0.05
                30                                                                                  0.10                                                                     0.00
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                10
                                                                                                                    Population size                                                     Population size   MD=40 cM
                                                                         G                                          MD= 40 cM           H                                               MD= 40 cM
                                                                                                    0.70                                                                     0.50
                 0                                                                                                                                                                                         PVE=1%




                     Standard error of estimated effect
                                                                                                    0.65                                                                     0.45                          PVE=2%
                                                                                                    0.60
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                         Estimated genetic effect




                                                                                                                                                                             0.40                          PVE=3%
                                                                                                    0.55
                                                                                                    0.50                                                                     0.35                          PVE=4%
                                                                                                    0.45                                                                     0.30                          PVE=5%
                     PVE=1%     PVE=2%          PVE=3%          PVE=4%                              0.40   PVE=5%         PVE=10%     PVE=20%                                0.25   PVE=30%                PVE=10%
                                                                                                    0.35                                                                                                   PVE=20%
                                                                                                    Population size
                                                                                                    0.30
                                                                                                                                                                             0.20
                                                                                                                                                                             0.15                          PVE=30%
                                                                                                    0.25
                                                                                                    0.20                                                                     0.10
                                                                                                    0.15                                                                     0.05
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                                                      Zhonglai Li, Institute of Wang, Agriculture – Institut international d’agriculture tropicale – www.iita.org
                                                                                        Population size                                Population size
Huihui Li, Sarah Hearne, Yunbi Xu, Marianne Bänziger,International & JiankangTropicalHeredity in press
MAS versus        MAS
GWS                Only track significant markers
                  GWS
                   All markers have value

                  Which is optimal?
                  How many cycles of selection?
                  Best estimate?
                      BLUE (GxE), BLUP (no GxE but
                      marker by marker)
                  Selection index?




             International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
MAS versus                                                               Simulations
     GWS                                              Fig.1 1a
                                                       Fig.


                                                                        360    YB 400MM BLUE   YB 40MM BLUE                              30
                                                                               YA 400MM BLUE    YB 400MM BLUP
                                                                               YB 40MM BLUP    YA 400MM BLUP




                                                                                                                                                EPP (number)
                                                                        355                                                              25


                                                                                     P
                                                                        350        EP                                                    20
                                                  GY (grams per plot)




                                                                        345                                                              15



                                                                        340                                                              10

                                                                                     Y
                                                                                    G
                                                                        335                                                              5




                                                                                                                                              ASI (days)
                                                                                    ASI
                                                                        330                                                              0



                                                                        325                                                              -5
                                                                               0          1    2          3        4    5        6
                                                                                                   Cycle of selection



Cerón-Rojas, J. J., Crossa, J., Alvarado, G., Burgueño, International Institute of Tropical Agriculture – S. J. & Davenport, G., F., Sub Crop Sci – www.iita.org
                                                         J., Wang, J., Atlin, G., Bänziger, M., Hearne, Institut international d’agriculture tropicale
MAS versus                                                                        GWS better than MAS in all situations
                      GWS                                                                               400 markers better than 40

                                                                                                        BLUP better than BLUE when looking at
    Fig.1 1a
     Fig.
                                                                                                        well watered environments
                      360   YB 400MM BLUE   YB 40MM BLUE                     30
                            YA 400MM BLUE    YB 400MM BLUP
                            YB 40MM BLUP    YA 400MM BLUP
                                                                                    EPP (number)




                      355                                                    25



                      350       EP
                                  P
                                                                             20
                                                                                                        BLUE better than BLUP when looking at
                                                                                                        drought stressed environments
GY (grams per plot)




                      345                                                    15



                      340                                                    10

                                  Y
                                 G
                      335                                                    5
                                                                                  ASI (days)




                                 ASI
                      330



                      325
                                                                             0



                                                                             -5
                                                                                                        Genetic gain for grain yield up to cycle six
                            0          1    2          3        4    5   6
                                                Cycle of selection




                                                                                                   International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Three years-           Maize molecular breeding
outputs and                   projects, methodologies
outcomes                      applications

Maize                  Maize genetic diversity
Cowpea                        global diversity
Cassava                Striga
Musa
                                         distribution, diversity
Striga
                                         pathogenicity

                       Resource development and use
Some highlights
                              cowpea, cassava and musa


                       Plans for the future

                  International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Maize diversity        Maize from Americas, Africa, Asia, Europe
                       and teosintes
                       Group of collaborators from ten different
                       institutes
                       Population geneticists, breeders, genebank
                       Curators, molecular geneticists, GIS
                       specialists
                       How has maize migrated across the
                       globe?

