ICRISAT Annual Report 2009

 

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Over the past few decades, major advances in the field of information technology coupled with advances in genomic technologies, have led to more efficient applications of genomics in crop improvement programs.

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aerial view of icrisat headquarters patancheru india all photos in this publication are copyrighted to icrisat.

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contents message from the director general message from the chairman food security and diversification in the drylands bioinformatics tools for molecular breeding orphan legume crops are not orphan anymore pearl millet diversity in west africa stalking striga the cereal killer understanding the drivers of development the west africa seed alliance wasa assessing the watersheds of china and india nourishment from nutriplus about icrisat icrisat governing board 2009 financial summary icrisat ratings under the cgiar performance measurement system icrisat senior staff and collaborative staff members partnerships publications and awards development investor partnerships initiated in 2009 research scholars during 2008 research scholars during 2009 workshops conferences meetings during 2008 workshops conferences meetings during 2009 training courses during 2008 training courses during 2009 publications list available on cd version icrisat in the news awards 2009 2 3 6 8 10 12 14 16 18 20 22 24 26 27 31 44 48 54 58 61 65 70 71 72 included here as these reports were not published in the 2008 annual report due to a change in the publication date icrisat annual report 2009

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message from the director general z eno the greek philosopher who died in 264 bc said the goal of life is living in agreement with nature reminding us that although we live in a diverse world with diverse needs it is imperative that we live in harmony with nature however the unabated loss of biodiversity taking place today reveals the imbalance between human needs and nature s capacity loss of genetic diversity could endanger agriculture the irish potato famine and the soviet wheat loss are striking examples while effective conservation efforts begin in the fields forests and watersheds complementary governmental efforts are also needed as is international cooperation given the global nature of the biodiversity crisis general interest in biodiversity has grown rapidly in recent years in parallel with the growing concern about nature conservation largely as a consequence of natural habitat loss degradation and the extinction of species it is our duty to safeguard the variety of life on earth icrisat s mission is to reduce poverty enhance food and nutritional security and protect the environment of the semi-arid tropics by empowering the poor through partnership-based science with a human face our report for 2009 portrays our multipronged efforts to ensure food security in the semi-arid tropics biotechnology and bioinformatics facilitate giant steps in research and we employ these modern science tools to delve into the mysteries of genetics towards creating new and more vigorous crop varieties while we are still trying to overcome an old enemy in the dreaded striga weed we are also elated with our partnership successes and the resultant improved varieties not only are we developing improved varieties of food crops we are also providing the infrastructure for development of healthy foods through our agri-science park our efforts in natural resource management are fostering diversified vegetation in hitherto barren lands drawing attention from governments who seek our expertise to help develop viable watersheds at the community level our seed systems promise the availability of good seed for the poor farmer and of course our research is guided by the village dynamics studies that help us to focus on our mission the cgiar is going through a change process and although the framework for the new cgiar is laid there is still an air of uncertainty about the role individual centers will play have we done our part to make our strengths known how relevant will we be in the future whatever the final analysis we know that we must play a larger role in strengthening capacities reducing poverty and enhancing livelihoods we recognize that our interventions will not necessarily be limited to mandate crops but we are certain that it is our mission goals that will finally guide our actions the institute is in the process of mapping out a new strategic plan to 2020 the conservation and use of mandate crop biodiversity is a high priority as always we acknowledge the support and guidance given to us by our governing board our donors our partners and the immense loyalty and hard work of our staff members who contribute to the fulfillment of our mission william d dar director general 2 icrisat annual report 2009

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message from the chairman n the one year that i have been board chair i have witnessed the enormous mission of icrisat to help empower 600 million poor people to overcome hunger poverty and a degraded environment in the dry tropics through better agriculture in that short period i have also been very impressed with the successes of team icrisat president dwight d eisenhower famously said farming looks mighty easy when your plow is a pencil and you re a thousand miles from the corn field the complexity of agricultural research the very real problems faced by poor farmers and the enormity of our responsibility to use science to find solutions hits home when one takes a close look at the activities of agricultural research institutes such as icrisat one of my heroes the novelist douglas adams once said it is a mistake to think you can solve any major problems just with potatoes icrisat does not claim to be a problem-solver with just its scientific research i am very proud of the fact that icrisat has pursued strategic partnerships to both develop agricultural solutions and to disseminate its knowledge and findings i laud the fact that in addition to the scientific research being done in asia and in sub-saharan africa icrisat efficiently transfers information knowledge and benefits from one continent to the other research institutes must always be looking for ways of doing things better the research thrusts must also change with changing needs and new knowledge i see that icrisat is living up to its expectations icrisat has developed climate ready crops to help poor farmers adapt i to climate change icrisat is discovering and developing alternate uses for the crops it researches icrisat is linking with partners to diversify the farming systems where necessary so long as it satisfies its mission to improve the livelihoods of poor farmers in the semi-arid tropics we have a large task ahead of us we must remember the 600 million poor people we have committed to help i would like to paraphrase the words of the chair of the cgiar consortium board carlos perez del castillo who said that agriculture is an essential element in all the crises we face today ­ food security energy crisis persistent poverty we need collective action against these global challenges we need collective responsibility and collective ownership i am confident that icrisat and its excellent leadership is up to the task and extend my very sincere and best wishes to the institute for success in their noble mission nigel poole chairman governing board icrisat annual report 2009 3

