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v More than 200 breeders and agriculturists from NARS trained to use modern breeding management and decision tool (Fig. 1) v Establishment of nodes and migra@on of historical data from several breeding programs in Africa into the BMS tool v 15 research scien@sts trained in Demand-led variety design approach v SSR genotyping of tubers (yam, cassava), cereals (rice, maize), tree crops (mango, eucalyptus), vegetable (biJer leaf), forage, fish and livestock (caJle, goat) from sub Saharan Africa, USA and Ecuador (Fig 2) v SNP genotyping of 3230 samples including forage, maize, rice, sorghum, fish and sheep from CG centers (70%), Na@onal Agricultural Research System (NARS) (15%) and the Program for African Seed System (PASS) (15%) (Fig. 3). v Genomic assisted breeding jointly implemented with partners in Tanzania and Eritrea Molecular Breeding Pla0orm at the BecA-ILRI Hub: Suppor>ng breeders in the region *Nasser Yao, Mary Wambugu, Francesca Stomeo, Mark Wamalwa, Appolinaire Djikeng and *Josephine Birungi Biosciences eastern and central Africa-InternaFonal Livestock Research InsFtute, (BecA-ILRI) Hub,Nairobi, Kenya About the Molecular Breeding Pla0orm The Breeding plaWorm at the BecA-ILRI Hub aims at enhancing plant breeding and livestock research using modern breeding tools. The plaWorm is built around three key components: the Breeding Management System (BMS), the Integrated Genotyping Service and Support (IGSS) and the Demand-led variety design. BMS is a suite of comprehensive tools, embedded in a single place, and commonly used by breeders for their day to day breeding ac@vi@es. IGSS is an innova@ve genotyping service and support to local plant/livestock breeding programs and small and medium enterprises in sub- Saharan Africa to accelerate the rate of gene@c gain, development and release of new crop varie@es and improved livestock. Through the demand-led variety design approach, the breeding plaWorm aims at making plant breeding in Africa a business model responsive to market demand. The plaWorm also generates and manages genomic and marker data and provides support to breeders and other scien@sts in integra@ng DNA marker assays and genomic tools into their breeding program and research ac@vi@es for both cul@vated and orphan crops and livestock species. Major fields covered under the plaWorm include: 1) training of breeders to make efficient use of breeding decision support tools (BMS and IGSS), 2) provision of advice and guidance in elabora@ng an holis@c breeding strategies (demand-led variety design) using modern breeding tools, 3) genome sequencing-based gene@c profiling and genera@on of various genotyping data types from low to high throughput facili@es, 4) support in popula@on development and data management followed by required analyses, interpreta@on of result and suppor@ng scien@sts to get the suitable breeding decision for the next step, 5) genome wide associa@on study and 6) genomic selec@on. *For more informa@on contact Dr Nasser Yao/Dr Josephine Birungi [email protected]/[email protected] ● hub.africabiosciences.org Funding: Bill and Melinda Gates Founda@on (BMGF) Syngenta Founda@on for Sustainable Agriculture (SFSA) This document is licensed for use under a Crea@ve Commons AJribu@on –Non commercial-Share Alike 3.0 Unported License February 2016 Partnerships Outputs v Modern breeding tool adopted and used in several breeding programs in eastern, central and southern Africa including Ethiopia, Uganda, Tanzania, Sudan and Kenya v Breeders and agriculturists beJer integra@ng historical and manual data directly into BMS to accelerate breeding efforts v Major QTL for Maize Lethal Necrosis (MLN) iden@fied and used to develop maize MLN resistant lines v Gene@c profiling of 350 rice accessions, comprising a unique collec@on of the African Oryza and key rice germplasms used by the rice community as parental lines or elite material, now serving several breeding purposes at the Africa Rice Centre v Ins@tu@ons (Naliendele Agricultural Research Ins@tute (NARI) in Tanzania and the Hamalmelo College of Agriculture, Eritrea) implemen@ng genomic-based/ molecular assisted breeding Outcomes • Gene@c profiling of key crop and livestock commodi@es from breeding programs in Ethiopia, Kenya, Rwanda, Tanzania and Uganda • Design of product profiles for major crops/livestock • Development of cul@var development pipelines for major crop/livestock • Linkage with the Global Open-source Breeding and Informa@cs Ini@a@ve (GOBII) and Diversity Seek (DivSeek) ini@a@ves Poten>al to scale-up 0 10 20 30 40 50 60 70 80 90 100 Private Sector CG center ABCF NARS University Number of trainees per ins>tu>on Figure 1: Number of trainees per country and per ins>tu>on Figure 3: Number of samples processed per commodity and per ins>tu>on under IGSS 0 50000 100000 150000 200000 250000 300000 2009 2010 2011 2012 2013 2014 Number of samples Years Trends in Genotyping Service Provision Figure 2: SSR genotyping service provision and trend from 2009 to 2014 0 5 10 15 20 25 30 35 40 Zambia Benin Cote d'Ivoire Cameroon DRC Burundi Rwanda Eritrea Tanzania Ethiopia Kenya Sudan Uganda Number of trainees per country