                       What is the pattern of global diversity?




                  International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Maize diversity        Maize from Americas, Africa, Asia, Europe
                       and teosintes
                       Group of collaborators from ten different
                       institutes
                       Population geneticists, breeders, genebank
                       Curators, molecular geneticists, GIS
                       specialists
                       How has maize migrated across the
                       globe?

                       What is the pattern of global diversity?




                  International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Maize diversity        Globally landraces are in general tropical
                       in origin

                        Twelve main landrace clusters exist in the
                        world




Africa




                  International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Maize diversity        Western Sub-Saharan Africa -tropical
                       maize
                       Diversity data strongly supports hypothesis
                       of introduction via Portuguese slave
                       West Africa very distinct - Sao Tome and
                       Cape Verde – groups originating from both
                       can be defined:- rapid differentiation of
                       original gene pools- environment and
                       human uses
Africa
                       East Africa – data suggests direct diffusion
                       of US maize after World War II – potential
                       replacement of tropical landraces



                  International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Mir, C., Warburton, M.L., Taba, S., Bedoya, C., Franco, J.,Zhang, S., Xie, C., Prasanna, B.M., Hearne, S., Muthamia, Z., Yunus, M., Cuong,
B.M., and Charcosse. In Prep

                                             International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Three years-           Maize molecular breeding
outputs and                   projects, methodologies
outcomes                      applications

Maize                  Maize genetic diversity
Cowpea                        global diversity
Cassava                Striga
Musa
                                         distribution, diversity
Striga
                                         pathogenicity

                       Resource development and use
Some highlights
                              cowpea, cassava and musa


                       Plans for the future

                  International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Striga               Striga is one of the most significant biotic
                     constraints to maize production in SSA
-from the parasite   Striga sp., while often lumped together have
perspective          distinct and different breeding systems. S.
                     asiatica is inbreeding species while S.
                     hermonthica is self incompatible and is highly
                     outbreeding in nature.
                     These differences have implications on diversity
                     within and between parasite populations per se
                     and also has implications control technology
                     efficacy from region to region – be that host
                     resistance and tolerance to parasite or herbicide
                     tolerant germplasm.

                                                                                       Hearne, Pest Mgmt Sci, 65, 2009
                     International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Striga               Surveying Striga endemic areas in Nigeria, DRC
                     and Kenya. In 2011 survey Tanzania.
-from the parasite
perspective          Taking basic farmer perception data and
                     collecting Striga leaf and seed samples from
                     individuals and populations to assess parasite
                     diversity.

                     Using location data to prepare and atlas of Striga
                     distribution working with GIS




                     International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Striga               Pilot project completed assessing diversity of S.
                     hermonthica in Kenya using SSR markers
-from the parasite
perspective          Within population variation contributed to some
                     95.89% of the total variance with only 4.11%
                     being due to among populations. High even for
                     an allogamous species.

                     The total heterozygosity observed across all
                     markers and populations was very high at
                     0.72054, within population heterozygosities
                     ranged from 0.4829 to 0.73988.



                     International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Striga               The level of heterozygosity may reflect the
                     obligate out-breeding nature of the species and
                     the level of population diversity needed to ensure
-from the parasite   fitness
perspective
                     Marker availability for Striga is limited – 8
                     informative SSR markers
                     Link with evolutionary biologist, Claude de
                     Pamphilis at Penn State on NSF initiative to
                     sequence parasitic plant ESTs
                     Striga tissue collected from diverse sources in
                     Nigeria and sent to US for RNA isolation and
                     sequencing using 454 Titanium sequencing



                     International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Striga               Assemblies being constructed – mine for SNP
                     and polymorphic SSR to conduct further studies

-from the parasite   Claude using data to complete the Striga
                     chloroplast genome and construct a mitochondrial
perspective          genome – understand evolution of parasitism
                     across parasitic plants – Striga, Alectra,
                     Orobanche

                     Use new markers to evaluate within and between
                     population S. hermonthica diversity. SSR in
                     Ibadan and SNP at Kbiosciences.

