Part II
Pursuing the Vision and Strategy

Chapter 3

Producing more and better food at lower cost through genetic improvements (System Priority 2)

Maintaining and enhancing yields and yield potential of food staples (Priority 2A)

Staple food crops of the SAT

ICRISAT mandate crops – sorghum, pearl millet, chickpea, pigeonpea and groundnut – are important for ensuring future food nutritional security and enhancing the livelihoods of poor people in the SAT. Of the global sorghum area of 43.7 M ha, Africa accounts for 57% (25 M ha) and Asia 26% (11.2 M ha). Globally 34.6 M ha of millets (pearl millet + minor millets) are grown, of which Africa accounts for 20.9 M (60%) and Asia 12.1 M ha (35%).

Chickpea (11.2 M ha globally) is mostly grown in Asia (10.2 M ha, including Central Asia and West Asia), with around 0.5 M ha cultivated in the African continent. Similarly pigeonpea is grown mostly in Asia (4.1 M ha, 90%), although Africa has 0.4 M ha of pigeonpea. Groundnut (24.6 M ha) is much more widely distributed across continents, with Asia accounting for 54% of area (13.3 M ha) and Africa 42% (10.2 M ha).

Enhance the capacity and efficiency of genetic improvement programs through approaches linking characterization and use (Priority 2 A: Specific Goal 1)

Overview

ICRISAT believes in the potential of biotechnology to enhance the speed, precision, efficiency and value addition in many aspects of its crop improvement efforts. This is especially true in addressing the complex traits that have remained intransigent to conventional breeding approaches. In addition, many of the crops under ICRISAT's mandate have had little attention paid to them, especially in the biotechnology arena. Where possible we will seek the assistance of other advanced scientific partners who may have greater access to appropriate knowledge or technology, for example, in the transformation or mapping of sorghum or pearl millet.

Specific target traits and crops are determined in collaboration with other crop improvement specialists and with ICRISAT's many partners. These close interactions ensure that the highest priority traits are being addressed in each crop, as well as the most appropriate technologies are being used in each case. In certain instances, a high priority trait may not be a high priority for biotechnology applications given available conventional solutions and/or a lack of biotechnology approaches.

Potential impact: All breeding efforts using biotechnological tools will improve the rate and efficiency of bringing new genetic resources to the continuing fight against rapidly evolving fungi, bacteria, andviruses that are the casual agents of many biotic stresses. As such they are useful tools for the breeding community that will grow in importance over the next decade.

Predominant capability: ICRISAT is one of the very few organizations in the SAT which are capable of running a full scale, broad spectrum biotechnology project. With a dedicated genomics laboratory with an annual capacity of 1 million DNA samples per year and comparable laboratory and staff in wide crossing, genetic engineering and bioinformatics plus access to the SAT principal genebank for ICRISAT mandate crops and substantive field facilities for accurate phenotyping --- ICRISAT rightly claims that it exercises a predominant capability in this research area.

Counterfactual: The absence of ICRISAT's biotechnology activities would have a major effect in reducing the present and future efficiency of cereal and legume breeding programs for semi-arid environments in Africa and Asia which would in turn significantly compromise the likelihood of the achievement of MDG 1.

Wide crosses

Currently, ICRISAT has good techniques for embryo rescue, culture and plant regeneration for chickpea, pigeonpea and groundnut. These provide options to develop intra- and inter-specific hybrids and backcross materials in each of these crop species. The program will focus on producing hybrids that require significant laboratory techniques (e.g., embryo rescue, chromosome doubling). Inter-specific crosses in chickpea will be developed and evaluated for insect resistance as natural levels of resistance are lacking. Inter-specific crosses in pigeonpea will be evaluated to provide additional genetic diversity for several traits, as the molecular evaluations have indicated extremely low levels of diversity within the cultivated species. In groundnut, specific attention will be given to producing “synthetic groundnut” germplasm. Being a tetraploid (AABB genome), it is feasible to cross the AA and BB genome species to “recreate” the conventional tetraploid species. Such an approach has been extremely successful in other polyploidy species such as wheat, and would produce tremendous diversity for further backcrossing and selection for numerous traits of interest.

Specific objective: Enhance the genetic diversity of ICRISAT's crops through the introduction of genomic segments from wild species.

Outputs and outcomes to 2015

Outputs:

Outcomes:

Structural and functional genomics

The major objective of structural and functional genomic applications is to identify, isolate and manipulate genes for traits of interest in ICRISAT's mandated crops. To accomplish this, it is necessary to have a number of genomic resources available. Molecular markers of various types (e.g., RFLPs, AFLPs, SSRs, SNPs) are necessary for analyzing the molecular diversity in a species, and for locating specific genes and QTLs in the genome. Markers such as AFLPs can be developed from generic resources available commercially, while markers such as RFLPs, SSRs and SNPs require significant investment to develop. For ultimate ease of use in breeding, marker types based on simple PCR techniques (SSRs, SNPs) are desirable. The availability of each of the more important marker types for each mandated crop is listed in the table below.

