Making genetics work for Africa by increasing genetic gains in farmers’ fields

Making genetics work for Africa by increasing genetic gains in farmers’ fields

Gary Atlin Global Development, Ag R&D 3rd Africa Rice Congress Yaoundé, Cameroon, Oct. 22, 2013

© 2012 Bill & Melinda Gates Foundation |

Rate of genetic gain:

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§  Annual rate of productivity increase in farmers’ fields due to genetic improvement

§  Measured in experiments where cultivars released in different eras are planted side by side under common management.

§  Rate of gain is plotted against year of release §  Should be measured on-station and on-farm §  Genetic gains are very rarely measured, but achieving them

in farmers’ fields is why we invest in breeding

© 2012 Bill & Melinda Gates Foundation | 3 October 22, 2013

Why are we so concerned about genetic gains?

§  Steady, long-term improvement from effective breeding programs transforms agriculture

Yields after 20 years of breeding and varietal turnover with rates of gain of 1, 2, and 3%

Initial yield After 20 years at: 1% 2% 3%

1 t/ha 1.22 1.49 1.81 2 t/ha 2.44 2.97 3.61


The problem (diagnosed at the genetic gains convening, San Diego, Jan 17-19 2013):

•  Inadequate technical and managerial performance is resulting in low rates of genetic gain and low adoption rates that can and must be improved

•  Public-sector breeding serving smallholders in the developing world are achieving sub-optimal rates of genetic gain


Consistently high rates of genetic gain, coupled with rapid turnover of new varieties, result in:

§  Productivity increases leading to poverty alleviation •  A reduced environmental footprint for agriculture •  Effective and constant adaptation to a changing climate

The farmers who are best protected from climate change are those using cultivars bred in the current climate!


Rate of genetic gain in farmers’ fields is a function of:

•  Annual rate of genetic gain measured under farmer management

•  Proportion of the cropped area on which improved varieties are adopted

•  Annual rate of turnover of improved varieties in farmers’ fields

§  These are generic metrics for crop improvement and seed systems investments


The impact of poor rates of genetic gain, low adoption, and slow variety turnover: the example of maize in Africa

Proportion of area planted to improved varieties: 50%1

Rate of genetic gain for improved varieties on-station: 1.2%2

Portion of on-station gain expressed on-farm: 50%3

1Smale, Byerlee and Jayne, 2011 2Badu-Apraku et al., 2013 3G. Atlin rough guess

Overall rate of genetic gain in farmers’ fields: 0.3%


Rate of genetic gain is the key measure of breeding program effectiveness, but it’s hard to measure directly because: • Gains in any one breeding cycle are usually no more than 10% • Breeding cycles are a minimum of 3 – 4 years, but usually at least twice that, resulting in gains per year of 1-2% • It’s difficult to measure yield differences of 10% or less against year-to-year and field-to-field noise • ERA experiments comparing old and new varieties in the same field are the “gold standard” but are difficult, expensive, and need varieties from >10 years


Measuring genetic gains: maize yield under optimal conditions in ESA

Year of first tes4ng in regional trials

Grain yield (t ha-‐1)

y = 5.80+ 0.196x Pr t > 0 = 0.08

2000 2010 2002 2001 2003 2004 2005 2006 2007 2008 2009

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Es#mated gene#c gains in very high-‐yield trials: 196 kg ha-‐1 yr-‐1

9 loca4ons across Zimbabwe, Zambia and

Malawi

PhD study of Benhilda Masuka (Zimbabwe)


Estimates of rates of genetic gain in several crops on-station

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Species Region Period

Rate of gene2c gain (kg ha-‐1 yr-‐1) Reference

Maize (Pioneer) Corn Belt 1930-‐2010 89 Smith (personal communica4on)

Irrigated rice (IRRI) Philippines 1966-‐1995 0* Peng et al. (2000) Wheat (CIMMYT)

High-‐yield envs 1977-‐2008 64 Lopes et al. (2012)

Low-‐yield envs 1977-‐2008 10 Lopes et al. (2012) Maize (IITA) West Africa-‐

drought 1988-‐2010 14 Badu-‐Apraku et al. (2013)

West Africa-‐ High-‐yield envs 1988-‐2010 40

Badu-‐Apraku et al. (2013)

§  Very few programs have measured rates of genetic gain in farmers’ fields * Peng et al have observed in several studies that irrigated rice yields in

tropical Asia cannot be shown to have increased since the Green Revolution when the effects of disease are controlled in older varieties © 2012 Bill & Melinda Gates Foundation | 11