                     Data analysis, Sarah, Jorge and GIS




                     International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Striga   Pathogenicity work – implication of
         diversity?

         First need a system for maintaining the discrete
         Striga populations collected in the field

         Working with Mike Timko, U . Virginia to look at
         methodologies for inter population mating to
         maintain population diversity. Working on
         Nigerian isolates of Striga

         NSF proposal to sequence Striga genome – great
         resource to start to understand parasitism and
         pathogenicity at the genomic level




         International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Striga-host    Field screening $, uses only one or two populations of
               Striga and does not provide an understanding of the
interactions   mechanisms of tolerance / resistance seen

               Implemented medium and high throughput lab and
               screenhouse based phenotyping protocols to assess
               the Striga-host interaction at biochemical, physiological
               and morphological levels.

               Assess resistance at germination, haustorial initiation,
               attachment and post attachment stages

               Enable improved selection of favorable recombinants
               and facilitate studies of gene action
               Integrate these assays with current molecular breeding
               work to identify molecular markers for key traits of
               interest

               International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Three years-           Maize molecular breeding
outputs and                   projects, methodologies
outcomes                      applications

Maize                  Maize genetic diversity
Cowpea                        global diversity
Cassava                Striga
Musa
                                         distribution, diversity
Striga
                                         pathogenicity

                       Resource development and use
Some highlights
                              cowpea, cassava and musa


                       Plans for the future

                  International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Marker           Program of EST sequencing projects – cowpea,
                 cassava and musa
development
                 Generated:-
                 Cowpea-
JCVI, ILRI, UC   41949 sequences
Riverside        3367 putative SNP
                 1805 putative SSR, 916 di- and trinucleotide repeats

                 Cassava
                 5046 sequences (41173)
                 2699 putative SSR
                 2486 putative SNP

                 Musa
                 5494 sequences (52907)
                 1937 putative SSR
                 28815 putative SNP

                 International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Marker development                    HarvEST cowpea database - 17 libraries -
                                         Two IITA libraries, 12 UCR libraries.
Consolidation and
utilization of EST                    HarvEST cassava database - 17 libraries -
                                         Two IITA libraries, 12 UCR libraries.

                                      HarvEST musa database - 17 libraries - Two
                                         IITA libraries, 12 UCR libraries.




                                               http://harvest.ucr.edu/

                     International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Marker                    Developed Illumina Goldengate SNP assay
                                IITA Reference collection, breeders lines, bi-
development and                 parental populations
use                             IITA reference collection encompassed genetic
                                diversity assessed using SNP
Cowpea                          Ref set and additional germplasm extensively
                                phenotyped – tool for allele mining


                          Development of consensus genetic map of
                          cowpea, and synteny with soybean and Medicago
                                Provides genomic framework for identification of
                                marker trait association, map-based cloning,
                                selection of markers for assessment of genetic
                                diversity, association mapping


            Muchero, W., Diop, N., Bhat, P., Fenton, R., Pottorff, M., Hearne, S., Ndiaga, C., Fatokun, C., Ehlers, J.,
            Roberts, P., Close,T. 2009. PNAS
                          International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Marker               410 EST derived SSR - Xu et al 2009, Molecular
                     breeding
development
                     Mike Timko’s group compared EST with GSS
Consolidation and    data
utilization of EST           Determine the gene discovery rate Timko et al
                             2008 BMC Genomics
                             Predict open reading frames for the genes (oligos)
                             used to create a cowpea microarray – 385k.
                             Microarray used to study cowpea-Striga
                             interaction- Li et al 2009 Pest Mgmt Sci




                     International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Three years-           Maize molecular breeding
outputs and                   projects, methodologies
outcomes                      applications

Maize                  Maize genetic diversity
Cowpea                        global diversity
Cassava                Striga
Musa
                                         distribution, diversity
Striga
                                         pathogenicity

                       Resource development and use
Some highlights
                              cowpea, cassava and musa


                       Plans for the future

                  International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Building on good         Breeding
foundations
                                                          Musa                  Yam
      Genome sequence
      ESTs                                                                             Cassava
                                                 TLI                  TLII

                                  DTMA                DTMA                 DTMA                 DTMA



                         Adapt and apply know how to achieve
                         rapid advances in other IITA crops