For crops such as sorghum and chickpea, a large number of molecular markers are already available and the number is expected to continue to increase, especially for sorghum where it has recently been announced by the US Department of Energy that the sorghum genome will be sequenced starting in 2006. Pearl millet and groundnut have a number of markers available, although a much larger number is required to provide adequate coverage of the genome. For pigeonpea and most of the minor millets, the number is extremely limited and considered inadequate for most mapping and breeding purposes.

Molecular markers can be developed via a number of different strategies (e.g., from EST and/or BAC libraries). The specific strategy to be employed will depend on the status of various other genomic resources in the targeted species. In some cases, it will be desirable to target specific genomic regions to saturate a region known to contain gene(s) of interest. Some targeting could benefit from a comparative approach using a species such as rice, maize or soybean that have available high-density maps. It is envisioned that marker development would be developed in partnership with public (and private) collaborators in developed and developing countries (e.g., sorghum and pearl millet with USA; chickpea and pigeonpea with India; groundnut with Brazil, India and USA).

Specific objective: Public availability of genome-wide molecular markers for ICRISAT's crops for use in molecular tagging and selection programs.

Outputs and outcomes to 2015

Outputs:

Outcomes:

Gene/QTL mapping

A major application of genomics is the use of molecular markers as indirect selection tools in a breeding program. Essentially, the goal is a better prediction of a particular phenotype from a determined genotype. To accomplish this, it is necessary to determine molecular markers that have a high predictive value for a particular phenotype or trait. Development of such markers requires that:

Priority traits have been identified in collaboration with the Regional Programs and Crop Improvement Global Theme. In most cases, adequate phenotyping methods are available, although for some traits such as drought and salinity, these will be firmly established by 2007. Contrasting germplasm for use in developing segregating populations are available and in many instances, the required populations at various levels of inbreeding are available. Statistical packages for analyzing the molecular and phenotypic data are available and are being incorporated into a bioinformatics system (iMAS) to allow efficient handling of these datasets.

Specific objective: Public availability of reference maps and identified linked molecular markers for traits/genes of interest in ICRISAT's crop species

Outputs and outcomes to 2015

Outputs:

Outcomes:

Marker-assisted selection (MAS)

Ultimately, the goal of identifying linked markers is their use as indirect selection tools in the breeding programs. In addition to the identified linked markers, it is necessary to have a low-cost, high-throughput marker service facility and often to consider alternative breeding strategies to most effectively incorporate molecular approaches. The Global Theme will continue to evaluate marker methods and adopt those that provide lower cost and higher throughput. At the moment, SSR markers are considered appropriate for most species. It is predicted that SNP markers may become attractive in the next few years and technology will need to be established in-house. A major limitation in MAS is the cost to select for the recurrent genome in the backcrossing programs (normally, only markers linked to the trait/gene of interest are used). Chip-based technologies such as DARTs or chip-based genotyping may provide an effective system and will be evaluated for possible use. As MAS becomes a routine strategy, it will be necessary to establish a Service Lab to provide the high-throughput marker services on-demand to the breeding programs.

Specific objective: Marker-assisted selection for multiple traits of interest in crops

Outputs and outcomes to 2015

Outputs:

Outcome: Partner breeders make enhanced use of markers globally to improve the efficiency of their breeding programs

Genetic engineering

For effective genetic engineering of any crop, it is necessary to have a number of tools available. These include:

ICRISAT is fortunate in that most of these issues are ether available or are being addressed. The only current limitation is an effective transformation system for sorghum and pearl millet, although such systems do exist in other laboratories and ICRISAT has used biolistic transformation to produce a few transgenic sorghum lines. A strength of ICRISAT is its ability to transform chickpea, groundnut and pigeonpea using an Agrobacterium transformation system. Appropriate biosafety containment greenhouses are available, and options for increasing the number of these do exist given appropriate resources. ICRISAT has also had experience with the initial field evaluation of transgenic chickpea, groundnut and pigeonpea on its campus at Patancheru, Andhra Pradesh, India. A number of biosafety applications have been submitted and all approved by the internal and Indian biosafety committees.

Efforts to date have focused on developing transformation systems and gaining experience in the evaluation of transgenic materials under approved greenhouse and field conditions. A number of traits have been targeted with various genes and promoters. Successful incorporation of these genes into the target species has been accomplished and greenhouse and field trials conducted for many. Some genes have been determined to be promising and will be selected for product development. This will require the production of a large number of transgenic events, effective phenotypic and molecular screening of these, small and large-scale field trials for target trait and agronomic performance, and the development of the required regulatory dossiers.

