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a Dep. of Plant Pathology, 321 Plant Science, Cornell Univ., Ithaca, NY, 14853
b Dep. of Plant Breeding, 313 Bradfield Hall, Cornell Univ., Ithaca, NY, 14853
c Center for Environmental Science and Policy, Stanford Univ., Encina Rm. 418E, Stanford, CA, 94305
* Corresponding author (mmj9{at}cornell.edu)
Abbreviations: EST, expressed sequence tag • MAS, marker-assisted selection • QTL, quantitative trait loci
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INTRODUCTION |
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 TOP INTRODUCTION Scientific Opportunities for...Science in ContextREFERENCES |
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In addition to a small number of well-known major global crops such as maize (Zea mays L.), rice (Oryza sativa L.), and wheat (Triticum aestivum L. em. Thell.), many more crops are regionally or locally important for nutrition and income in poor regions. Crops such as plantain and bananas (Musa sp. L.); root and tuber crops such as cassava (Manihot esculenta Cranz.), sweet potato [Ipomoea batatas (L.) Lam.], and yam (Dioscorea sp. L.); millets such as pearl millet [Pennisetum glaucum (L.) R. Br]), finger millet [Eleusine coracana (L.) Gaertn.], and foxtail millet [Setaria italica (L.) Beauv.]; legumes such as cowpeas [Vigna unguiculata (L.) Walp], groundnut (Arachis hypogaea L.) and Bambara groundnut [Vigna subterranea (L.) Verdc.]; and tree crops. Moreover, indigenous crops such as tef [Eragrostis tef (Zucc.) Trotter], quinoa (Chenopodium quinoa Willd.), and many types of vegetables are critical for food security and nutrition on a regional or local basis.
Twenty-five such "orphan" crops within developing countries total some 240 million hectares, with an additional 70 million hectares planted to fruits and vegetables (Naylor et al., 2004). In Sub-Saharan Africa, for example, sorghum [Sorghum bicolor (L.) Moench.] and pearl millet are more important than rice and wheat, both in area (41 million ha. vs. 9 million ha.) and in contribution to diet. Roots and tubers are essential staples in Africa, where cassava is the third most important source of calories overall. The underresearched crops are nutritious, valued culturally, adapted to harsh environments, and diverse in terms of their genetic, agroclimatic, and economic niches. Attention to locally important crops takes on added urgency given that 38% of Sub-Saharan Africa's population is undernourished, and the number of undernourished children in that region is expected to increase from present levels by 39% by 2020 (Pinstrup-Anderson et al., 1999).
A large discrepancy exists between the potential role of these crops in improving food security and livelihoods, and the low levels of investment they have received. One reason for this may be that research on orphan crops may appear to have relatively low returns when measured by gross economic and welfare impacts, a view that stems in large part from inadequate measurement. The use of alternative metrics, e.g., human capital development, cropping system stability, the promotion of genetic diversity, all of which increase the capability of agricultural systems to withstand major biotic, abiotic, policy- or economic-induced shocks—provides even greater incentives to fund orphan crop germplasm improvement (Conway, 1997). While we believe these arguments offer compelling justification to enhance investment levels in crops other than wheat, rice, maize and soybean [Glycine max (L.) Merr.], clearly the contributions of major crops to human well-being are immense. No argument in this paper should be interpreted as suggesting that current research on them is excessive or even close to adequate.
Advances in crop genomics have resulted in a more unified understanding of the biology of the entire plant kingdom, as well as a powerful set of molecular and bioinformatic tools and methods. Such advances provide an opportunity for efficient transfer of information systems from model species and major crops to orphan crops (Naylor et al., 2004). As a result, relatively small investments in the transfer of advanced science from major crops to larger sets of orphan crops may potentially result in disproportionately high payoffs in terms of crop production, yield stability, and food security in least developed countries. It is important to emphasize that investment in genomics for a given species is only likely to be useful if a strong conventional breeding effort exists (and unfortunately, this prerequisite is too often not fulfilled).
There may also clearly be reciprocal benefits of genomics research on orphan crops for improvement of major crops, derived from insights into the genetic bases for their distinctive attributes. That is, some of the orphan crops can provide good models for traits not possessed by the model crops. Superior alleles for drought resistance, for instance, might be found in pearl millet and utilized by direct gene transfer in rice or wheat (Goodman et al., 1987). Alleles contributing tolerance to poor soils might be found in cowpea and used in other legumes.
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Scientific Opportunities for Applying Advanced Technologies to Orphan Crops |
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TOPINTRODUCTIONScientific Opportunities for...Science in ContextREFERENCES |
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Farmers and plant breeders have used visual selection as a fundamental tool in crop improvement for millennia. MAS has been demonstrated for a modest but increasing number of cases, and is most likely to be useful when genetic variability is obscure, phenotypes are difficult or expensive to evaluate, or where detectable variation is result of complex interactions of many genes and/or gene products. In only a few cases has a rigorous cost–benefit analysis been presented (e.g., Dreher et al., 2003).
Existing genetic variability in species can now be both identified and used in new ways for germplasm improvement. For example, any two plants from a group sharing a similar phenotype may or may not have genetic differences that would make it possible to recombine their genes to achieve a superior combination. Molecular techniques permit the visualization of molecular variation, which may allow a breeder to select the best possible parents for a crossing program. Useful gene variants may be present in plants with unpromising phenotypes, and molecular analysis of specific loci may allow cryptic but potentially useful genes to be discovered. Both these situations undoubtedly contribute to the phenomenon long apparent to plant breeders as "transgressive segregation" (Frantz and Jahn, 2004; de Vicente and Tanskley, 1993).