                    International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
Be brave and        In farmers fields plant are subject to
look at             multiple stresses
complexity          Start looking at the basis of stress
                    tolerance resistance. Then look at
                    complexes of commonly occurring
                    stresses




               International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
We have a bright future




Thank you
                    International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org

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Harnessing interdisciplinary approaches for germplasm development

  • 1. “IITA - the appliance of science” Harnessing interdisciplinary approaches for germplasm development Sarah Hearne International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 2. The bottom line Development of varieties that are: High yield potential High yielding under farmer conditions Pest and disease resistant Resistant to abiotic stress Effective use of nutrients Market preferred characteristics Nutritious Desired duration International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 3. Physiology Pathology Weed science Breeding Entomology Agronomy Nematology IPM Biotechnology Biometrics Bioinformatics International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 4. Tools to Phenotyping accelerate / Methodologies better target / Benchmark sites improve efficiency of Molecular tools -markers germplasm improvement Statistical methodologies Breeding and selection methodologies Data management, analysis and decision support tools International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 5. How these tools Rapid targeted selection of segregants Molecular breeding support Rapid integrated data analysis breeders? Selection of parents Heterotic grouping Diversity assessment – allelic / general Predictive breeding Variety production and seed systems DUS (distinct, uniform, stable)& VCU (value for cultivation and use) Seed purity Impact assessment Stress interactions / host-pest interactions Target breeding for specific stress complexes / pest genotypes International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 6. Three years- Maize molecular breeding outputs and projects, methodologies outcomes applications Maize Maize genetic diversity Cowpea global diversity Cassava Striga Musa distribution, diversity Striga pathogenicity Resource development and use Some highlights cowpea, cassava and musa Plans for the future International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 7. DTMA Interdisciplinary team with many talents working across centers! International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 8. DTMA Multiple interconnected themes within the initiative Genomics Breeding Seed systems Impact assessment Drought Polygenic with high degree of epistasis GxE issues Phenotyping complexity – precision issues Can’t apply markers across populations for MAS International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 9. Phenotyping Increase throughput Enhance precision Benchmark sites with precision irrigation -Nigeria, Kenya, Zimbabwe, Zambia, Mexico International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 10. Phenotyping Biomass/ senescence Spectroradiometry – NDVI – rapid biomass assessment New tools implemented Collaboration with breeders and physiologists Transpiration Leaf / canopy temperature Water use efficiency / NIRS & ash content effectiveness International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 11. Molecular DTMA- largest public sector molecular breeding project for maize in the world breeding Monitor and coordinate phenotyping, genotyping, data analysis and breeding turnaround across projects Work with physiologists on phenotyping methods and site characterization Work with molecular team on genotyping technologies and bottlenecks Work with biometricians on issues of pop size and marker number and on simulations of new approaches using real data Work with bioinformaticians on issues of data handling and processing International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 12. Molecular What strategy to use for molecular breeding? breeding What markers to use? How to do the genotyping? What traits to look at using markers?: Make adapted materials more drought tolerant Make drought tolerant materials more disease tolerant International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 13. Molecular What strategy to use for molecular breeding? breeding Classic QTL ABQTL MARS GWS What markers to use? For breeding - SNP How to do the genotyping? What traits to look at using markers?: Both drought and disease -list of diseases and populations International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 14. Molecular Molecular breeding training course 2008 breeding DTMA scientists NARS and private sector partners Side meetings Breeding strategy? Evaluated our own QTL data and looked at