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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
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