The Gates Foundation views genetic gains in farmers’ fields as a key metric for investments in crop improvement

We are: §  Seeking to understand the critical drivers of genetic gain §  Developing scorecards and metrics by which to assess the

programs we invest in with respect to their ability to deliver high rates of genetic gain

§  Seeking ways to support more effective delivery of steady rates of gain to farmers

October 22, 2013 © 2012 Bill & Melinda Gates Foundation |

What are the routes to increased genetic gains? 1.   Bigger programs (= higher selection intensity)

−  Mechanization, automation, digitization

2.   Adequate genetic variability −  Donors, elite but exotic materials

3.   More accurate selection (=higher heritability) −  Higher-quality phenotyping, better experimental designs, more reps, MAS

4.   Faster breeding cycles −  State of the art program design, genomic prediction

5.   Management that is empowered and accountable for product delivery −  Research managers lead product development, planning, monitor progress, provide supportive

environment, and ensure effective coordination among teams

6.   Well-trained staff who understand product development −  Training of plant breeders needs to be modeled on engineering training, with a focus on

quantitative analysis, mechanization, internships in commercial and high-quality public sector programs

© 2012 Bill & Melinda Gates Foundation | 13

Revolutionary management tool 1: pipeline thinking (i) trait development pipelines

October 22, 2013

§  Big, visible “step changes” caused by major genes are very rare (eg Sub1) but critical

§  There are many QTLs with smaller effects, but that still warrant delivery as tools to breeders

§  Public research systems have done a poor job of delivering traits

§  Effective trait pipelines that quickly deliver production markers for QTLs must be aggressively managed

§  Trait pipelines need highly coordinated teams cooperating on phenotyping, mapping, bioinformatics, and cloning, with clear roles and hand-offs

§  Role of research managers on the effectiveness of trait pipelines is critical; trait pipelines cannot be managed like basic biological research programs (publish and declare victory).


The IRRI abiotic stress trait pipeline is delivering markers for QTLs with large effects on:

Anaerobic germination

Submergence tolerance


§  Drought tolerance


Revolutionary management tool 1: pipeline thinking (ii) cultivar development pipelines

October 22, 2013

§  Between big “step changes” we need steady, incremental concentration of hundreds of alleles with small but favorable effects

§  The products of this cultivar development pipeline are the varieties in which the “step-change” traits are delivered to farmers.

§  Products of the trait pipeline are incorporated into cultivar platforms

§  Private sector programs in maize and soy have scaled up and accelerated their line development pipelines through

i)  Mechanization and digitization of field operations to support huge scale (testing at 100s of locations, in 100,000s of plots

ii)  Databases and analysis tools that are fast and breeder-friendly iii)  Constant measurement of progress against competitors iv)   Highly specialized and integrated teams enabled by managers v)   … and new genomic selection algorithms linking phenotypic and

genotypic data on huge populations to predict performance in the field?


To increase rates of gain, management must: §  Evaluate scientists based on their contribution to product

development rather than on publication §  Evaluate scientists as members of breeding teams rather than as

individual researchers §  Develop clear product concepts and breeding targets § Monitor team performance against genetic gain metrics, and ensure

that product pipelines function §  Provide consulting and mentoring support for scientists

October 22, 2013

Revolutionary management tool 2: managing teams for product delivery


Challenge: Outcome metrics for crop improvement are difficult to capture

•  Seed sold or disseminated

•  Productivity of specific populations

•  Adoption of new varieties

•  Average age of varieties on-farm

•  Welfare benefits


Solution: Intermediate process metrics for plant breeding programs in routine use in the private sector •  Size of program •  Breeding cycle time •  Quality of measurement (repeatability of trials) •  Quality of data management •  Performance against checks on-farm •  Rates of genetic gain on-farm •  Existence and effectiveness of research management and accountability

systems

Intermediate performance metrics are relatively easy to capture and will be built into new Gates Foundation grant agreements


Changes needed to double genetic gains in smallholders’ fields

Management, capacity, metrics, and incentives 1.   Education of new breeding professionals and upgrading skills of the

current cadre to enable the exploitation of the new technologies 2.   Enabling informed management with clear goals and responsibility 3.  Application of intermediate metrics in monitoring, evaluation, and

program management towards goals 4.  A scorecard system that that models good management and identifies

national and international programs with high performance 5.  Sustained support for systemic transformation of breeding programs 6.   Longer-term funding cycles that facilitate sustainable systems change