necessary population sizes and marker numbers – NO classic QTL Private sector present advising ABQTL and MARS breeding strategies Defined a template for population planning and molecular breeding implementation Worked with breeders to define possible populations – 35 potentials International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 15. Marker assisted recurrent selection: MARS -new lines Select Genotype populations parents Using 200-300 polymorphic Make SNP markers populations Phenotype test cross populations in 3 or more Genotype parents multilocation trials Find marker trait Using ~1500 SNP markers associations for drought tolerance Recombine the best materials using marker data to stack or Isolate new lines Use lines to pyramid favorable markers and phenotype create new for two or more cycles under drought drought tolerant (no phenotyping) varieties Seed based DNA extraction International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 16. Y1 Molecular breeding Power of MARS Y2 Sel C0 Breeder lines Y3 MARS C2S1 lines mid p If you have 20 regions under selection, freq of optimum genotype goes from 1 per trillion in cycle 0 to 1 in 5 in cycle 3 International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 17. Marker assisted recurrent selection: MARS -new lines Select Genotype populations parents Using 200-300 polymorphic Make SNP markers populations Phenotype test cross populations in 3 or more Genotype parents multilocation trials Find marker trait Using ~1500 SNP markers associations for drought tolerance Recombine the best materials using marker data to stack or Isolate new lines Use lines to pyramid favorable markers and phenotype create new for two or more cycles under drought drought tolerant (no phenotyping) varieties Seed based DNA extraction International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 18. Molecular Annual meeting 2008 breeding Scheduling of phenotyping and genotyping and cost of genotyping Some seasons ~6500 individuals to genotype 3 weeks to extract DNA and genotype Genotyping option Illumina golden gate – 1536 SNP markers International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 19. Illumina golden gate – 1536 SNP markers Molecular breeding International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 20. Molecular Workshop Feb 2009 breeding SNPlex no longer an option BeadXpress Illumina system 384 markers Single plex assays – KBiosciences DTMA – buy BeadXpress Analysis of throughput and cost Discussion with private sector Visit to KBioscience Presented data at 2009 DTMA annual meeting in Zim - use KBiosciences International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 21. Molecular DTMA – 20 molecular breeding projects. 18 MARS/GWS (explained in next slide), 2 ABQTL (line breeding conversion) – WA had 5 MARS/GWS populations Two genotyping platforms- Illumina golden gate- One diverse 1536 illumina OPA, 1330 good SNP KASPar – single plex primer extension based assays designed for 1111 SNP Will be using new 60k infinium assay in 2010 Genotyping by sequencing under evaluation International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 22. Building on MARS Some of the hit list:- populations We have high MSV breeding value segregating Striga hermonthica populations We have GLS genotype data Nematodes What other high value traits we can phenotype for… International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 23. Molecular Tolerance to MSV breeding Breeder, Virologist, Biometrician and Mol Geneticist Abebe + – populations, field phenotyping Lava – Screenhouse phenotyping and indexing, field phenotyping Sarah – Candidate marker identification, population genotyping, tracking, data curation Guy – Data handling and manipulation Sarah and Jose – Data analysis and marker identification Contribute knowledge and markers for simple traits to incorporate into breeding work International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 24. Molecular Resistance and tolerance to Striga breeding Breeders, Physiologist, Biometrician and Mol Geneticist Abebe and Baffour – populations, field phenotyping Sarah – Screenhouse phenotyping Sarah – Candidate marker identification, population genotyping, tracking, data curation Sarah and Jose – Data analysis and marker identification Contribute knowledge and markers for identified traits to incorporate into breeding work International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 25. GLS Field phenotyping issues - Reliability Not a simple trait – or a single species (Lava) Development of improved phenotyping e.g. HTP detached leaf assay for GLS evaluations with pathologist - Ranajit Enable controlled infestation with different genotypes of pathogen (pathotypes / species with agroecological niches) International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 26. CML 488 maize inbred line Nematodes Pratylenchus Meloidogyne Black Lesions Reduced root mass “Root galling” Un-infected Meloidogyne infested International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 