Specific objective : Effective, commercializable and farmer-friendly transgenic events for high priority traits

Outputs and outcomes to 2015

Outputs:

Outcomes:

Bioinformatics

ICRISAT and its partners have generated extensive information on the genetic resources of its mandated crops. Recent and emerging developments in modern science, especially molecular genomics, have led to the generation of large datasets of genotypic and phenotypic information. In addition, enormous quantities of data already exist in databases and files generated by researchers for their own use. To be of optimal use by all scientists working on these crops and other crops specific to the semi-arid tropics, all of this data must be collated and made accessible. Therefore, a major focus of the bioinformatics efforts will be to develop an information management system that provides the required entry, query and access interfaces to meet the demands of ICRISAT globally.

Currently, a workflow laboratory information management system (LIMS) is available that manages sample tracking of DNA through the genotyping process. The genotyping data from this system flows into a database (ICRIS) that has user interfaces for retrieving and generating simple reports from the genotypic data. Future efforts will focus on enhancing the existing LIMS and ICRIS systems with additional functionality and user interfaces. By 2010, it is projected that this system will be in place and functioning in ICRISAT's global locations.

Specific objective: Public, web-accessible crop information system for ICRISAT's mandated species.

Outputs and outcomes to 2015

Outputs:

Outcome: Researchers and other partners worldwide have the ability to access and use information on ICRISAT's crops

Identification and development of pro-poor traits in crops (Priority 2 A: Specific Goal 2)

Potential impact (generic): The potential impact of ICRISAT improved germplasm for its five mandate crops in the public domain is exemplified by the very high proportion of newly released, improved cultivars worldwide that contain significant proportions of ICRISAT-bred material. This is mirrored by ICRISAT's major contribution to capacity building in this field worldwide. These two factors make a substantial contribution to the potential achievement of MDG 1.

Predominant capability (generic): ICRISAT's crop breeding experience in all it's mandate crops now exceeds thirty years in most instances and this incorporates experience from all the main crop growing environments in sub-Saharan Africa and South Asia. This is coupled to its expertise in biotechnology, its unique germplasm banks and extensive field facilities for the development and testing of improved parental gives it a clear advantage to undertake development of varieties and hybrids both conventionally and biotech-assisted breeding in SAT environments.

Counterfactual (generic): Should ICRISAT cease its hybrid and varietal breeding programs in its five mandate crops, the impact on partner breeding programs would be very substantial. Breeding progress in such crops would be much slowed down, less biodiversity would be used and the probability of new, improved material being treated as IPGs would be strongly diminished. The capacity and knowledge base of partner institutions to undertake this type of research would be diminished and the global crop improvement networks contributed to by ICRISAT would not function as well as at present. Thus the likelihood of MDGs 1 and 8 being achieved would be severely threatened.

Sorghum is a staple crop for millions of poor farmers in the SAT regions of Africa and Asia. Sorghum yields have decreased by 14% during the 1980s, before rising slightly in the 1990s. Production has been stagnant in many sorghum-growing countries in Asia, despite adoption of improved cultivars and crop management practices mainly due to a shift of the sorghum crop to marginal lands with poor soils (replaced by soybean and maize). Sorghum is a staple crop in the diet in all the major growing areas (ranging from 20 kg to 120 kg per capita per year). However, per capita consumption is declining due to a shift in consumer preferences brought about by subsidy for rice & wheat, urbanization, and non-availability sorghum products (flour) in the markets. A portion of sorghum grain is used as animal feed, while the green fodder and stover are fed to cattle. Demand for fodder and grain for animal feed is increasing due to increased demand for milk, egg and meat. Sorghum grain is also used in making alcoholic and non-alcoholic beverages. Other alterative uses of sorghum include processed foods (bread, biscuits, etc.) and starch for industry. Sweet sorghum is emerging as a renewable source of ethanol for the biofuel industry.

Asia

As a result of release of 50 varieties (+ around 40 hybrids in India alone) by national programs using ICRISAT-bred germplasm, production has been stabilized using less land area. However, if sorghum has to remain as a competitive crop, crop productivity and stability (by incorporating resistance to major pests and diseases) needs to be enhanced.

Eastern and Southern Africa

West and Central Africa

Outputs: Annually, hybrid parents and varietal material with improved traits to counteract the principal constraints to sorghum growth and productivity in the SAT.

