Phenotyping in Breeding Programs for biotic stresses

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9 September 2015, Workshop on Implementation of IITA’s Genetic Improvement Strategy, IITA, Ibadan, Nigeria
Phenotyping in Breeding Programs
Biotic Stresses
Lava Kumar et al.,

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Team
Abuelgasim Elzein (Microbiology / striga)
Augusto Joao (Pathology)
Danny Coyne (Nematology)
Georg Goergen (Entomology)
George Mahuku (Pathology)
Harun Maruthi (Pathology)
James Legg (Virology / vector entomology)
Joseph Atehnkeng (Pathology)
Lava Kumar (Virology / Germplasm health)
Kolade Olufisayo (Phenotyping)
Manu Tamu (Entomology)
Maria Ayodele (Pathology)
Ranajit Bandyopadhyay (Pathology)
Rachid Hanna (Entomology)
Crop breeders / Geneticists
NARS staff / Students

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1.Current status
2.What could/should be done
3.Opportunities
4.Resource requirements
5.Way forward
Outline

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MLND/MCMV
FoC TR4
• Breeding for resistance is a major tactic to control
pests and diseases of IITA ‘mandate’ crops
• Six crops; at least 40 different targets
• Pre- and postharvest pests and pathogens
• Fungi, Viruses, Bacteria and Phytoplasma
• Insects, Acarids and Nematodes

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Crop Diseases Insects and
acarids
Other
Cassava Mosaic, brown streak, bacterial
blight, anthracnose, phytoplasma
Whitefly, mealy
bug, green mite,
root scales
Mycotoxins
Yam Mosaic, anthracnose, tuber rots Mealybugs
beetles
Nematodes,
mycotoxins
Banana
and
plantain
Bacterial wilt, Fusarium wilt,
bunchy top, Sigatoka
Weevil, aphid Nematodes
Taro and
cocoyam
Blight, mosaic
Cacao Phytophthora, swollen shoot Mirids,
mealybug
Mycotoxins
*Potential future targets in italics
Phenotyping targets for biotic stresses:
Vegetatively propagated crops

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Crop Diseases Insects and
acarids
Other
Maize Streak, Lethal necrosis, gray leaf
spot, ear rot, wilt, leaf rust,
downy mildew, leaf blight
Stalk and corn
borers,
leafhopper,
aphids, thrips
Striga,
aflatoxins,
fumonosins
Soybean Rust, mosaic, phytoplasma
Cowpea Bacterial blight, mosaic, wilt Maruca, aphid,
thrips, weevils
Striga
*Potential future targets in italics
Phenotyping targets for biotic stresses:
Vegetatively propagated crops

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Region-wise phenotyping
B = Banana
C = Cassava
Co = Cowpea
M = Maize
S = Soybean
Y = Yam

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Plant microbe interactions
Host response
Gene regulation
Genes
Phenotyping approaches
Vector biology
Survival and spread
Environmental factors
Biochemical, molecular &
biological Properties
Bioassays
Serological &
Nucleic-acid assays
Pathogen / Pest
Biology, ecology and
diversity assessment
Establishment of isolates
Identification of
environments/locations
Diagnostic tools
Germplasm screening
Transgenics Conventional /
MAS Breeding
Variety development, trait discovery & mechanisms of host response

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Phenotyping approaches
Genotype assessment
Infection rate (incidence)
Disease / damage severity (assessed using quantitative scale)
Single time point assessment
Multiple assessment over a period of time (means / AUDPC)
Often visual (manual)
Sometimes digital imaging used

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Measurement of total surface area
-
Measurement of non-infected area
(All tuber surface area–
non-infected area)/
All tuber surface area=
Infected area
Infection area 41.9%
Modification for reading
labels with OCR
Fortunus Kapinga (PhD student)
Phenotyping approaches

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•Virulence variation in pathogen populations within the region and
across the regions
•Soybean rust (Phakopsora pachyrhiz)
•Yam anthracnose
•Cassava mosaic begomoviruses
Phenotyping approaches
•Type isolates are being used to the extent possible or location specific
evaluation

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CMD: Caused by a complex of 9 species either alone or in mixed infection
•African cassava mosaic virus (ACMV)
•East African cassava mosaic virus (EACMV)
•South African cassava mosaic virus (SACMV)
•EACMV-Cameroon, EACMV-Malawi, EACMV-Kenya, EACMV-Zanzibar
EACMV-Uganda (Recombinant virus)

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Phenotyping approaches
We don’t see a lot
Understanding
underlying
mechanisms is vital
to improve
precession and
accuracy of selection,
especially to move
towards MAS, GS, etc

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(A), AR40-6 (B), Kibaha (C), NDL06/132, Kiroba (E), Albert (F) and non-template control (G).
Relative titers of CBSVs in cassava
CBSV UCBSV
What we could / should do better
Source: Kwasei et al.
Pathogen – host interactions

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What we could / should do better
Gene regulation
in resistance /
susceptible
response

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•Modernizing phenotyping methods
•Introduction of digital tool (non-invasive methods)
•Spectral imaging
•Benchmark sites
•Annual (season) incidence and severity; and weather data
•Long term data collection; can help climate change studies
•Meta data analysis
•Data from field books on pests and diseases can be utilized
•Harmonization of definitions and scoring scales
What we could / should do better

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•Moving targets
•Pathogen/pest shifts
•Emergence of new pathogens
•Maintenance of isolates / diagnostic tools
•Recurring cost (depleting funding)
•Vulnerability of conservation facility
•Temperature fluctuations / maintenance problems
•Sub-optimal facilities
•Poor screen houses
•Lack of environmental control chambers
•Misting screen house for bacteria and fungi inoculations
•Insufficient funding
•Depletion of W1 and W2
•W3 funding is specific and linked to critical problems
•Future CRP operational model is similar to W3
•Staff
•Thinly stretched
•Affects throughput
Challenges

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•Insufficient facilities for phenotyping in Central and Southern Africa
Challenges

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Way forward
Phenotyping – genotyping pipeline
Transcriptome
Genome & Proteome
Metabolome
Phenome
Database
Trait diversity Resistant varieties Mechanisms Tools
Trait-specific markers / modeling
tools for genomic selection /
GWAS / QTLs / Genes / MAS / Breeding
Omics
applications
&breeding
Striga
Cassava
Maize
Banana & Plantain
Taro & Cocoyam
Cowpea & wild Vigna
Soybean
Yam
Oomycetes
Nematodes
Bacteria
Insects & acarids
Fungi
Mycotoxins
Phytoplasma
PathogensVirus
Germplasm collections /Breeding lines / Transgenic lines
Controlled infections
/ Multienvironmental
testing
Type isolates for
phenotyping
Assays, tools and
protocols for
phenotyping and data
acquisition
Data storage and
analysis
Cacao
Phenotypingforbioticstresses

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Partnerships
Existing
NARS
Universities
CGIAR centres
ARIs
Private sector
Potential
UK National Plant Phenomics Centre
EPPN: European Plant Phenomics Network
Private sector
& Other

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Acknowledgments
GENEBANKS