27. Nematodes Nematode and drought interaction Breeders, Nematologist, Physiologist, Interaction Biometrician and Mol Geneticist between drought Abebe and Baffour – lines – parents of MARS and nematode – populations flowering date Danny – Screenhouse phenotyping- and ASI nematodes Sarah – Screenhouse phenotyping- drought Sarah and Jorge – Data analysis Contribute knowledge and markers for identified traits to incorporate into breeding work International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 28. What other Selection of parents applications to Heterotic grouping support Diversity assessment – allelic / general Predictive breeding breeders? Genotyping of potential parents Variety production and seed systems DUS (distinct, uniform, stable)& VCU (value for cultivation and use) Seed purity Impact assessment Testing the quality of outgrower produced hybrid seed in Zimbabwe Genotyping IITA released maize lines using 60k SNP chip to facilitate tracking of IITA germplasm for impact assessment International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 29. Numbers, Molecular breeding is a balancing numbers act everywhere… $ How do we balance competing demands for funds and optimize genetic gain? International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 30. A MD= 5 cM B MD= 5 cM 0.70 0.50 PVE=1% Standard error of estimated effect 0.65 0.45 PVE=2% 0.60 Estimated genetic effect 0.40 PVE=3% 0.55 0.50 0.35 PVE=4% 0.45 0.30 PVE=5% 0.40 0.25 PVE=10% 0.35 0.20 PVE=20% 0.30 0.15 PVE=30% 0.25 Analysis of pop 0.20 0.15 0.10 0.10 0.05 0.00 size and marker 20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 360 380 400 420 440 460 480 500 520 540 560 580 600 20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 360 380 400 420 440 460 480 500 520 540 560 580 600 Population size Population size C MD= 10 cM D MD= 10 cM 0.70 0.50 density on QTL PVE=1% Standard error of estimated effect 0.65 0.45 PVE=2% 0.60 Estimated genetic effect 0.40 PVE=3% 0.55 0.35 PVE=4% detection 0.50 0.45 0.40 0.30 0.25 PVE=5% PVE=10% 0.35 0.20 PVE=20% 0.30 0.15 PVE=30% 0.25 0.20 0.10 0.15 0.05 0.10 0.00 20 40 60 80 20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 360 380 400 420 440 460 480 500 520 540 560 580 600 100 120 140 160 180 200 220 240 260 280 300 320 340 360 380 400 420 440 460 480 500 520 540 560 580 600 Population size Population size 100 E F 0.70 MD= 20 cM 0.50 MD= 20 cM 90 PVE=1% Standard error of estimated effect 0.65 0.45 MD=5 cM PVE=2% 0.60 80 Estimated genetic effect 0.40 PVE=3% 0.55 0.35 PVE=4% 70 0.50 Power (%) 0.45 0.30 PVE=5% 60 0.40 0.25 MD=10 cM PVE=10% 0.35 0.20 PVE=20% 50 0.30 0.15 PVE=30% 0.25 40 0.20 0.10 MD=20 cM 0.15 0.05 30 0.10 0.00 20 20 40 60 80 20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 360 380 400 420 440 460 480 500 520 540 560 580 600 100 120 140 160 180 200 220 240 260 280 300 320 340 360 380 400 420 440 460 480 500 520 540 560 580 600 10 Population size Population size MD=40 cM G MD= 40 cM H MD= 40 cM 0.70 0.50 0 PVE=1% Standard error of estimated effect 0.65 0.45 PVE=2% 0.60 40 40 40 40 40 40 40 40 440 240 440 240 540 140 340 540 140 340 240 440 240 440 140 340 540 140 240 340 540 140 340 540 140 340 440 240 440 240 440 540 140 340 540 140 340 540 240 440 Estimated genetic effect 0.40 PVE=3% 0.55 0.50 0.35 PVE=4% 0.45 0.30 PVE=5% PVE=1% PVE=2% PVE=3% PVE=4% 0.40 PVE=5% PVE=10% PVE=20% 0.25 PVE=30% PVE=10% 0.35 PVE=20% Population size 0.30 0.20 0.15 PVE=30% 0.25 0.20 0.10 0.15 0.05 0.10 0.00 20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 360 380 400 420 440 460 480 500 520 540 560 580 600 20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 360 380 400 420 440 460 480 500 520 540 560 580 600 Zhonglai Li, Institute of Wang, Agriculture – Institut international d’agriculture tropicale – www.iita.org Population size Population size Huihui Li, Sarah Hearne, Yunbi Xu, Marianne Bänziger,International & JiankangTropicalHeredity in press
  • 31. MAS versus MAS GWS Only track significant markers GWS All markers have value Which is optimal? How many cycles of selection? Best estimate? BLUE (GxE), BLUP (no GxE but marker by marker) Selection index? International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 32. MAS versus Simulations GWS Fig.1 1a Fig. 360 YB 400MM BLUE YB 40MM BLUE 30 YA 400MM BLUE YB 400MM BLUP YB 40MM BLUP YA 400MM BLUP EPP (number) 355 25 P 350 EP 20 GY (grams per plot) 345 15 340 10 Y G 335 5 ASI (days) ASI 330 0 325 -5 0 1 2 3 4 5 6 Cycle of selection Cerón-Rojas, J. J., Crossa, J., Alvarado, G., Burgueño, International Institute of Tropical Agriculture – S. J. & Davenport, G., F., Sub Crop Sci – www.iita.org J., Wang, J., Atlin, G., Bänziger, M., Hearne, Institut international d’agriculture tropicale