Pearl millet is a major staple cereal for millions of poor in the SAT of Asia and Africa, grown especially in the marginal environments. It is grown in the harshest environments where maize and sorghum cannot be cultivated, and hence is important for the food and nutritional security of the poor people living in these critically dry and hotter parts of the SAT. Pearl millet grains have good storage quality, and are highly nutritious (10.6% protein) and also contribute about one third of iron and zinc requirements. Grains are mostly used for food. The crop residue is used as dry fodder for cattle and also as building materials. Area and production in WCA have been increasing slightly, but yield per ha has been stagnant. In ESA also yields have not increased because production is being pushed to marginal areas with poor soils. However, production in India has increased (5.7 to 6.9 M t) despite a reduction in area (from 12.1 to 9.4 M ha) due to increase in yield from 473 to 740 kg/ha during 1970 and 2001. Food use has declined slightly in both Africa and Asia due to availability of subsidized food, and change in food habits of people due to urbanization. A small proportion of the grain is used for poultry feed in Asia and the Americas. With increasing demand for dairy products, the demand for pearl millet fodder will increase substantially, especially in Asia.

Asia

Constraints to pearl millet production vary considerably, although it remains a low input, subsistence crop in most areas. As indicated earlier, substantial progress has been made in India by improving productivity. However, with pearl millet being relegated to marginal areas, efforts will be to sustain and increase yields by reducing losses due to various constraints. There is a noticeable trend of irrigated pearl millet production during the summer in India, and this will need increased heat tolerance during flowering and seed set. The following research areas will be emphasized:-

West and Central Africa

Past research has produced improved OPVs, and these will be popularized through appropriate seed systems. Future strategy to increase pearl millet production and marketing in WCA will be based on the IGNRM approach. Participation of all stakeholders in technology development will be essential to achieve sustainable capacity building and long term impact of R&D. The crop improvement research will focus on:

Eastern and Southern Africa

Pearl millet is a comparatively minor crop in the ESA region (2 M ha), with scattered production in areas with low rainfall and poor soils. Crop improvement efforts will be carried out in close collaboration with NARS partners in countries where this is a major crop:

Groundnut

Groundnut is an important food and cash crop for the resource-poor farmers in Asia and Africa. It is primarily grown for edible oil (48-50%) as well as for direct consumption as food by people. Groundnut haulms are excellent fodder for cattle, and groundnut cake (after oil extraction) is used as animal feed, and also helps to improve soil fertility through nitrogen fixation. It contributes significantly to household food security and cash income through sale of groundnut products. Groundnut productivity in WCA and ESA is below the world average yield of 1.4 t/ha. Although the groundnut productivity in Asia (1.8 t/ha) is above the world average, it is still lower than the yields in developed countries (3 t/ha). Area under groundnut in ESA has increased dramatically from 2.3 to 3.3 M ha during 2000 to 2004; in Asia also there is an increasing trend in China and Vietnam, but a decline in India during 1991-2004. There is slight decline in area in WCA. Although the productivity globally has shown a positive trend, much more needs to be achieved in future.

Asia

The overall projection for area, production and productivity for groundnut in Asia is positive. However, further increase can be possible through both genetic and crop management to address production constraints:

.Eastern and Southern Africa

• Developing early maturing cultivars for short-season environments with erratic rainfall will continue. Early-maturing Spanish varieties with fresh seed dormancy is required where the crop may be exposed to rain at maturity. In addition, we will also concentrate on medium-duration varieties for areas with good rainfall regimes and favorable growing conditions.
• Continued efforts are needed for breeding cultivars with resistance to groundnut rosette disease. Good sources of resistance are available. Combining resistance to the three factors responsible for resistance to rosette disease (GRAV, GRV, and its satellite RNA) and resistance to the aphid vector will be pursued vigorously.
• Resistance to foliar diseases (especially early and late leaf spot, and to rust) is essential in all breeding material (both short and medium duration cultivars). Some of the Arachis species have high levels of resistance to ELS and these need to be incorporated into cultivated groundnut using wide-hybridization techniques.
• Integrated management is essential to reduce aflatoxin contamination
• Incorporating drought tolerance is essential for erratic rainfall areas

West and Central Africa

Groundnut is important for food and income generation in WCA, as it generates up to 60% cash earnings and up to 70% rural employment in many countries. However, productivity and incomes have remained low due to various production constraints. Hence, genetic enhancement activities will be geared towards alleviating some of these constraints in the next decade, so that groundnut production becomes more profitable to small-holder farmers:

Outputs: Annually, varietal material with improved traits to counteract the principal constraints to groundnut growth and productivity in the SAT.

Chickpea is the third most important legume globally, and second in importance in Asia. It is also an important legume crop in Eastern and Southern Africa (Ethiopia, Kenya, Malawi, Mozambique and Sudan). About 90% of global area and 88% of production is in Asia. Chickpea has one of the best nutritional compositions of any dry edible legume, and is mainly used for human consumption. The desi type (colored seed coat) is usually de-hulled & split to make dhal or flour (Besan), while Kabuli types (white or cream colored seed coat) is often cooked as whole grain. The haulms are used for animal feed. Chickpea improves soil fertility through nitrogen fixation (up to 140 kg N ha -1 ). Chickpea area has slightly decreased globally, but has been stable at 9 M ha in Asia for the past 25 years. However, production in Asia has increased by 39% due to 32% increase in productivity. Even then, the current average yield in Asia (0.8 t ha -1 ) is low, and far below the potential yield (5 t ha -1 ), or research station yields (3.5 t ha -1 ). The global demand for chickpea in 2010 is estimated at 11.1 M t (from the current 8.6 M t). A combination of productivity enhancement through crop improvement and integrated crop management and expansion of area to new niches and production systems can help achieve this target.

