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Through collaboration among CIMMYT, IITA, advanced research institutes, the Generation Challenge Program (GCP), national research systems, and small‐ and medium‐size seed enterprises, this Strategic Initiative will also refine the new breeding tools and develop strategies to permit their use by small breeding programs to address the problem of increasing productivity in tropical and subtropical maize production environments. Integration of advanced tools within breeding programs in Africa, Asia, and Latin America will result in increased genetic gains, more rapid development of resilient, high‐yielding hybrids and open‐pollinated varieties, and increased food security and incomes for millions of the maize‐dependent poor. The aim is to double rates of genetic gains within the six‐year life of this project. Use of these new tools will result in more competitive national and regional seed companies and increase the availability of elite germplasm from public international agricultural research centers. Maintaining diverse sources of elite maize germplasm in the public domain is critical to the survival of local and regional seed companies and to the existence of competitive seed markets that serve the needs of a wide range of farmers and, in particular, poor smallholders. Progress to date and lessons learned Both breeding behavior (Carena et al. 2009) and QTL analysis (Ribaut et al. 2008) indicate that genetic control of drought tolerance in maize is complex and polygenic. Methods that reduce breeding‐cycle time are needed to increase genetic gains for such “difficult” traits. CIMMYT is developing tropical doubled haploid (DH) inducers and rapid‐cycle marker‐based recurrent selection protocols for this purpose. DH inducers obtained from the University of Hohenheim (Germany) have been used to develop tropically‐adapted inducers that will be available for distribution within 1.5 years. The cost of genotyping with single‐nucleotide polymorphism (SNP) markers is no more than 10% of the cost of simple sequence repeat (SSR) markers per data point, and the availability of efficient, rapidturnaround commercial SNP genotyping services means that breeding programs no longer need (nor would find cost effective) in‐house genotyping capacity. Even small NARS and commercial breeding programs can afford to genotype and apply marker‐assisted selection in variety development. Both CIMMYT and IITA are now outsourcing most genotyping. Application of marker‐driven, rapid‐cycle recurrent selection methods has been demonstrated to increase breeding progress in commercial programs in the US (Eathington et al. 2007), but have not yet been applied to maize breeding in developing countries (Prasanna et al. 2010). CIMMYT has initiated over 30 marker‐assisted recurrent selection populations to test these methods in breeding programs for Africa and Asia. Genotyping costs are expected to drop by several orders of magnitude more in the coming year, as sequencing technologies are applied to genotyping. CIMMYT’s elite East African germplasm will be genotyped at a density of approximately 1,000,000 polymorphic features in 2010 by the pioneering “genotyping by sequencing” technology developed by the Buckler Lab at Cornell University. Routine high‐density genotyping of all breeding lines in the CIMMYT and IITA programs, and extension of this technology to research partners, will transform maize breeding for poor smallholders, allowing the development of breeding systems based on genomic selection. High‐density marker genotypes can be used to predict genotypic value (Heffner et al. 2009) and have been shown to be highly effective in predicting maize yield under stress in CIMMYT germplasm with as few as 1300 SNP markers (J Crossa, unpublished data). CIMMYT has links with the laboratory of E. Buckler (Cornell University, USA) to apply new, state‐of‐the‐art genotyping by sequencing (GBS) methods to permit rapid‐cycle genomic selection in its African breeding programs, beginning in 2010. High‐density, low‐cost markers allow the application of GS in multi‐parent populations with better prospects for long‐term gains than bi‐parental populations. CIMMYT and IITA breeders are assembling multi‐parent populations for this purpose. An 152
innovative “open‐source” breeding system has been planned that will permit smaller NARS and commercial breeding programs to use these tools to increase gains. These systems rely heavily on lowcost tissue sampling and DNA extraction; simple dry‐seed chipping systems have been successfully implemented by CIMMYT and IITA and are ready to be shared with partners. Why international agricultural research? The new tools that are transforming commercial plant breeding in developed countries are not currently accessible to national research and extension systems and small‐ and medium‐sized seed companies in the developing world, because their effective use requires strong capacity in biometrics, bioinformatics, high‐density genotyping and doubled haploid systems. Few national systems or small companies have the needed depth of capacity in all these fields. Currently, only the largest multinational seed companies have been able to integrate these elements effectively into a product development pipeline. Multinational seed companies consider their integrated molecular breeding pipelines highly proprietary. While they are increasingly open to collaboration with the CGIAR, they usually restrict the sharing of their technologies with third parties. They also cannot be relied on to deliver the products of these pipelines to the developing world where small and fragmented markets and low purchasing power of poor smallholders make breeding investments commercially unattractive. CIMMYT and IITA are public institutions with strong breeding, biometrics, and genetics capacities, and close links to both advanced research institutes and national research and extension systems. In collaboration with the GCP, they are well‐placed to merge the new genotyping, phenotyping, informatics, and DH systems into an integrated public platform attuned to the needs of national systems and small‐ and medium‐sized companies engaged in maize breeding. Association mapping panels consisting of inbred lines with adaptation to all major tropical and subtropical target mega‐environments have been assembled at CIMMYT for the specific purposes of detecting genes with effects on drought tolerance, disease resistance, and tolerance to infertile soils (Lu et al. 2009; Yan et al. 2009). These panels have been or are being phenotyped for many different traits in a wide range of environments and phenotyping systems; they are a unique, freely available resource for the maize research community and their value increases as they are phenotyped for more traits and in more environments. CIMMYT and IITA provide the natural platform for linking small and technologically isolated NARS and small private sector breeding programs into “open‐source” genomic selection networks, wherein a central breeding program cycles the selection populations, driving them towards improved allele frequencies on the basis of selection for genotype only; they also provide high‐precision phenotyping in managed stress screens. By contrast the commercial and NARS “hubs” provide phenotyping for the training population in the target environment, and receive unique, genotyped proprietary DH lines preselected on the basis of GEBV for adaptation, stress tolerance, and yield potential in their own target markets. Only CIMMYT and IITA, in the public sector, have the international mandate and linkages, germplasm, and bioinformatics and biometrics capacity to implement such networks. Researchable issues Optimizing marker‐assisted recurrent selection (MARS) and genomic selection (GS) systems, in particular for multiple complex traits (e.g. yield potential, drought tolerance, mycotoxin resistance) that are essential in many tropical maize‐growing environments, including: o Analyzing the power of high‐density haplotype indices to predict phenotypic performance for multiple complex traits. o Translating reduced cycle time of MARS/GS into increased gains in stress‐prone environments. 153
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MAIZE ‐ Global Alliance for Impro
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Abbreviations 1 AFLP CA CBO CEO CGI
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Executive summary Recurrent food pr
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All SIs include capacity building t
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essentially the same land area whil
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Competing uses for a staple grain A
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Figure 3. Annual global yield fluct
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environments and capacity building.
