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Enhancing agricultural productivity in those areas of the world bypassed by the …

Biology Articles » Agriculture » Agriculture in the developing world: Connecting innovations in plant research to downstream applications » Harnessing the New Sciences for Crop Improvement

Harnessing the New Sciences for Crop Improvement
- Agriculture in the developing world: Connecting innovations in plant research to downstream applications

Agriculture will never truly thrive in places like subSaharan Africa unless solutions are found for fundamental issues, such as lack of roads, weak input and output markets, the low level of general health and education of poor farmers, poorly functioning extension services, and gender inequity that places a disproportionate burden on women in agriculture, all critical issues that cannot be solved by biotechnology and are well beyond the scope of this article. Even in the specific area of crop improvement, there are great opportunities to apply conventional breeding that do not need to draw on the very latest discoveries in plant biology. One of the first rules of our Food Security Team at the Rockefeller Foundation is, “If the breeders can solve the problem, let them do it.” In places like subSaharan Africa, once breeders began tailoring their efforts to breeding targeted specifically to African conditions, it became apparent that significant crop improvement is possible through conventional approaches (11).

The Increasing Power of Molecular Breeding. With respect to the recent advances in the plant sciences, as the sequences of many plant genomes become known, the power of genomics for applied breeding has to be one of the most exciting advances of recent years. Extremely valuable to breeders in the national agricultural research systems is the ability to genotype their collections to get a clear picture of their diversity and how such diversity might be enhanced through sharing and access to global collections. The use of marker-assisted selection in cases where phenotyping presents a challenge or to trace introgression of known genes or important regions from wild relatives should also become part of every serious national breeding program.

Complete sequence information, maps, and a huge array of molecular markers exist for rice; with more sequence information for other crops, new techniques for assessing allelic diversity, and a better understanding of synteny (12), these are now being adapted for the breeding of other crops. Yet, for orphan crops like cowpea, common bean, the millets, tef, and cassava, we still have insufficient numbers of ESTs, bacterial artificial chromosome libraries, molecular maps, and markers (13). Programs such as the Generation Challenge Program and crop-specific initiatives such as Phaseomics are beginning to address these limitations, but a glance at the number of ESTs available for different organisms (www.ncbi.nlm.nih.gov/dbEST/dbEST_summary.html) indicates that more funds and efforts are clearly warranted. Good value can also be had through sequencing of the genomes of major plant pathogens. In addition, there are many challenges in creating the needed infrastructure, including high-throughput analysis systems and critical high-speed Internet access to the tools of bioinformatics; development of a pool of breeders well-versed in the use of these tools also still limits progress on this front. Networks in Asia that brought together rice (the Asian Rice Biotechnology Network, ARBN) and maize breeders (the Asian Maize Biotechnology Network, AMBIONET) to build capacity and better interactions among molecular breeders have been most successful; a similar fledgling network called AMMANET (African Molecular Marker Applications Network), which holds promise for African breeders, is another welcome development.

A new regional center in Nairobi called Biosciences for East and Central Africa (BECA) is intended to serve as a center of excellence for agricultural biotechnology that will interact with and serve the various universities and national agricultural research systems of the region. At BECA, the modern tools of genomics can be shared with breeding programs through training, provision of markers, high-throughput analysis coupled with a sophisticated bioinformatics platform, and joint efforts to genotype key crops and identify projects suitable for marker-assisted selection. For example, a recent meeting at BECA brought together 28 sorghum and millet breeders from national agricultural research systems representing 14 countries of the region and specialists in molecular breeding and genomics from the U.S., Europe, and the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). The purpose of the meeting was to learn about the genomics tools available to them from both public and private sources and to discuss and draft project proposals for application of marker-assisted selection in African sorghum and millet breeding programs. More extensive promotion of such collaborations and other forms of imaginative human capacity building is clearly warranted.

The use of molecular markers has helped highlight the importance of genes from wild relatives for use in crop improvement (14, 15) and, as evidenced by recent work on tomato improvement, the results can sometimes be spectacular (16). African farmers are showing real enthusiasm for new interspecific hybrids that combine the best of both Asian and African rices (17). For complex traits, the identification of quantitative trait loci (QTL) has advanced to a considerable degree, to the point where it is now becoming somewhat more feasible to identify specific genes that control the traits underlying the QTL (e.g., see ref. 18 and refs. therein). Advances in genomics should also be able to contribute new insights to our currently vague understanding of that most important of traits, heterosis (hybrid vigor). Can the recent work showing how inbred lines of maize differ strikingly in gene sequences (e.g., ref. 19) and gene expression patterns (20) provide some clues? Can such understanding help us determine whether there is good value in promoting the development of hybrid sorghum and millets for Africa and to explore further the potential of heterosis in many crops beyond maize? Certainly, development of hybrid seed is one way to promote viable seed markets for crops. But do we understand well enough the cost–benefit equations for small farmers with respect to purchase of high-quality seed (hybrid or not) vs. the saving of seed, and is the development of a strong private-sector seed business a necessary part of moving such farmers beyond the subsistence level? Such questions go beyond the realm of science into that of sociology and economics, but good answers clearly require input from the scientific community.