In ESA, chickpea is cultivated after a cereal crop (maize, rice or wheat) and under residual soil moisture. The production in Africa has been increasing significantly as farmers embrace the idea of crop diversification. Presently, it is produced in Ethiopia, Kenya, Malawi, Tanzania and Mozambique. Large commercial enterprises, for instance Mozambique Leaf Tobacco, are interested in including eco-friendly legumes crops such as chickpea in rotation with tobacco. The major constraints in chickpea production in ESA are diseases namely fusarium wilt, and stunt virus. Helicoverpa pod borer, nematodes and bruchids are major pests whereas drought is the main abiotic stress. The strategy would be to identify specific constraints in prospective agro-ecological zone in ESA and initially evaluate germplasm from India in these production areas. Most of the constraints are being addressed at the ICRISAT, Patancheru chickpea breeding program. Advanced lines are received for agronomic performance testing and release. Later, a breeding program will be initiated in the region with backstopping from India.

ICRISAT has the global mandate for chickpea research, whereas ICARDA has a regional mandate for West Asia and North Africa. Much of the basic crop improvement for both Asia and ESA (and other continents) is conducted at ICRISAT-Patancheru. Advanced generation breeding lines are evaluated by NARS (through a Regional Program in ESA for the countries in the region) for further selection, evaluation and release for farmer cultivation:

Outputs:

Annually, varietal material with improved traits to counteract the principal constraints to chickpea growth and productivity in the SAT

Outcomes:

Partner breeders and NGO/CBO agencies in the public sector access improved germplasm at their request and improve the efficiency and quality of their breeding and seed-multiplication efforts on behalf of farmers in the SAT

Pigeonpea

In ESA, pigeonpea is cultivated as an intercrop in cereal-legume systems in which there is little or no competition for soil moisture while the cereal benefits from the fixed nitrogen. Partly because of the increase in the frequency of droughts in ESA, small-holder farmers have preferred this highly drought tolerant crop in order to secure food supplies in these situations where traditional cereal crops fail . Although ICRISAT has developed varieties with resistance to some pathogenic races of wilt disease, the presence of different races in the region has imposed limitations on breeding for resistance

Pigeonpea is sensitive to photoperiod and temperature. The period from sowing to flowering and to maturity which are important for productivity and adaptation, are both affected by the two factors. Short -duration (SD) types are relatively insensitive to photoperiod but sensitive to temperature (optimum is 24 o C), with low temperatures (<20 o C) causing significant delay in flowering and maturity, thus preventing the growing of SD in cool areas . Both medium-duration and long-duration types are sensitive to photoperiod and temperature. Long-duration lines are sensitive to temperature with high temperature delaying or inhibiting flowering, thus rendering them prone to terminal drought. In cool areas, maturity in long-duration pigeonpea is accelerated and severe competition occurs between intercropped maize whose maturity is delayed and pigeonpeas resulting in yield reduction of both crops.

The major portion of pigeonpea improvement effort is at ICRISAT-Patancheru, with limited crop improvement work (especially for photoperiod and temperature sensitivity for highlands) in ESA in Kenya. The Asia program targets hybrid parents breeding (using newly identified CMS lines) with limited varietal improvement research (for all regions globally), while ESA targets varietal development, with the possibility of hybrids in the future:

Networking and capacity building

Resources for crop breeding are declining both at the national and international institution levels, particularly in sub-Saharan Africa. Preliminary ICRISAT achievements towards pursuance of efficiency in crop breeding include --- broad delineation of agro ecological zones, stratification of sites to identify and use of only a few key representative testing sites. The strategy of engaging NARS scientists to take leadership in agreed regional activities is pursued as the lead NARS approach and also through networking of NARS and led by one NARS. This approach is expected to bring efficiency in crop improvement strategies.

Output: Sustainable regional breeding networks for cereals (sorghum and millets) and legumes (groundnuts, pigeonpea and chickpeas) established and capacity for NARS and partners enhanced.

Outcome: Countries with weak NARS breeding programs in ICRISAT mandate crops benefit from shared knowledge regionally precipitated by ICRISAT's IPG mode of collaborative action.

Improved forage and fodder cultivars

ICRISAT and its partners will contribute to augmenting income from livestock through breeding for dual-purpose cereals, legumes and oilseeds that have higher fodder yields and superior fodder quality and reduced aflatoxin content. Increase in the digestibility coefficient of fodder is directly related to higher milk yields and hence higher incomes for resource poor farmers. Recent studies at ICRISAT have shown that improvement in the yield of groundnut and sorghum haulm/stover quality has contributed to higher productivity of animal products.