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vision improved well-being of the poor of the semi-arid tropics mission to reduce poverty enhance food and nutritional security and protect the environment of the semi-arid tropics by helping empower the poor through science with a human face goal to mobilize with partners cutting edge science and institutional innovations for poverty alleviation food security human development and environmental protection for poor rural families in semi-arid production systems of asia and sub-saharan africa 4 icrisat annual report 2009

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food security and diversification in the drylands

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bioinformatics tools for molecular breeding data capture through handheld electronic fieldbooks the first step in the journey to icis ver the past few decades major advances in the field of information technology coupled with advances in genomic technologies have led to more efficient applications of genomics in crop improvement programs today large and complex sets of data are being routinely generated bioinformatics tools for the capture curation integration and analysis of these large volumes of data are therefore a necessity for increased efficiency and improved quality within the molecular breeding process to efficiently manage the extensive amounts of information generated by icrisat and its partners a number of bioinformatics tools are currently being developed and implemented these tools and technologies are part of the analytical pipeline being developed under the integrated breeding platform ibp of the cgiar s generation challenge program gcp o crop information systems chickpea and sorghum implementations of the international crop information system icis are currently being evaluated for the management and integration of global information on genetic resources and germplasm improvement icis provides for the integration of phenotypic traits and genotypic genes information which is crucial for modern breeding electronic data capture through handheld electronic fieldbooks is also being implemented in collaboration with other gcp `crop lead centers established as a part of the ibp laboratory information management system one of the major constraints in molecular breeding projects is the timely and accurate availability of information from the laboratory to scientists who may be geographically dispersed icrisat has developed a highly customized workflow 6 icrisat annual report 2009

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based laboratory information management system lims that allows efficient tracking of samples in the genomics laboratory as well as availability of the data to collaborating scientists through the internet the lims ensures that the process of collecting genotypic information is validated and traceable for quality assurance purposes it also facilitates standardization of protocols and methods within the laboratory reviewing the development of the ismab system information system for marker-assisted breeding data visualization is becoming critical in agricultural research because of the large amount of complex data generated in genomics and crop breeding a major challenge in crop improvement programs is in interpreting and decision making from large data sets that combine information on genotypes phenotypes and environments visual analytics allow breeders to view their information in a graphical environment where they can more easily understand the relationships underlying the data identify trends and patterns and make discoveries based on information visualization the information system for marker-assisted breeding ismab focuses on visualization of marker-assisted backcrossing experiment datasets to provide a workbench that can integrate information from various experiments across generations and identify the best individuals by visual analysis computational architecture molecular breeding projects have an inherent requirement to connect to various sources of publicly available information and databases in order to facilitate the querying and interaction between and across databases as well as species especially within the ibp a layer of computational architecture is being developed collaboratively this is based on a consensus blueprint of a scientific data model as well as standardization through common and controlled vocabularies ie so that a pearl millet panicle can be equivalent to a sorghum head crop vocabularies for sorghum and chickpea have already been developed at icrisat and these are now being used to further develop trait dictionaries to be used within the crop information systems mentioned above due to the specifics of different crops and breeding schemes there is no one-size-fits-all solution however with the current tools under development at icrisat and the collaboration with a consortium of partners through the ibp a learn-by-doing approach is proving most useful in designing data management and informatics for molecular breeding analyzing and managing complicated breeding data has become a demanding issue for the community of plant breeders data sources and software applications developed at icrisat will help breeders to keep track manage and efficiently analyze large amounts of data generated in breeding programs these tools will also help to interpret large and complex data sets by combining information on genotypes phenotypes and across multiple environments and different generations understanding the relationship underlying the data identifying trends and patterns and making new discoveries by analyzing breeding data in silico will definitely benefit the crop improvement programs in realizing their goals to accelerate the rate of genetic gain and lead to more productive varieties in a shorter time icrisat annual report 2009 7