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Page 1: Molecular Breeding Platform at the BecA-ILRI Hub: Supporting breeders in the region

v More than 200 breeders and agriculturistsfromNARStrainedtousemodernbreedingmanagementanddecisiontool(Fig.1)

v Establishment of nodes and migra@on ofhistorical data from several breedingprogramsinAfricaintotheBMStool

v 15researchscien@ststrainedinDemand-ledvarietydesignapproach

v SSR genotyping of tubers (yam, cassava),cereals (rice, maize), tree crops (mango,eucalyptus), vegetable (biJer leaf), forage,fish and livestock (caJle, goat) from subSaharanAfrica,USAandEcuador(Fig2)

v SNP genotyping of 3230 samples includingforage,maize,rice,sorghum,fishandsheepfromCGcenters(70%),Na@onalAgriculturalResearch System (NARS) (15%) and theProgram for African Seed System (PASS)(15%)(Fig.3).

v Genomic ass isted breeding jo int lyimplementedwithpartnersinTanzaniaandEritrea

MolecularBreedingPla0ormattheBecA-ILRIHub:Suppor>ngbreedersintheregion

*NasserYao,MaryWambugu,FrancescaStomeo,MarkWamalwa,AppolinaireDjikengand*JosephineBirungiBioscienceseasternandcentralAfrica-InternaFonalLivestockResearchInsFtute,(BecA-ILRI)Hub,Nairobi,Kenya

AbouttheMolecularBreedingPla0ormTheBreedingplaWormattheBecA-ILRIHubaimsatenhancingplantbreedingandlivestockresearchusingmodernbreedingtools.TheplaWormisbuiltaroundthreekeycomponents:theBreedingManagementSystem(BMS),theIntegratedGenotypingServiceandSupport(IGSS)andtheDemand-ledvarietydesign.BMS is a suiteof comprehensive tools, embedded in a singleplace, and commonlyusedbybreeders for their day todaybreedingac@[email protected]@vegenotypingserviceandsupporttolocalplant/livestockbreedingprogramsandsmallandmediumenterprisesinsub-SaharanAfricatoacceleratetherateofgene@cgain,developmentandreleaseofnewcropvarie@esandimprovedlivestock.Throughthedemand-ledvarietydesignapproach,thebreedingplaWormaimsatmakingplantbreedinginAfricaabusinessmodelresponsivetomarketdemand.TheplaWormalsogeneratesandmanagesgenomicandmarkerdataandprovidessupport tobreedersandotherscien@sts in integra@ngDNAmarkerassaysandgenomic tools into theirbreedingprogramand researchac@vi@es forboth cul@vatedandorphan cropsand livestock species.Majorfields coveredundertheplaWorminclude:1)trainingofbreederstomakeefficientuseofbreedingdecisionsupporttools(BMSandIGSS),2)provisionofadviceandguidanceinelabora@nganholis@cbreedingstrategies(demand-ledvarietydesign)usingmodernbreedingtools,3)genomesequencing-basedgene@cprofiling and genera@on of various genotyping data types from low to high throughput facili@es, 4) support in popula@on development and datamanagementfollowedbyrequiredanalyses,interpreta@onofresultandsuppor@ngscien@ststogetthesuitablebreedingdecisionforthenextstep,5)genomewideassocia@onstudyand6)genomicselec@on.

*Formoreinforma@oncontactDrNasserYao/[email protected]/[email protected]●hub.africabiosciences.orgFunding:BillandMelindaGatesFounda@on(BMGF)SyngentaFounda@onforSustainableAgriculture(SFSA)ThisdocumentislicensedforuseunderaCrea@veCommonsAJribu@on–Noncommercial-ShareAlike3.0UnportedLicenseFebruary2016

Partnerships

Outputsv Modernbreedingtooladoptedandused

inseveralbreedingprograms ineastern,central and southern Africa includingEthiopia, Uganda, Tanzania, Sudan andKenya

v Breeders and agriculturists beJerintegra@ng historical and manual datadirectly intoBMStoacceleratebreedingefforts

v Major QTL for Maize Lethal Necrosis(MLN) iden@fied and used to developmaizeMLNresistantlines

v Gene@c profiling of 350 rice accessions,comprising a unique collec@on of theAfrican Oryza and key rice germplasmsused by the rice community as parentallines or elite material, now servingseveral breeding purposes at the AfricaRiceCentre

v  Ins@tu@ons (Naliendele AgriculturalResearchIns@tute(NARI)inTanzaniaandthe Hamalmelo College of Agriculture,Eritrea) implemen@ng genomic-based/molecularassistedbreeding

Outcomes

•  Gene@c profiling of key crop and livestock commodi@es from breedingprogramsinEthiopia,Kenya,Rwanda,TanzaniaandUganda

•  Designofproductprofilesformajorcrops/livestock

•  Developmentofcul@vardevelopmentpipelinesformajorcrop/livestock

•  Linkage with the Global Open-source Breeding and Informa@cs Ini@a@ve(GOBII)andDiversitySeek(DivSeek)ini@a@ves

Poten>altoscale-up

0 10 20 30 40 50 60 70 80 90 100

PrivateSector

CGcenter

ABCF

NARS

University

Numberoftraineesperins>tu>on

Figure1:Numberoftraineespercountryandperins>tu>on

Figure 3: Number of samples processed per commodity and perins>tu>onunderIGSS

0

50000

100000

150000

200000

250000

300000

2009 2010 2011 2012 2013 2014

Num

bero

fsam

ples

Years

TrendsinGenotypingServiceProvision

Figure2:SSRgenotypingserviceprovisionandtrendfrom2009to2014

0 5 10 15 20 25 30 35 40

ZambiaBenin

Coted'IvoireCameroon

DRCBurundiRwandaEritrea

TanzaniaEthiopiaKenyaSudan

Uganda

Numberoftraineespercountry

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