Are GM Crops the Answer? A fierce debate continues over the potential of GM crops to solve the problems of hunger in the developing world. At one extreme, proponents argue that these new technologies will be the panacea needed to solve hunger, whereas the other extreme argues that the technologies are unsafe to both humans and the environment and are being promoted simply as a means to further the interests of the large multinational companies that market them. Those arguments are not the focus of this article, except to say that most reasonable people understand the truth lies somewhere between these extremes and, at best, GM crops are only one of many approaches available to solve world hunger, and developing countries should be free to assess their worth within the context of their own needs and priorities. It can be argued that all new advances, including the undoubted success of the Green Revolution, can have their downsides. A recent example is the Roundup Ready soybean, which has been a huge success for the farmers of Argentina and Brazil but may be promoting a debatably dangerous trend toward monoculture and expansion of farming into valuable sites for biodiversity. Whatever one's opinion on these issues, there seems to be little doubt that the endless, and often shrill, GM debate has limited the development of crops that could be very relevant to poor farmers by reducing the number of donors willing to support such efforts, raising concerns over liability in companies considering the provision of their technologies for use in public-sector projects and creating confusion and uncertainty about whether to allow even simple testing of the efficacy of new transgenic crops in developing world countries. A key consequence of this debate has been to lower the level of engagement of skilled scientists in key laboratories who should be building better capacity in this field.

Most of the discussions on GM crops are much too narrowly framed and focus just on the current situation, wherein only four major GM crops, with only two traits, represent the bulk of the GM market today. These traits are insect and/or herbicide resistance in soybeans, maize, canola, and cotton, a very limited repertoire that was designed by the private sector for use in large-scale agriculture. First, I shall discuss the extent to which this limited repertoire may be suitable and beneficial for use in the developing world. Then I shall make the argument that there are many other opportunities for crop improvement besides the current GM crops that could be developed by taking a more imaginative look at the recent advances in gene discovery.

The Relevance of Current GM Traits and Crops for the Developing World. In subSaharan Africa, maize is clearly the major staple human food crop in many countries, and cotton is grown as a commercial crop even by the poor in countries like Mali, South Africa, India, and China. For these crops, a strong commercial market for GM seed is developing that, at least in principle, targets both large- and small-scale farmers. Accumulating evidence indicates that the current GM crops can clearly prove beneficial to small as well as large farmers. Varieties of cotton with the toxin gene from Bacillus thuringiensis (Bt) are proving their worth to poor farmers in South Africa (21) as well as parts of Asia (22, 23), and Bt rice is performing well in late-stage trials in China (24). The benefits of these crops can be quite different depending upon circumstances. In China, where yields of conventional cotton and rice are maintained through heavy use of pesticides, the benefits are in savings on the costs of these inputs and on the health of workers from pesticide poisoning and protection of the environment through the use of fewer chemicals. In South Africa and India, where costs of pesticides are prohibitive for the poorest farmers, the benefits are more clearly seen in substantial yield increases when pests are controlled through Bt technology. However, quite worrisome for the developing world is the serious issue of illegal seed movement and/or sales for GM crops, which occur widely in countries like Brazil, India, and China, which has lowered the incentive of the private sector to continue their involvement, weakened the private seed sector within these countries, and also lowered the quality of seed available to farmers (e.g., see ref. 25).

In contrast to Bt, where the trait is embedded in the seed, herbicide tolerance is a trait more beneficial to large-scale farmers who can afford to buy chemical inputs. Yet, several developments may require some rethinking of this belief. One of these is the increasing shift in Asia from growing rice in paddies that provide good weed control to aerobic conditions. In Africa, cost considerations, as well as the variety of crops grown on a single small plot, make the idea of herbicide tolerance seem less attractive for small-scale farmers. Yet, as shown in Argentina, herbicide-tolerant crops certainly favor the development of no-till agriculture, which can control erosion, save water, and sometimes allow for double-cropping; furthermore, in Africa, hand-weeding occupies much of a farmer's time and, with the severe labor shortages developing as a result of the HIV/AIDS epidemic, the science community should perhaps think about promoting cropping systems that save the time and energy of the farmer.