  • 33. MAS versus GWS better than MAS in all situations GWS 400 markers better than 40 BLUP better than BLUE when looking at Fig.1 1a Fig. well watered environments 360 YB 400MM BLUE YB 40MM BLUE 30 YA 400MM BLUE YB 400MM BLUP YB 40MM BLUP YA 400MM BLUP EPP (number) 355 25 350 EP P 20 BLUE better than BLUP when looking at drought stressed environments GY (grams per plot) 345 15 340 10 Y G 335 5 ASI (days) ASI 330 325 0 -5 Genetic gain for grain yield up to cycle six 0 1 2 3 4 5 6 Cycle of selection International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 34. Three years- Maize molecular breeding outputs and projects, methodologies outcomes applications Maize Maize genetic diversity Cowpea global diversity Cassava Striga Musa distribution, diversity Striga pathogenicity Resource development and use Some highlights cowpea, cassava and musa Plans for the future International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 35. Maize diversity Maize from Americas, Africa, Asia, Europe and teosintes Group of collaborators from ten different institutes Population geneticists, breeders, genebank Curators, molecular geneticists, GIS specialists How has maize migrated across the globe? What is the pattern of global diversity? International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 36. Maize diversity Maize from Americas, Africa, Asia, Europe and teosintes Group of collaborators from ten different institutes Population geneticists, breeders, genebank Curators, molecular geneticists, GIS specialists How has maize migrated across the globe? What is the pattern of global diversity? International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 37. Maize diversity Globally landraces are in general tropical in origin Twelve main landrace clusters exist in the world Africa International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 38. Maize diversity Western Sub-Saharan Africa -tropical maize Diversity data strongly supports hypothesis of introduction via Portuguese slave West Africa very distinct - Sao Tome and Cape Verde – groups originating from both can be defined:- rapid differentiation of original gene pools- environment and human uses Africa East Africa – data suggests direct diffusion of US maize after World War II – potential replacement of tropical landraces International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 39. Mir, C., Warburton, M.L., Taba, S., Bedoya, C., Franco, J.,Zhang, S., Xie, C., Prasanna, B.M., Hearne, S., Muthamia, Z., Yunus, M., Cuong, B.M., and Charcosse. In Prep International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 40. Three years- Maize molecular breeding outputs and projects, methodologies outcomes applications Maize Maize genetic diversity Cowpea global diversity Cassava Striga Musa distribution, diversity Striga pathogenicity Resource development and use Some highlights cowpea, cassava and musa Plans for the future International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 41. Striga Striga is one of the most significant biotic constraints to maize production in SSA -from the parasite Striga sp., while often lumped together have perspective distinct and different breeding systems. S. asiatica is inbreeding species while S. hermonthica is self incompatible and is highly outbreeding in nature. These differences have implications on diversity within and between parasite populations per se and also has implications control technology efficacy from region to region – be that host resistance and tolerance to parasite or herbicide tolerant germplasm. Hearne, Pest Mgmt Sci, 65, 2009 International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 42. Striga Surveying Striga endemic areas in Nigeria, DRC and Kenya. In 2011 survey Tanzania. -from the parasite perspective Taking basic farmer perception data and collecting Striga leaf and seed samples from individuals and populations to assess parasite diversity. Using location data to prepare and atlas of Striga distribution working with GIS International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 43. Striga Pilot project completed assessing diversity of S. hermonthica in Kenya using SSR markers -from the parasite perspective Within population variation contributed to some 95.89% of the total variance with only 4.11% being due to among populations. High even for an allogamous species. The total heterozygosity observed across all markers and populations was very high at 0.72054, within population heterozygosities ranged from 0.4829 to 0.73988. International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 44. Striga The level of heterozygosity may reflect the obligate out-breeding nature of the species and the level of population diversity needed to ensure -from the parasite fitness perspective Marker availability for Striga is limited – 8 informative SSR markers Link with evolutionary biologist, Claude de Pamphilis at Penn State on NSF initiative to sequence parasitic plant ESTs Striga tissue collected from diverse sources in Nigeria and sent to US for RNA isolation and sequencing using 454 Titanium sequencing International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 45. Striga Assemblies being constructed – mine for SNP and polymorphic SSR to conduct further studies -from the parasite Claude using data to complete the Striga chloroplast