phenotyping in breeding programs for biotic stresses

A member of CGIAR consortium www.iita.org

9 September 2015, Workshop on Implementation of IITA’s Genetic Improvement Strategy, IITA, Ibadan, Nigeria

Phenotyping in Breeding ProgramsBiotic Stresses

Lava Kumar et al.,


TeamAbuelgasim 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 / GeneticistsNARS staff / Students


1.Current status

2.What could/should be done

3.Opportunities

4.Resource requirements

5.Way forward

Outline


MLND/MCMVFoC 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


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


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


Region-wise phenotyping

B = BananaC = CassavaCo = Cowpea M = Maize S = SoybeanY = Yam


Plant microbe interactionsHost responseGene regulationGenes

Phenotyping approaches

Vector biologySurvival and spreadEnvironmental factors

Biochemical, molecular & biological Properties Bioassays

Serological &Nucleic-acid assays

Pathogen / Pest

Biology, ecology and diversity assessment

Establishment of isolatesIdentification of

environments/locations

Diagnostic tools

Germplasm screening

Transgenics Conventional / MAS Breeding

Variety development, trait discovery & mechanisms of host response



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


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)



• Virulence variation in pathogen populations within the region and across the regions• Soybean rust (Phakopsora pachyrhiz)• Yam anthracnose • Cassava mosaic begomoviruses


• Type isolates are being used to the extent possible or location specific evaluation


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)



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


(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



Gene regulation in resistance / susceptible response


• 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



• 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


• Insufficient facilities for phenotyping in Central and Southern Africa

Challenges


Way forwardPhenotyping – genotyping pipeline

TranscriptomeGenome & Proteome

Metabolome

PhenomeDatabase

Trait diversity Resistant varieties Mechanisms Tools

Trait-specific markers / modeling tools for genomic selection /

GWAS / QTLs / Genes / MAS / Breeding

Om

ics applications &

breeding

Striga

Cassava

Maize

Banana & Plantain

Taro & Cocoyam

Cowpea & wild Vigna

Soybean

Yam

Oomycetes

Nematodes

BacteriaInsects & 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

Phenotyping for biotic stresses


Partnerships

Existing NARSUniversities CGIAR centres ARIs Private sector

Potential UK National Plant Phenomics CentreEPPN: European Plant Phenomics NetworkPrivate sector & Other


Acknowledgments

GENEBANKS

phenotyping in breeding programs for biotic stresses

Government & Nonprofit