Improving Sorghum Adaptation in West Africa with Genomics-Enabled Breeding

Geoffrey Morris | Kansas State University | Sorghum in the 21st Century

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Our genomics-enabled breeding network

Daniel Fonceka (CERAAS/CIRAD)Jean-Francois Rami (CIRAD)Aziz Saidou (U Maradi)Geoffrey Morris (KSU)

Ndiaga Cisse (ISRA/CERAAS)Aissata Mamadou (INRAN)Magagi Abdou (LSDS)Eva Welztien (ICRISAT)Niaba Teme (IER)

Bassirou Sine (CERAAS)Falalou Hamidou(ICRISAT)

Breeding Genetics

Physiology

Jack AkataTogo

CERAAS

Cyril DiattaSenegal

CERAAS

Ardaly OusseniNiger

INRAN/WACCI*

Fanna MainaNigerKSU

Jacques FayeSenegal

KSU

Marcus OlatoyeNigeriaKSU*

* SMIL-funded data and/or training, not PhD

PhD Trainees

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Successes and roadblocks from 50 years of West African sorghum breeding

• Senegal & Niger national programs: Focus on dual-purpose (grain & biomass) purelinevarieties for Sahelian and Soudano-Sahelian zones

• Development of varieties that have been adopted

– Modest adoption: wide→old (e.g. IRAT204), new→narrow (e.g. Nganda) (Ndjeunga et al. 2015 DIVA)

• Marker-assisted breeding implementation (Striga, stay-green)

– No pipeline for local discoveries in local germplasm

• Breeding programs have supportive physiology programs (CERAAS, ICRISAT)

– No in-house genetics support to link physiology to breeding

• Common theme? Breeders lack connectivity

– Build a decentralized breeder network, with genomics facilitating and linking(Cooper et al. 2014 Crop & Pasture Sci)

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Overview of specific objectives and workflow

Genomics-assisted breeding

• Marker-assisted recurrent selection

• Evaluation of GS

Genomics toolkit for breeding

• Trait-predictive & local background markers

• Convert GBS-to-KASPPhenotyping & trait mapping

• Senegal: Pre/post flowering drought, grain mold resistance

• Niger: Post flowering drought, Striga resistance

Multi-parent populations

• West Africa Sorghum Association Panel

• Senegal & Niger mini-NAM families

Gender integration

• Balance in training• Participatory rural appraisal

Long & short term training

• PhD training (n = 4 + 2)• Workshops (genomics, seed)

Genomic characterization

• Niger & Senegal germplasm• Other WA (Mali, Togo, Nigeria)

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Multi-parent populations for West African germplasm

WASAP Population structure• WASAP: West African Sorghum Association Panel

– 800 landraces & breeding lines

– Senegal (ISRA/CERAAS), Niger (INRAN), Mali (IER), Togo (ITRA)

• Mini-NAM (Nested Association Mapping) populations (n = 600 x 2)

– Senegal (F6): Nganda X Sureno, Macia, CSM63

– Niger (F4): Mace De Kunya X SRN39, ICSV745, L153

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Genomic characterization of West African germplasm

Genotyping-by-sequencing at 400,000 SNPs

• WASAP (DNA extracted in Senegal, n = 800)

• Genebank accessions from Senegal, Niger, & Nigeria (n = 1500)

• Mini-NAMs (in process)

Genomic analyses and PhD training

• Identify diverse parents for combining ability study (Akata et al. 2017 Afr Crop Sci J)

• Characterize local adaptation, identify variety-specific markers (Maina et al. 2018 Genome)

• Genome regions underlying precipitation adaptation in Nigeria (Olatoye et al. in review)

• Genomic regions underlying Sahelian vs. Soudanianadaptation (Faye et al. in prep.) Jacques Faye

Partitioning the factors shaping genomic variation in Senegal

Clinal climate adaptation

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Increased phenotyping capacity for Striga resistance, integrated into genomics-enabled breeding

• Farmer/seed producer/breeder selections from MDKxSRN39 mini-NAM family (Adbou & Mamadou)

• Striga resistance & SRN39 markers (Ousseini & Maina) (LGS1; Gobena et al. 2017 PNAS)