genome and construct a mitochondrial perspective genome – understand evolution of parasitism across parasitic plants – Striga, Alectra, Orobanche Use new markers to evaluate within and between population S. hermonthica diversity. SSR in Ibadan and SNP at Kbiosciences. Data analysis, Sarah, Jorge and GIS International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 46. Striga Pathogenicity work – implication of diversity? First need a system for maintaining the discrete Striga populations collected in the field Working with Mike Timko, U . Virginia to look at methodologies for inter population mating to maintain population diversity. Working on Nigerian isolates of Striga NSF proposal to sequence Striga genome – great resource to start to understand parasitism and pathogenicity at the genomic level International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 47. Striga-host Field screening $, uses only one or two populations of Striga and does not provide an understanding of the interactions mechanisms of tolerance / resistance seen Implemented medium and high throughput lab and screenhouse based phenotyping protocols to assess the Striga-host interaction at biochemical, physiological and morphological levels. Assess resistance at germination, haustorial initiation, attachment and post attachment stages Enable improved selection of favorable recombinants and facilitate studies of gene action Integrate these assays with current molecular breeding work to identify molecular markers for key traits of interest International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 48. Three years- Maize molecular breeding outputs and projects, methodologies outcomes applications Maize Maize genetic diversity Cowpea global diversity Cassava Striga Musa distribution, diversity Striga pathogenicity Resource development and use Some highlights cowpea, cassava and musa Plans for the future International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 49. Marker Program of EST sequencing projects – cowpea, cassava and musa development Generated:- Cowpea- JCVI, ILRI, UC 41949 sequences Riverside 3367 putative SNP 1805 putative SSR, 916 di- and trinucleotide repeats Cassava 5046 sequences (41173) 2699 putative SSR 2486 putative SNP Musa 5494 sequences (52907) 1937 putative SSR 28815 putative SNP International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 50. Marker development HarvEST cowpea database - 17 libraries - Two IITA libraries, 12 UCR libraries. Consolidation and utilization of EST HarvEST cassava database - 17 libraries - Two IITA libraries, 12 UCR libraries. HarvEST musa database - 17 libraries - Two IITA libraries, 12 UCR libraries. http://harvest.ucr.edu/ International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 51. Marker Developed Illumina Goldengate SNP assay IITA Reference collection, breeders lines, bi- development and parental populations use IITA reference collection encompassed genetic diversity assessed using SNP Cowpea Ref set and additional germplasm extensively phenotyped – tool for allele mining Development of consensus genetic map of cowpea, and synteny with soybean and Medicago Provides genomic framework for identification of marker trait association, map-based cloning, selection of markers for assessment of genetic diversity, association mapping Muchero, W., Diop, N., Bhat, P., Fenton, R., Pottorff, M., Hearne, S., Ndiaga, C., Fatokun, C., Ehlers, J., Roberts, P., Close,T. 2009. PNAS International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 52. Marker 410 EST derived SSR - Xu et al 2009, Molecular breeding development Mike Timko’s group compared EST with GSS Consolidation and data utilization of EST Determine the gene discovery rate Timko et al 2008 BMC Genomics Predict open reading frames for the genes (oligos) used to create a cowpea microarray – 385k. Microarray used to study cowpea-Striga interaction- Li et al 2009 Pest Mgmt Sci International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 53. Three years- Maize molecular breeding outputs and projects, methodologies outcomes applications Maize Maize genetic diversity Cowpea global diversity Cassava Striga Musa distribution, diversity Striga pathogenicity Resource development and use Some highlights cowpea, cassava and musa Plans for the future International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 54. Building on good Breeding foundations Musa Yam Genome sequence ESTs Cassava TLI TLII DTMA DTMA DTMA DTMA Adapt and apply know how to achieve rapid advances in other IITA crops International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 55. Be brave and In farmers fields plant are subject to look at multiple stresses complexity Start looking at the basis of stress tolerance resistance. Then look at complexes of commonly occurring stresses International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org
  • 56. We have a bright future Thank you International Institute of Tropical Agriculture – Institut international d’agriculture tropicale – www.iita.org