Outputs and outcomes to 2015

Outputs: High-yielding forage hybrid parents and varieties, and hybrid parents and varieties with improved stover quality in elite, diverse genetic backgrounds resistant/tolerant to major biotic stresses made available for use by partners and associated capacity building measures completed

Outcomes: Hybrids and varieties bred by private and public sector organizations with improved forage/fodder yield and ruminant nutritional quality under evaluation in national trials by 2010 -2015 and capacity of partner breeder organizations enhanced

Potential impact: Cropping system diversification and increased household incomes of poorer farmers, through better exploiting opportunities for increasing animal production using improved dual- purpose food-feed crops.

Counterfactual: Reduced options for small, poor farmers to increase production and nutritional quality of animal feed reducing opportunities for diversification of household income sources.

Predominant capability: ICRISAT's joint programs with the International Livestock Research Institute focusing on improvement of fodder resources in Asia and SSA, with its unique access to crop genetic resources, excellent scientific facilities, linkages to private and public sector national programs, and focus on IPGs, can not be easily substituted for within the national programs in the SAT.

Tolerance to abiotic stresses (Priority 2B)

Abiotic stresses severely limit agricultural production. In groundnut, drought is supposed to be responsible for about 500 Million USD losses in India alone. There is a clear consensus that drought, salinity and low phosphorus availability are among the most severe stresses, in Asia, ESA and WCA. They are also those that ICRISAT crops face repetitively. The needs/challenges in the area of abiotic stress research are to:

Drought

Water capture by roots and water use efficiency are probably two of the components of yield architecture that are important for crops growing under terminal drought conditions, which is the case for most SAT crops. Drought avoidance (i.e. getting more water or using it more efficiently) will be likely to be the major trait of interest to expand the production to presently uncropped areas and post-rainy fallows in Asia.

For root traits, we need progress in understanding in those crops where roots have already proved to be beneficial for yield under terminal drought (chickpea), and then explore in those crops where little information on roots has been acquired (the other mandate crops). Specifically, there is a need to understand the dynamics of roots, how roots contribute to the overall water budget, and in particular how they contribute at the time of grain filling. Recent results by ICRISAT indicate that deeper rooting correlates with a higher harvest index (HI) in chickpea in conditions of more severe drought. Recent results tend to lead to a similar conclusion in pearl millet, where deep rooting is involved in the QTL for high panicle harvest index (thereby a link between roots, i.e. the “T” component of the yield architecture and HI).

Regarding transpiration efficiency (TE), our current state of the art is observed in groundnuts, where TE is addressed both through a MAS and a conventional breeding approach which should increase the chances of reaching our goals. The comparative advantage of ICRISAT in this area is the availability of trained manpower in India and the availability of genetic resources (in particular for roots). However, effective exploitation of this subject would probably require a quantum leap in our phenotyping capacities, as well as in the methods used to investigate root traits.

Soil salinity is an important limiting factor for crop yield improvement, which affects 5-7% of arable lands, i.e. approximately 77 M ha worldwide. Most crops are sensitive to salt stress at all stages of plant development, including seed germination, vegetative growth and reproductive growth. Legumes, in general, are sensitive to salinity, and within legumes, chickpea, faba bean and pea are more sensitive than other food legumes. The salinity problem is increasing, in particular in areas where irrigation is a common practice. Management options exist to alleviate salt effects. However, management options are often in contradiction with the immediate economic choices of the concerned farmers and crop improvement for salt tolerance appears to be the only alternative.

The problem of salinity is basically two-fold. In one case, soil is saturated with sodium (Na) and soil pH remains within an optimal range for crop growth. This type of salinity refers to coastal or dry land salinity. These are soils that get saturated with sodium because an existing saline ground water table is rising (proximity to the sea or salt that have accumulated down in the soil profile), bringing the salt at the surface. In a second case, soil is both saturated with Na (exchangeable sodium percentage, ESP, > 6) and pH has reached levels above 8.5-9.0. This type of salinity is also called transient salinity, and is thereafter referred to as sodicity or sodic soils . In this case, the sodium saturation brings about the same effect as salinity, but the high pH dramatically affects the availability of micronutrients (low availability/solubility of micronutrient salts at these pH levels), the soil structure and porosity (poor drainage, tendency for water logging, little oxygenation, because of saturation of the exchange complexes in the soil by sodium). Most studies have focused on salinity , and only a few on sodicity .

Despite the importance of salinity on the crop production worldwide, and the abundance of knowledge gathered about the effect of salinity on plant growth and development, there has been surprisingly little effort to breed for improved salinity tolerance, except a few exceptions like wheat, rice, barley, alfalfa or claims of soybean. Breeding tolerant crop varieties is therefore urgently needed.