Technology • Engineering support for mechanization, automation, and digitization of field operations in CG, SME, and NARS stations. • Support to national programs and CG Centers to upgrade research stations into world-class phenotyping hubs. • Support for adoption of breeding information management systems that allow rapid data analysis and effective decision support • A consultancy to help breeding institutions optimize line and trait development pipelines and reduce breeding cycle times • A world-class “back office” for developing genomics tools and genomic selection pipelines for use in CG, NARS, and SME programs

Changes needed double genetic gains in smallholders’ fields

© 2012 Bill & Melinda Gates Foundation | © 2013 Bill & Melinda Gates Foundation | 22 October 22, 2013

Three elements of an evolving initiative to increase rates of genetic gain

1. Donors will need to incorporate key genetic gains pre-requisites and metrics in grants via grant agreements and strategic results frameworks

§  Prerequisites will include modern database, seed storage, irrigation, capable staff, support of program leadership, product concept, target environment, pipeline plan

§  Metrics include measures of program size, testing effort, repeatability for key traits, data return rate, yield relative to widely-used baseline checks, rate of genetic gain.

© 2012 Bill & Melinda Gates Foundation | © 2013 Bill & Melinda Gates Foundation | 23

October 22, 2013

2: Develop a structure to support increased rates of gain in public breeding in SA and SSA, supported by three “pillars”:

Standards of effectiveness modeled, disseminated, by a scorecard system and monitored by regional bodies

Funding for agreements with research organizations for improvement plans to reach standards

Consultancies to help plan and implement improvement plans


Plant breeders in Africa receive little mentoring, and little IT, engineering, or biotech support. They need to be highly independent! To grow, African seed companies need breeders who can independently design and operate a breeding pipeline. Breeders need: -  Genetics and breeding theory -  Mechanization and data collection automation skills -  Quantitative breeding pipeline analysis skills -  Computer programming and database skills -  Ability to source and use molecular data (not to run gels) -  Ability to analyze end user needs, develop product concepts, and conduct

participatory evaluation -  Seed production skills -  Willingness to work at remote locations for reasonable salary

3: A reformed training model for crop improvement specialists to meet the needs of a growing seed industry in Africa


Training reforms needed §  High-quality, practical MS §  Strong focus on mechanization, database, and programming §  Strong focus on quantitative and statistical analysis §  Internships in successful, product-oriented breeding programs §  Exposure to methods used outside home station §  Exposure to commercial pipeline thinking §  High-quality e-learning materials

These reforms are being piloted at three universities (KwaZulu-Natal, KNUST, and Makerere) in a new PASS-led project


2013 2018 2023 2028 2033

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Enabling and accountable management Pipeline and network optimization (training, consultancy) Integrated breeding informatics (database, statistics) Improved phenotyping quality and throughput (station upgrades, engineering support Basic marker applications High-density genomics

System change and technical innovations needed to increase rates of genetic gain


The importance of rapid varietal turnover §  Across Africa and South Asia, farmers are using improved varieties

that are 20+ years old (often 30 years since the cross was made) § We can’t deliver genetic gains unless farmers change varieties §  The best adaptation to climate change is a breeding and seed

system that rapidly develops, deploys, and then replaces varieties §  National release and seed policies need to be assessed for their

impact on genetic gains an poverty alleviation

October 22, 2013


Examples of policy interventions to increase the rate of variety turnover §  Cease production of breeder and foundation seed of obsolete

varieties §  Provide seed subsidies only for varieties released in the last 5

years §  Eliminate release requirements (as has been done in South Africa,

the US, Canada, and many other countries) §  Use average age of varieties produced by national seed

corporations as a performance metric §  Provide companies with small grants to help cover the cost of

replacing obsolete varieties

October 22, 2013 © 2012 Bill & Melinda Gates Foundation | 29 October 22, 2013

Key conclusions

§  A high and sustained rate of genetic gain is a key component of agricultural transformation

§  Rate of genetic gain delivered in farmers’ fields is the key measure of effectiveness of a crop improvement system

§  The public crop improvement system is lagging in technology and management methods, and is underperforming

§  Research leaders, scientists, and the donor community must take responsibility for increasing the rate of genetic gain

§  CG, NARS, and SME breeders need sustained support to apply modern breeding technology and optimize breeding pipelines.

§  The CG centers need to grasp a leadership role in supporting modernization of the international public breeding system

•  National seed systems need to be designed for rapid varietal turnover

§  The Gates Foundation is committed to helping the international crop improvement system modernize and increase rates of gain.

Thanks!

Making genetics work for Africa by increasing genetic gains in farmers’ fields

Technology

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