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productivity while reversing widesp
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Target Group 3: Poor consumers and
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poverty reduction, food insecurity,
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Methods Innovative approaches to a
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Methods Aggressive development, va
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Outcomes Novel tools will empower N
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Based on the maize systems describe
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Program‐level product delivery Pr
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Impact pathways Impact pathways are
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Outcomes for MAIZE as a whole shown
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The portfolio of Strategic Initiati
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Table 2. Summary of impacts of MAIZ
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allocate their time to more product
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fall short of making up the differe
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Priority setting to plan future rev
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Strategic Initiative SI 2. Sustaina
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Strategic Initiative SI 4. Stress t
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Strategic Initiative SI 7. Nutritio
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Partnership principles While the pa
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Based on current staff and partner
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Oversight Committee: This committee
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Review and refine priorities, targe
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Price Trade Policy REDD, PES, Reser
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CGIAR Research Program Outputs from
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Climate change strategy The impact
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Process monitoring will include par
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Given the high costs and difficulti
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the uptake of outputs and the inten
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CIMMYT has developed such partnersh
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12. Decision makers understand and
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Scaling up and out of methodologies
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Bilateral funding: Following the Co
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Table 7A. Income and expenses for S
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Expenses by Strategic Initiative: T
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References Alston, M.J., Norton, W.
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MAIZE Strategic Initiatives Strateg
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Targeting resource‐poor farmers i
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Knowledge of the structure and func
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2014: Analysis of policy options an
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Strategic Initiative 2. Sustainable
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stress‐tolerant germplasm, better
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Researchable issues Effective appr
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Key milestones 2011: Maize‐based
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Modernizing agriculture through use
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coherent exploratory diagnostic tri
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universities, the private sector (i
Page 110 and 111: What's new in this initiative? To
Page 112 and 113: Strategic Initiative 4. Stress‐to
Page 114 and 115: (mycotoxins) also contaminate grain
Page 116 and 117: CIMMYT and IITA breeding programs a
Page 118 and 119: Institutional weaknesses affecting
Page 120 and 121: Research and development partners C
Page 122 and 123: What's new in this initiative? Dro
Page 124 and 125: Gerpacio, R.V. and Pingali, P.L. 20
Page 126 and 127: gain per year. The physiological ba
Page 128 and 129: Intellectual property management of
Page 130 and 131: Other producer‐ or consumer‐rel
Page 132 and 133: considered “women’s” crops, a
Page 134 and 135: subtropical, mid‐altitude, transi
Page 136 and 137: mycotoxin monitoring capacity of re
Page 138 and 139: 4. Hubs and protocols to phenotype
Page 140 and 141: Assuming that low‐cost storage fa
Page 142 and 143: Mugo, S., Likhayo, P., Karaya, H.,
Page 144 and 145: More than two‐thirds of the globa
Page 146 and 147: Commercial QPM seed is currently av
Page 148 and 149: Outputs 1. High‐throughput and lo
Page 150 and 151: Linkages with other SIs SI 7 will m
Page 152 and 153: Meenakshi JV, Johnson N, Manyong V,
Page 154 and 155: Compared with the genomes of other
Page 156 and 157: Breeding programs will achieve more
Page 158 and 159: Strategic Initiative 9. New tools a
Page 162 and 163: o Generating predictive power of ha
Page 164 and 165: generated from CIMMYT and IITA bree
Page 166 and 167: Strategic Initiatives 1-9. Summary
Page 168 and 169: Techniques of good quality seed pro
Page 170 and 171: Annex 1. Population, poor and maize
Page 172 and 173: Bolivia, CIF Botswana, Department A
Page 174 and 175: Swaziland, Ministry of Agriculture
Page 176 and 177: India, Meerut, Sardar Vallabah Bhai
Page 178 and 179: Uganda, NASECO Seeds 1996 Ltd Ugand
Page 180 and 181: Annex 3. Impact pathways for MAIZE:
Page 182 and 183: Main outputs of MAIZE SIs 4. Instit
Page 184: Annex 4. CIMMYT maize mega‐enviro
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