All these facts indicate there definitely can be a positive role for the private sector for the sale of seed for these major crops with these traits in at least some areas of the developing world. Experience tells us that if farmers benefit, if they have the cash, or if they can be helped through microcredit schemes, and if strong regulatory systems are in place (as in the U.S., Argentina, and South Africa), they will buy such quality seed. But if governments, as was the case in Brazil with the Roundup Ready soybean, delay approval of a GM crop that farmers clearly want, the farmers often find a way to get it illegally, compromising both the quality of seed available, the viability of private seed sector, and the ability of a government to provide adequate regulation.

In terms of strategy, one has to strongly question whether the public sector should waste its precious resources developing any product that duplicates what the private sector can make available. However, similar benefits could be imagined for these same traits in a number of crops that are traditionally outside the formal seed sector and of no interest to the large private-sector companies. Targets where Bt genes could potentially be used to address the constraints of poor farmers include the pod borers that attack cowpea and pigeon pea; the stem borers of rice, weevils, and/or nematodes that attack banana or sweet potato; the diamondback moth that affects cabbage; or the fruit and shoot borers of eggplant. For maize, the larger grain borer has become a serious storage pest for maize in Eastern Africa and is a target trait not likely to be addressed by the private sector (26). Techniques now exist for transformation of all of these crops, although some would certainly benefit from further optimization. Genes have clearly been identified to control most Lepidopteran pests such as the moths and pod, stem, and fruit borers. Searches are still ongoing to identify the most effective Bts that may control Coleopteran pests like large grain borer, weevils, and nematodes; these are cases where the application of gene shuffling techniques may be important for enhancing effectiveness.

Moving Beyond Bt and Herbicide Tolerance. The plant science community is discovering a vast array of genes that control all aspects of plant growth and development. Although GM crops based on many of these other genes may have little or no commercial potential, they can have a much different value when considered for certain crops important to the developing world. The creation of nutritionally enhanced crops such as Golden Rice is an obvious example (27, 28), but it should be possible also to enhance mineral content and improve the digestibility of crops like sorghum and to eliminate toxic compounds such as the cyanogenic glycosides of cassava. Although perhaps not quite ready for downstream application, the recent work on the identification of new genes that control phosphorous utilization or tolerance to aluminum offers future promise (7). Also worthy of more intense study are the arbuscular mycorrhizal fungi that form symbiotic relationships with >80% of all plant species and certainly contribute to the more efficient extraction of nutrients from the soil (29). A major problem in working with these has been the inability to culture these fungi in the absence of the host; in this regard, an exciting breakthrough is the recent identification of strigolactones as key stimulants of fungal development, which are secreted from plant roots in response to low phosphate; this work may also have significance for research on the parasitic weed Striga, because similar compounds also stimulate Striga seed germination (29, 30).

Through the classic studies of coat-protein-mediated resistance (31) and, more recently, using RNA interference, we know it is entirely feasible to control RNA viruses such as ringspot, which attacks papaya (32); similar approaches can potentially be used with great benefit for the brown streak virus of cassava or against cucumber mosaic virus, which affects many vegetable crops. The ssDNA geminiviruses that cause devastating diseases of cassava, maize, banana, and tomato, because they do not involve an RNA-based intermediate for replication, were thought not to be controllable by this approach, but recent evidence suggests they may nevertheless be targets for posttranscriptional gene silencing (33); other targets for control are also being explored (e.g., refs. 34 and 35).

Bacterial and fungal diseases represent an enormous challenge, because they cause such huge losses to farmers who lack the labor and skills needed for good field management and the money for effective pesticides (36). Breeding for resistance can clearly solve some of these problems, but development of pathogen resistance is a persistent problem, so the plant community needs to unite to come up with more and better strategies to achieve durable forms of resistance, a goal I would list as one the highest priorities for future plant research for the developing world.