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orphan legume crops are not orphan anymore a scientist inspecting the development of a high density marker array being held by a research technician l egumes are the third largest family among flowering plants accounting for 27 of the world s crop production with grain legumes eg beans chickpea groundnut lentils peas peanut/groundnut alone contributing 33 of the dietary protein needs of humans grain legumes are also a rich source of essential vitamins minerals and important amino acids grain and forage legumes are grown on some 190 million hectares and their production is about 300 million metric tons globally however legumes are often grown in marginal environments of the semi-arid tropic sat regions by smallholder farmers where the production of these crops is heavily challenged by a range of biotic and abiotic stresses researchers have been working for many years to improve crop productivity by using traditional breeding strategies and better crop management practices and several improved varieties including hybrids eg pigeonpea have been developed by icrisat and its partners still we need to increase the speed at which we can develop better varieties and icrisat believes that one way to accomplish this is through the application of modern genomics 8 importance of genomic interventions in legume breeding recent advances in the area of genomics offer several opportunities to enhance breeding for many biotic and abiotic constraints that affect crop production while a significant amount of genomic resources have been developed for a few legume species most of the legume species important in the sat have not had sufficient resources for modern breeding approaches as a result these legume crops were often referred to as orphan crops however during the last five years as a result of several national and international initiatives concerted efforts have been made to develop genomic resources in the legume crops of the sat and as a result these crops are now turning into resource-rich crops use of next generation technologies novel sequencing technologies such as roche 454 flx and illumina/solexa are being used to sequence the genes of chickpea and pigeonpea using 454 flx sequencing over 100,000 chickpea and nearly 500,000 pigeonpea gene sequences have been icrisat annual report 2009

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generated further analysis of these sequences has resulted in over 100,000 tentative unique sequences for chickpea and over 125,000 sequences for pigeonpea similarly the illumina/solexa sequencing approach has resulted in around 120 million sequences for chickpea and 180 million sequences for pigeonpea efforts are now underway to assemble all of the sequence data into a genome map for chickpea and pigeonpea just a few years ago this would have seemed impossible for such species but today it is a reality icc 4958 icc 1882 total rna of the variation for several root traits efforts are now underway at icrisat to cross this major root trait qtl into three elite chickpea lines jg 11 chefe and kak 2 in collaboration with egerton university kenya ethiopian institute of agricultural research eiar ethiopia lake zone agricultural research institute lzari tanzania and indian institute of pulse research iipr india erstwhile orphan legumes have a prosperous future next generation sequencing clearly significant progress has been made towards developing genomic resources in model species medicago and lotus alignment with ta advances in trait mapping major legumes soybean and molecular breeding common bean and peanut given the low level of as well as so called orphan thousands of snps genetic variation and crops cowpea chickpea and a paucity of molecular pigeonpea while some legume markers the development crops now enjoy the availability selection of hundreds of of dense genetic trait maps of initial genome sequences eg informative snps were difficult for the sat soybean medicago and lotus legumes however with the legume species important in the development of large-scale sat regions now have appropriate genomic resources described numbers of molecular markers above it has been possible and genetic maps for use in to develop the genetic maps breeding and research programs development of illumina goldengate assay with sufficient marker density similarly large amounts of for example a genetic map genome and gene sequence data has been developed using is available for several legume a segregating population crops and will be expanded application in genetics and breeding of cultivated groundnut several fold in the coming combining this map with years due to increasing use of data from field experiments next generation sequencing technologies analysis and use of this `tsunami of that analyze the effects of drought on the genomic information is going to be an even more population has indicated that drought tolerance challenging task than generating the resources in the in groundnut is controlled by many genes termed first place icrisat and its partners are up to this task quantitative trait loci or qtl each contributing a and look forward to continuing the efforts to apply the small amount of drought tolerance on the other best technology in the improvement of crops critical for hand qtl analysis for root traits in a population the livelihoods of smallholder farmers in the semi-arid of chickpea has revealed a single genomic region tropics that contains several qtl contributing up to 36 millions of transcript tags solexa tags icrisat annual report 2009 9