Imagine, for instance, that a researcher would like to improve the starch or vitamin content of a certain crop about which relatively little is known. Typically, the breeder has access to a large germplasm collection that has not been well characterized or utilized. It would make sense to analyze the collection for the phenotype of interest. Once a large group of individuals with known phenotypes has been established, it may be worthwhile to characterize the plants with a panel of markers representing the genes controlling starch and vitamin biosynthesis. Genotypes with different gene variants might be good candidates for entry into a breeding program.
To what extent is this process possible in current practice, for any crops? Progress in the area of plant genomics has been dramatic and the stage is set for efficient application of marker-assisted genetics, candidate gene analysis, and molecular breeding. Within plant families, similarities of genes and their physical organization on the chromosomes has already made it possible to use information from model species as a platform from which to pursue rapid progress on lesser-studied species. To date, however, the full impact of these technologies has yet to be felt in any crops, and it remains unclear how far-reaching results from one particular plant species will be across the whole plant kingdom.
Emerging evidence indicates that genomes for the entire plant kingdom have much in common in terms of gene content, biochemical pathways, and chromosome organization. Genes involved in many biochemical pathways and processes are similar across the plant kingdom (Thorup et al., 2000). Functions such as gene regulation, general metabolism, nutrient acquisition, disease resistance, general defense, flowering time, and flower development are largely conserved across taxa. Comparative mapping studies reveal that gene order is conserved for chromosomal segments among grass species (Bennetzen and Freeling, 1998; Gale and Devos, 1998; Devos and Gale, 2000). Though weaker, chromosomal colinearity is detectable between monocots and dicots (Bennetzen, 2000; Devos et al., 1999; Goff et al., 2002).
Most traits of importance to farmers and consumers are governed by multiple genes of relatively small individual effects. These "quantitative traits" are the most difficult to understand and improve. Molecular genetic approaches have begun to illuminate the genetic architecture of quantitative traits (Paterson et al., 1988; Kearsey and Farquhar, 1998). Although MAS for these traits using anonymous QTL-associated markers is more challenging than was initially projected, because of the imprecise localization of QTL and by inconsistent QTL expression, recent studies have provided encouraging evidence that MAS may be useful for enhancing these traits under certain circumstances (e.g., Han et al., 1997; Bouchez et al., 2002; Villanueva et al., 2002; Mithen et al., 2003; Zhou et al., 2003).
Candidate genes, genes known or suspected to be involved in conditioning the phenotype of interest, make it possible to localize desirable variants much more precisely. Credible candidate genes have now been identified for many plant traits, including quantitative (multiple gene) disease resistance in rice (Wang et al., 2001; Ramalingam et al., 2003), wheat (Faris et al., 1999), bean (Phaseolus vulgaris L.; Geffroy et al., 2000), and potato (Solanum tuberosum L.; Trognitz et al., 2002). A number of research approaches have converged to allow genes underlying QTLs to be cloned (Frary et al., 2000; Johanson et al., 2000; El-Assal et al., 2001; Thornsberry et al., 2001). Isolation of genes controlling quantitative traits will permit both the identification of potentially useful variants of agronomically important genes and the precise selection of the most useful alleles. The availability of the isolated genes could allow natural molecular variation to be analyzed efficiently in a range of genotypes, enabling the identification of potentially useful variants for future use.
Sequence data on expressed genes and on plant and crop genomes are rapidly accumulating and present powerful tools for plant science. The increasing availability of expressed sequence tags (ESTs) puts QTL cloning within reach. EST collections also provide the basis for microarray technology that allows patterns of gene expression to be investigated in various physiological conditions, another potentially promising source of candidate genes. Combining information on mapped QTLs and ESTs provides a step toward identifying the genes that underlie quantitative trait loci. Although sequence datasets are, in themselves, imposing and cumbersome, increasingly powerful and friendly databases (e.g., Yuan et al., 2001) allow researchers to access genetic information and identify and exploit natural variation in ways previously not possible. For orphan crops, however, numbers of ESTs are meager.
While it is often possible to associate a candidate gene with a QTL, it is not so easy to actually prove that the candidate contributes to the expression of the trait of interest (Glazier et al., 2002). The number of recombination events in a mapping population is often insufficient to permit the identification of genes underlying a QTL with high resolution. QTL estimation often spans several centimorgans, and hundreds of genes will underlie a region of this size. The size of such a region can be reduced through a number of approaches, such as the use of high-resolution crosses, or the development of near-isogenic lines for small chromosomal segments across the putative QTL region. Linkage disequilibrium mapping offers another alternative, exploiting the long history of recombination and rich allelic diversity in collections of diverse germplasm (Remington et al., 2001; Buckler and Thornsberry, 2002). For example, a specific polymorphism in the Dwarf8 gene (a gene known to affect plant height) was shown to associate with variation for flowering time in maize by this type of approach (Thornsberry et al., 2001).
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Science in Context |
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TOPINTRODUCTIONScientific Opportunities for...Science in ContextREFERENCES |
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Success will depend on investment but also on appropriate integration of knowledge gained (Naylor et al., 2004). Integration starts with linking advanced science with plant breeding and seed programs. While the link between science and plant breeding is key, so too is the link between plant breeding, farmers, delivery systems, and consumers. Successful application of genomics is conditional on connecting the science to downstream delivery efforts. For the poorest countries, such integration may take years to achieve. Even with appropriate integration and sustained research investments, the benefits from advanced science depend critically on institutional, human capital, economic, and political contexts in regions that require agricultural growth.
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ACKNOWLEDGMENTS |
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Received for publication July 23, 2003.
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REFERENCES |
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TOPINTRODUCTIONScientific Opportunities for...Science in ContextREFERENCES |
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