I think there is no field in plant biology that has a collection of more imaginative scientists than those who have discovered such an amazing amount of information about pathways invoked upon the response of plants to pathogens or insects. Surely the field can benefit from continued work on the complex events involved in early recognition, including further identification of interacting proteins and the role of proteolysis in the process (37, 38), and on the connections between and relative importance of basal and induced defense systems (38). For both breeding and transgenic approaches that target resistance (R) or avirulence (AVR) genes, a clearer understanding of the nature of the fitness costs of both the R genes of the plant (39) and AVR genes in the pathogen (40) is one avenue worthy of additional exploration. It is clear that the simple idea of constitutive overexpression of key genes in resistance pathways often leads to loss of plant vigor and yield penalties (41). At first glance, the idea of inducible overexpression of key transcription factors that control a range of downstream responses seems attractive for disease resistance (42) and may represent one of the best approaches for other complex traits, such as drought tolerance (43). Equally critical to the success of this approach would seem to be the type of promoter selected. Unfortunately, for all transgenic work, the pubic sector is woefully lacking in a suite of good promoters for both eudicot and monocot species that are tissue-specific, developmentally regulated, and/or inducible by environmental cues like stress, disease, or cheap and safe chemicals. But the use of transcription factors for the control of diseases may be more problematic than originally imagined because of the complexity of the response pathways and the discovery of negative crosstalk that sometimes occurs between the salicylic acid-regulated pathway for disease resistance and the jasmonate–ethylene-regulated pathways important for insect resistance (44). One key regulator that intersects both of these pathways is the NPR1 gene (45); understanding ways to modulate its location and/or function in either pathway might therefore provide one way to control at least one type of negative crosstalk. Yet this is one field where it seems the more we learn, the more complicated the challenge, and one longs for another magic bullet similar to the Bt genes that control insects so well and so durably. Perhaps scientists need to think more about creating, through molecular design, some imaginative killer genes like Bt that could target specific groups of plant pathogens.

We should also be able to draw on the fascinating findings from the world of plant development to improve certain crops. At the meeting that brought together bench and field scientists, breeders told molecular biologists that cassava is very poor at flowering and, even worse, two varieties one wants to cross often do not flower at the same time in the same breeding station. From this emerged a project to attempt to create cassava for breeding purposes that has a flower-inducing gene under the control of an ethanol-inducible promoter. Ideas also emerged for projects that could aim to dwarf the ungainly East African Highland Banana or the favorite cereal crop of Ethiopia called tef, to enhance drought tolerance through stress-induced changes in root architecture, and to ask whether RNA interference technology might be used to control the parasitic weed Striga by sending, through host–parasite connections, an engineered small RNA from maize to directly target a critical Striga gene. References too numerous to cite here indicate we now should be able, perhaps with single-gene changes, to control traits like tillering in cereals; alter root or shoot branching patterns; control the timing and extent of flowering and/or alter vernalization requirements; change seed size or number; control seed shattering; and perhaps even think about altering flower color, scent, structure, and/or time of opening to prevent gene flow by pollinating insects. In Africa, children are made to stay home from school to scare away the birds that steal exposed grains of crops like sorghum; perhaps a mutant gene like “Tassel Sheath” of maize might be transferred to sorghum to mimic the advantages found in the enclosed grain of maize. Finally, the new insights emerging daily on how microRNAs control development (46) should offer many other new approaches to changing plant form and function. The above are only some examples of what might be done today, given current technologies, and only hint at what might be done in the future when additional insights become available, although they do not take into account cost–benefit analyses for any given projects or other roadblocks that might need to be considered.

One recent impressive tour de force study with rice involving genes controlling development is instructive for the current debate about whether molecular breeding should be favored over a transgenic approach. Using all the tools of modern breeding, Ashikari et al. (18) identified a strong quantitative trait locus (QTL) that controls grain number, cloned the gene (a cytokinin oxidase) in an effort that involved the analysis of 13,000 F2 plants, and created transgenic plants with a larger grain number by overexpression of the gene. Having learned much about this gene and its relationship to other members of the same gene family through the transgenic approach, the authors (18) then returned to breeding to pyramid the locus for an enhanced grain number with that surrounding the semidwarf gene (sd1), resulting in a plant that should substantially enhance grain yield. Ashikari et al. (18) have impressively shown what can be accomplished through molecular breeding, particularly as one approach to the identification of candidate genes; however, one has to ask whether, once specific genes are identified (as they were for both the cytokinin oxidase and the dwarfing gene), it would not make more sense to pursue a targeted transgenic approach for pyramiding the genes. In the end, the goals of breeding and transgenic research are the same, the introgression of good alleles for crop improvement. With breeding, linkage disequilibrium is a reality that often (but certainly not always) can result in the transfer of unfavorable genes along with the targeted good gene, whereas the transgenic approach eliminates this problem. Once candidate genes (and/or or key alleles of promoters of genes) are verified for traits of interest, either through QTL or functional genomics approaches, it would seem the most obvious route for trait improvement should be to move each good allele (and, if two or more, preferably linked to each other) selectively to the crop. Even from a regulatory point of view, this should be more attractive, because one knows exactly what is being transferred. Unfortunately, under the current regulatory climate, any new variety containing one or two new genes produced through breeding can find an easy path to approval and release, whereas the same variety with the very same new genes produced through transgenic approaches may be held up for years, if not forever, awaiting the approvals necessary for release to farmers.

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