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pearl millet diversity in west africa diversity of wca pearl millet panicle traits note the 12 inch scale for comparison earl millet [pennisetum glaucum l r br is a highly stress-tolerant staple cereal grain for the hottest driest regions of sub-saharan africa and south asia west and central africa wca is the primary centre of origin and diversity for pearl millet the picture above illustrates the tremendous diversity of local pearl millets in wca for panicle characters representing also different ecotypes as all these ecotypes are cultivated in wca the picture also illustrates the diversity of farmer preferences and that there is no `one size fits all regarding farmer-preferred pearl millet cultivars in wca genetic diversity is the capital of each breeding program the icrisat-wca pearl millet improvement program together with its nars partners in burkina faso mali niger nigeria and senegal aims at a better understanding and use of the wca pearl millet diversity in the development of improved farmer-preferred cultivars thereby diversity is studied and exploited at different levels understanding the extent of phenotypic diversity and geographic differentiation and promoting regional germplasm exchange within the frame of the bmz-funded project mobilizing regional diversity 424 pearl millet landraces from all over wca were characterized in burkina faso mali niger nigeria and senegal the landraces revealed wide ranges for all morphological agronomic and resistance traits p assessed from these characterization trials each participating country identified promising landraces for breeding and morphologically contrasting germplasm groups for crossing this resulted into important diversification of breeding materials in each partner country linking phenotypic observations to the geographic origin of the pearl millet landraces revealed certain patterns of geographic differentiation flowering time was correlated to latitude reflecting higher frequency of early flowering accessions in the north and later flowering accessions in the south corresponding to the rainfall patterns in the region but the correlation is rather loose as two types of millets are usually grown in the wetter south ­ early millets to cover the `hungry period and late-maturing ones for higher productivity geographic differentiation for panicle length revealed two main groups 1 longer panicle accessions originating from west niger north-east benin north burkina faso and senegal and 2 shorter panicle accessions originating from east niger west benin cameroon central african republic south burkina faso and mali enhancing heterozygosity intra-genotypic diversity through heterotic grouping being highly allogamous outcrossing the natural stage of pearl millet is heterozygous ie it needs to have two different alleles at most of the genome loci to be performing the degree of heterozygosity in pearl millet cultivars can be enhanced by crossing 10 icrisat annual report 2009

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genetically distinct materials to identify genetically distinct parental materials heterotic groups were identified for wca pearl millet landraces in the bmz-funded project mobilizing regional diversity heterotic groups represent germplasm groups that are genetically distinct from each other and that produce superior hybrids when crossed the heterotic grouping was done through the study of agro-morphological differentiation and the characterization of genetic diversity at the dna level via molecular markers heterotic groups identified via diversity analysis were then validated through multi-location evaluation of putative intraand inter-pool crosses this enables identification of the optimal genetic distance among parental materials for attaining maximal hybrid vigor in pearl millet the detection and use of heterotic pools provide a basis for sustainable breeding of both open-pollinated and hybrid cultivars as both types profit from heterozygosity and hybrid vigor a first fruit of the heterotic grouping is a cross of genetically distinct landraces from niger and senegal tiouma × souna that revealed outstanding performance and high farmer-preference indices in on-station and on-farm trials in niger studying intra-varietal diversity as mechanism of adaptation to variable climates local landraces of pearl millet are not uniform but rather highly heterogeneous data gained from full-sib selection trials funded by the ifadpromiso project revealed that pearl millet landraces from niger dispose significant genetic variability eg for flowering time differences between the earliest and the latest full-sib families derived from the same landrace were 16 days at minimum in bondabia landrace and 39 days at maximum in bazagome such an intra-varietal diversity for adaptation traits can reduce the vulnerability of the landrace eg in the case of a dry spell not all plants will be hit in their most sensitive stage and therefore enhance yield stability it may not be by chance that wca pearl millet landraces are displaying such a populational buffering mechanism against environmental variability as this characteristic has evolved during farmers selecting their preferred varieties in participatory selection trials thousands of years of natural and human selection it must bear some advantage for survival grain yield performance and stability therefore plant breeders must also question how much genetic heterogeneity is desirable or necessary to obtain improved stable varieties that are able to out-yield local cultivars under extreme and variable growing conditions such as in the sahel offering diversity to the diversity of farmers and farming conditions growing conditions and farmer preferences in wca are highly diverse therefore icrisatniamey works together with partner nars in a mcknight-foundation­funded project to develop efficient participatory population improvement methodologies the aim is to offer diversity to the diversity of farmers the approach includes community management of diversified pearl millet populations and training women and men to select within these populations for target traits according to their specific production objectives this participatory breeding research contributes to development of farmer-preferred cultivars to maintenance of genetic diversity in farmers fields and even tries to develop concepts for in-situ conservation of crop genetic resources 11 icrisat annual report 2009