ICRISAT´s challenge with regard to salinity is to fill the gap between the knowledge acquired on plant responses to salinity and the paucity of efforts made to breed salt tolerant crops and to increase the effort in the field of sodicity (salinity + high pH), which accounts for more than half of the saline soil, in India in particular.

Outputs and outcomes to 2015:

Outputs:

Outcomes:

Predominant capability: ICRISAT with a team of full time crop physiologists enmeshed in a greater supporting group of biotechnologists and breeders is in a strong position to undertake the difficult task of providing abiotic stress tolerance. Coupled with the availability of the unique ICRISAT germplasm collection, knowledge of the structure of the collections, controlled environments and access to rain out shelters and root study facilities gives ICRISAT the ability to tackle these tasks in a professional manner. There will be few other institutions in the SAT with capacity of competing quality. The private seed sector is not very keen on developing these products for economic reasons. Collaborating NARS have solicited ICRISAT to take the lead in developing these types of products.

Counterfactual:

Sufficient micronutrients in the daily diet are one of the prerequisites for human health. Estimates suggest that some 815 million households worldwide suffer from micronutrient deficiency. The ill effects on human health are further compounded by the quality and safety of foods that can often be contaminated by microbial toxins due to improper pre- and post-harvest conditions in the SAT.

In view of the acute malnutrition present in the SAT and to help developing countries attain food security and reduce poverty and malnutrition, it is important that ICRISAT focuses its research in developing technologies that improve the nutritional and vitamin status of its mandate crops and provides safety measures to decrease the risk of food and feed contamination by mycotoxins. This has been an area somewhat neglected globally in the past and ICRISAT seeks to become one of the World Leading Institutions in this area that is so critical for the well being of the poor.

Increase the content of micronutrients in the edible parts of plants through improved biotechnologies and breeding (Priority 2C: Specific goal 1)

Micronutrient malnutrition, often called "Hidden Hunger", is primarily the result of diets poor in bio-available vitamins and minerals, results in clinical deficiency and associated diseases such as respiratory and immunodeficiency diseases, impaired cognitive development of children, childhood diseases such as measles besides blindness and anemia (and even death). Levels of anemia in the savannah zones of West Africa are alarming, the highest being amongst children (88%) and women of reproductive age (63%). Iron deficiency is one of the most important causes of childhood anemia and zinc deficiency ranks fifth among the leading 10 risk factors in developing countries. Iron and zinc deficiency with children inhibits optimal cognitive and motor-skill development, and chances for later recovery are limited. Childhood mortality is higher, since their weakened immune systems are unable to fight off malaria and diarrhea.

Three micronutrients, Fe, Zn and beta-carotene, are widely recognized as limiting by the World Health Organization (WHO). Deficiency of these micronutrients is highest in south and south-east Asia and sub-Saharan Africa. These are also the regions where ICRISAT mandate crops are cultivated and consumed as food by large numbers of people who have poor access to formal markets and health care systems. Past programs to combat micronutrient malnutrition have relied primarily upon food fortification and to some extent on supply of vitamins and mineral pills as a readymade source. Unfortunately, these approaches have not proven to be sustainable for various reasons including lack of funds and poor infrastructure and are not able to reach all the people at highest risk of malnutrition.

The strategy for enhancing micronutrient levels in the edible parts of staple food crops has become the greatest priority to sustain nutritional security. In the past, breeding efforts in crop improvement have largely focused on genetic enhancement of yield potential and resistance to biotic and abiotic stresses. The emphasis on biofortification of staple food crops has now been initiated and is expected to be further enhanced in the coming years. The introduction of crop varieties selected and/or bred for increased, Fe and Zn, beta-carotene contents through genetic enhancement approach will complement existing approaches to combat micronutrient deficiency and can complement the ongoing benefits throughout the developing world by taking advantage of the consistent daily consumption of large quantities of sorghum, pearl millet, groundnut and pigeonpea-based diets by people at a fraction of the recurring cost of food fortification achieved during processing.

Outputs and outcomes to 2015

Outcomes:

Predominant capability: The NARS currently do not have capability or capacity for undertaking work on crop biofortification especially through transgenic approaches. ICRISAT has a comparative advantage as over the years it has built in-house capacity to undertake such product development and training in terms of human resources and infrastructure, such as well-established analytical laboratories for Fe and Zn analysis, well-equipped tissue culture and genetic transformation laboratories with optimized protocols for transgenic research.

Counterfactual: Micronutrient enhancement in food grains is not a recognized priority in the national programs of Asia and Sub-Saharan Africa. The private seed sector has not shown any interest in this area since micronutrient dense hybrids/ varieties do not add any income due to lack of brand equity of such commodities. If ICRISAT does not carry out this research, it is likely that malnutrition risk groups in developing and undeveloped countries of SAT will be deprived of cheaper and sustainable source of micronutrients.