60 d 90 d# Striga plants

Aissata Mamadou

Validation of facilityStriga collections Striga phenotypingfacility

Ardaly Ousseini(INRAN/WACCI) to ICRISAT-Mali

Striga training

Collaborative selection

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Increased phenotyping capacity for drought tolerance, integrated into genomics-enabled breeding

Managed water stress (WASAP, n = 600)

Phenotypes: Bassirou Sine, Jack Akata. Genetics: Fanna Maina, Jacques Faye. Breeding: Cyril Diatta, Jack Akata, Nofou Ouedraogo

Well-watered

Water stressed

Phenotyped morphology & yield components

Trait mapping & marker development

Marker validation & breedingHighest performing lines

crossed to local elite (Senegal, Togo, Burkina)DO N

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Genomics toolkit for breeder-friendly markers• Make GBS SNPs available as KASP markers via Breeding Management System

• Identify variety-specific markers for more efficient background selection (FST scans)

High Fst SNP markers for “Mota”

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Transition to genomics-assisted breeding?

• Marker-assisted recurrent selection (MARS)

– Limited ability to detect loci for grain mold resistance in F4 mini-NAM

– Bi-parental populations will not include all customer-demanded traits

• Evaluation of genomic selection (GS)

– West African breeding programs do not have kinship needed for shared genomic predictions

– Separate GS programs for each country would be costly and limited in scope

• Next steps?

– Focus on marker-assisted introgression of known loci (Striga resistance, stay-green)?

– Increase connectivity to capture traits and facilitate genomic prediction?

Cyril Diatta

Grain mold mapping

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Next steps: Genomic-assisted recurrent selection?• Implementing genomic selection in Haiti, as model

for small developing countries (Gael Pressoir & Ed Buckler, SMIL)

• Recurrent selection scheme using nuclear male sterility (e.g. ms3) to facilitate crossing and increase recombination

• Recurrent selection populations integrate well with other approaches:

– Participatory breeding (Vom Brocke et al. 2008 Cahiers Agri)

– Trait-focused molecular breeding (Ongom & Ejeta 2018 G3)

• A platform for connected West African sorghum breeding programs?

Time (Years)

Genomic (3X/yr)Genomic (2X/yr)Phenotypic (1X/yr)

Genetic Gain

Kebede Muleta, et al.

Pop size = 200 10% selected # QTL = 500 h2 = 0.3

Improved genetic gain with GARS

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Thanks! Questions?

Daniel Fonceka (CERAAS/CIRAD)Jean-Francois Rami (CIRAD)Aziz Saidou (U Maradi)Geoffrey Morris (KSU)

Ndiaga Cisse (ISRA/CERAAS)Aissata Mamadou (INRAN)Magagi Abdou (LSDS)Eva Welztien (ICRISAT)

Bassirou Sine (CERAAS)Falalou Hamidou(ICRISAT)

Jack AkataTogo

CERAAS

Cyril DiattaSenegal

CERAAS

Ardaly OusseniNiger

INRAN/WACCI*

Fanna MainaNigerKSU

Jacques FayeSenegal

KSU

Marcus OlatoyeNigeriaKSU*

* SMIL-funded data and/or training, not PhD

PhD Trainees

This presentation is made possible by the support of the American People provided to the Feed the Future Innovation Lab for Collaborative Research on Sorghum and Millet through the United States Agency for International Development (USAID) under Cooperative Agreement No. AID-OAA-A-13-00047. The contents are the sole responsibility of the authors and do not necessarily reflect the views of USAID or the

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Physiology & GeneticsResearchDeliver knowledge that facilitates the breeding programs

BreedingDevelopmentDeliver varieties that meet a defined product profile

Towards a durable R&D network

Local adaptationMarker-assisted introgression of major effect loci into local landraces

Broad adaptationGenomic recurrent selection from multi-environment trialsin intercrossed germplasm

Genetic dissectionGenetic architecture, trait mapping, and markers

Sub-traits

Loci

Traits

Lines

MarkersTraitsModelsGermplasm

Physiological dissectionPhysiological mechanisms, component traits, and models

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