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stalking striga the cereal killer two views of an on-station trial showing the combined effect of sorghum resistance intercropping and organic amendments right compared to the control left urple witchweed the very name has a mysterious menacing ring to it this is the common name of striga hermonthica the dreaded parasitic weed that infects and feeds on the roots of cereal crops and wild grasses and commonly referred to as striga s hermonthica is arguably the most important biological constraint to production of rainfed cereals of the semi-arid tropics sat in sub-saharan africa it thrives in fields with a high frequency of cereal cropping and very low soil fertility attacking pearl millet sorghum maize and upland rice the effect of the parasite on these crops is devastating and yield losses for pearl millet and sorghum are estimated at between 40-80 where infestations are high a single mature striga plant can produce up to 200,000 tiny dust like seeds that will spread easily with contaminated crop seeds farm tools wind water and animals and that may stay viable in the soil for up to ten years or more many potential options to control striga have been developed through research efforts in the last 30 years fig 1 despite these efforts adoption of 12 p control options by farmers has been limited and the infestation area and density of striga has increased on the one hand options such as mineral fertilizer and resistant varieties are not readily available to farmers and on the other hand many farmers are not aware of the available options intercropping cereals with legumes at a high density furthermore some options may not be effective or practical for farmers if applied as a single control method while any individual technique may not be effective a combination of options could reduce the striga population to manageable or even acceptable low or no damage levels providing increased crop yields and profitability of the cropping system research to find effective control options for an integrated striga and soil fertility management issfm strategy is necessary to improve adoption by farmers icrisat efforts icrisat and its partners in mali niger and nigeria are using on-station breeding and experimentation modeling and participatory on-farm research to develop effective applicable and profitable issfm icrisat annual report 2009

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1 resistant host-cultivars 12 prevention 2 intercrop host/non-host 11 biological control 3 rotation non-host 10 herbicides integrated striga management 4 weeding 9 herbicidecoated crop seed 5 organic amendments icrisat annual report 2009 fig ur e1 8 delayed sowing 6 fertiliser 7 deep sowing po ten tia m l contr her ol strategies for s ca thi on strategies for resource-poor farmers in the west and central africa region icrisat is also searching for and selecting sources of resistance to striga in pearl millet in sorghum good striga resistance found in a poorly adapted variety is being introgressed into farmer-preferred varieties using marker-assisted selection to produce adapted farmer-preferred striga resistant varieties striga resistant sorghum and pearl millet varieties will become an essential part of an issfm strategy fig 1 through on-station experimentation the efficacy of single and combined control techniques to increase crop yields and decrease striga seed bank densities the reserve of the viable seeds in a given volume of soil is being studied results from trials on sorghum indicate that there are clear benefits to the combination of control methods as compared to single control methods in terms of crop yields and s hermonthica control pictures on previous page data obtained from on-station trials will feed into a striga seed bank model to simulate and forecast long-term striga population dynamics and potential cereal crop yields already from simulations it is apparent that rigorous control of striga seed production is necessary to prevent striga population explosions and eventual damage to crop yields this stresses the importance of intensive monitoring of fields by farmers to prevent escaping s hermonthica plants from producing thousands of tiny seeds and infesting the field for years to come overcoming constraints to application besides efficacy of control options there are other constraints to the adoption of issfm by farmers such as limited knowledge and socio-economic results of a participatory cost-benefit analysis of issfm and farmer practice for a rigorous evaluation of issfm under farmer conditions constraints farmers are not always knowledgeable about the biology of striga its damaging potential for the cereal crop and the options for control this limited knowledge about the available control options and their effects is a very important constraint to the control of this parasite and the application of issfm by farmers to develop and test the efficacy of the issfm strategy we have found that it is best to apply and evaluate the strategy with the farmers themselves in their own fields to this end icrisat uses the cluster based farmer field school approach this approach provides a platform for farmers and scientists to exchange knowledge on striga biology and control options and to conceptualize and develop practical issfm strategies farmers are guided by the scientists in experimentation and observation of the striga control and evaluation of the strategy in agronomic and economic terms see picture above farmers in turn provide practical knowledge that catalyzes the innovative process in the search for efficient practical and profitable ways to control striga and improve soil fertility all these activities will lead to a broad range of information and data that is currently being gathered by icrisat and its partners a thorough analysis will enable us to understand the technological cognitive and socio-economical bottlenecks to the application of issfm by farmers and how to overcome these together we hope that one day africa could be free of the purple witchweed scourge 13

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