To reduce the content of constitutive or microbial toxins in selected staples that affect quality, food safety and human health (Priority 2C: Specific goal 3)

In addition to micronutrient malnutrition, several mycotoxins contaminate the food crops of the poor in the SAT. Among them, aflatoxins, which are toxic, carcinogenic, teratogenic and immuno-suppressive substances, are produced when toxigenic strains of the fungi Aspergillus flavus and A. parasiticus contaminate groundnut, maize, cotton, chillies, and many other agricultural commodities. About 4.5 billion people living in the developing countries are presently chronically exposed to largely uncontrolled amounts of these toxins. Blood tests have shown that very high percentages of the population are exposed to aflatoxins in several developing countries of Asia and Africa. Exposure to aflatoxins compromises immunity and interferes with metabolism of some proteins and micronutrients. They are highly toxic to livestock and are implicated in human diseases. Aflatoxins are well recognized as a cause of liver cancer. Chronic exposure to aflatoxin has major effects on the nutritional status of human beings and animals. It has been shown that humans, particularly children and animals that consume contaminated food/feed have reduced rates of growth. The interactions between vitamins and aflatoxin have also been studied and it has been reported that several vitamins including vitamin A levels decrease with increased level of aflatoxin in the livers of animals.

Aspergillus flavus that produces aflatoxin in groundnut is widely distributed in nature. Climatic factors, crop management and the genetic vulnerability of the plant all play a role in the susceptibility of crops to Aspergillus. Solutions to aflatoxin contamination are best provided through an integrated approach using aflatoxin tolerant cultivars, and implementing appropriate pre and post-harvest technologies that reduce the risk of aflatoxin contamination in food/feed. In spite of these efforts, aflatoxin contamination remains a problem in the SAT where a holistic approach is needed to translate technological breakthroughs into safer production and consumption patterns of, for example, groundnut. The great majority of farmers are unaware of the problems of Aflatoxin contamination. So information dissemination is critical. Once awareness is increased, preventive measures can be more easily adapted.

To deal with mycotoxin contamination, ICRISAT emphasizes an IGNRM strategy by developing mycotoxin-tolerant cultivars of mandate crops, particularly groundnut, and appropriate pre- and post-harvest technologies that reduce the risk of food/feed contamination. These involve genetic enhancement through both conventional plant breeding and biotechnology applications; better pre- and post-harvest crop management technologies including agronomic practices, biological control and post harvest techniques, development of simple and low-cost mycotoxin diagnostic tools.

There is also a need to profile the extent and intensity of mycotoxin contamination and related socioeconomic and health affects in different agro-eco systems of SAT Asia, on different staple and high value crops, including ICRISAT mandate crops. To motivate farmers to produce aflatoxin free crops it would be important to introduce, among other parameters, price determination based on aflatoxin contamination in the produce as is done in many developed countries. It is proposed that these activities will further enhance our efforts to improve the nutritional status and health of the poor in SAT by providing then with both a better quality and a better quantity of food.

Outputs and outcomes to 2015

Output 1: High quality and low cost diagnostic tools for estimating the risk of human exposure to aflatoxins and quantitative estimation of mycotoxins (aflatoxins, fumonisins and ochratoxin-A) in crops, processed foods, feeds and commodities, developed and widely disseminated for use by NARES, farmers, traders and processors in the developing countries of the SAT

Outcome 1: Mycotoxins better regulated in foods and feeds through continued and routine use of diagnostic tools by NARS and the private sector in various production, processing, supply and distribution chains.

Potential impacts:

Counterfactual: Food safety cannot be ensured; reliable enforcement of food safety regulations is reduced; farmers, traders and processors continue to suffer from trade restrictions and rejections of exports; processors in supply chain continue to waste resources on cleaning products; increasing overhead costs due to greater dependency on high-cost diagnostic tools from commercial suppliers; traders exploitation of farmers continue through arbitrary quality estimation. R&D programs on mitigating mycotoxin contamination in food and feed suffer because of high cost of aflatoxin detection from large number of farmers' production and therefore marketing will remain difficult therefore we need cost-effective diagnostic tools.

Outcome 2:

Predominant capability:

Counterfactual: Aflatoxin contamination in crops and crop-based products continue to be high and unchecked; human and animal health in marginal farming systems continue to be affected due to aflatoxin-related illnesses; outbreaks of human and animal mycotoxicoses cannot be prevented; confidence among exporters and importers remains low due to risk of contamination; trade restrictions on import of crop-based products from developing countries remain unlocked; threat of liver cancer due to aflatoxin accumulation especially among Hepatitis-B and C virus-affected patients remains high; aflatoxin contamination continues to be a major negative influence on health of children, human and animal productivity and ability of HIV-affected patients to cope with the illnesses.