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Checkbiotech: The role of genomics research in improvement of Crops
Posted by: DR. RAUPP & madora (IP Logged)
Date: December 09, 2004 07:51AM ;

The importance of agriculture to global food security goes beyond the need
for total growth in crop yields and production. Agriculture promotes food
security because it fulfills nutritional needs and/or contributes to local
incomes and employment. Poverty in the developing world remains most
pronounced in rural areas where agriculture is one of few sources of income
and employment. The world's poorest regions are typically those where
agricultural investments by the public and private sectors are extremely
low. There is an urgent need for mechanisms to enhance agricultural
development poor agrarian societies (Mosher, 1966), Dezember 2004.

In addition to a small number of well-known major global crops such as
maize (Zea mays L.), rice (Oryza sauva 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],
ground-nut (Arachis hypogaea L.) and Bambara groundnut [Vigna subterranea
(L.) Verde.]; 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 economicinduced 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

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.

Scientific Opportunities for Applying Advanced Technologies to Orphan Crops
Rationalizing investments in germplasm improvement for orphan crops requires
a shift in investment perspective from individual crops to whole sets of
crops with common genetic structures and from specific trait-crop
combinations to consideration of a particular trait and its component
attributes in a wide array of crops that may face similar production
constraints. How important will research on models-such as rice, maize,
Arabidopsis or Medicago truncatula Gaertn. -be for future improvements of
orphan crop species? Will upstream research on mechanisms of plant responses
to biotic and abiotic stress provide broadly applicable strategies for
limiting crop loss? Will it be possible to integrate new plant traits and
other findings into the ongoing, if limited, crop improvement efforts
already underway in least developed countries? The benefits of transferring
genomics information and techniques from model to orphan crops could take
one or more of several forms: (i) improved analysis of crop biodiversity and
identification of potentially useful variants, (ii) marker-assisted
selection (MAS) of desired alleles and allele combinations, and (iii)
cloning and direct transfer of desirable alleles among taxa.

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 costbenefit
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,

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 organi\zation. 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 (Paris 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

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).

Science in Context

Mass selection of landraces for desired traits generally has not kept pace
with globalization or even with changes in local conditions (including
population growth, changing tastes, new pest and disease pressures, and
abiotic stresses). To assist poor rural communities in generating local
opportunities and income, there exist great opportunities-and also major
challenges-for plant breeding interventions (DeVries and Toenniessen, 2001).
Insights and tools with practical utility for orphan crops can be obtained
from research into both basic and applied plant biology using model species
and major crops. Such transfer of technology from major or model crops to
orphan crops will be cost-efficient, but will still require significant
fixed costs up front in developing the basic biology of the orphan crops in

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.

REFERENCES and additional Information under:

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