new concepts and approaches to biodiversity

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NEW CONCEPTS AND APPROACHES TO BIODIVERSITY

D.F.Marshal1 and J.R. Hillman

Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA

1 INTRODUCTION

Biodiversity has become a word with a multiplicity of meanings that can be applied at

many levels of scale from global to local. It is a term that can be adapted to describe the

range of species in an ecosystem or to the levels of genetic diversity that are containedwithin a species.'

Biodiversity can essentially be thought of as the balance between the rate of generation

of new variation (by mutational and recombinational processes as well as speciation)

versus the rate of loss through local or global extinction of genetic variation within species

or of species themselves. Though most would agree with the notion that the maintenance

of biodiversity is a 'good thing', it is difficult to quantify biodiversity or even to identify an

optimum biodiversity level for a given habitat or to identify the optimum level of genetic

diversity within a particular species. Nevertheless there is now growing concern about the

increasing human impact on the rate of loss of biodiversity and the realisation that,

without modern technologies, species that go extinct are lost forever?.

The biological variation that we see is the manifestation of the expression of the range

of genes that are continually evolving in the global ecosystem, together with their

interactions with the changing biotic and physical environments in which they are found.

Much of the current public perception of the biodiversity issue is focused on 'visible'

biodiversity in terms of higher plant and animal species-richness. In reality, the biological

survival of an individual species is uniquely dependent on the genetic variation that it

contains and the microbial environment is a key, often overlooked, element of any

ecosystem.

In this article we shall focus for simplicity on the biodiversity of crop plants, though

we are aware that even a consideration of the impacts of crop plant biodiversity cannot be

treated in isolation from either their pests and pathogens or the other species in theiragricultural or natural ecosystems. As well as their role in food chains, human nutrition,

industrial feedstock and biomedicine, higher plants can be viewed as providing much of

the physical substance of the living landscape. In viewing these issues from a British

perspective most, if not all, of our visible landscape is the product of thousands of years of

human impact. Even here, the adoption of appropriate actions (e.g. a viable Biodiversity

Action Plan (BAP)) is required to mediate the impacts of modern agriculture and forestry

as well as other human activities.

Rapidly developing modern molecular technologies help deal with the biodiversity

issue. Traditional methodologies such as species inventories can yield valuable

information for the first stage of biodiversity analysis. PCR-based DNA technologiesprovide rapid screening tools to obtain relatively objective measurements of genetic

diversity within species, and can, for example, estimate biodiversity in the soil for

microbial species yet to be identified. For crop plants, molecular marker technologies have

enabled us to track the increasing loss of genetic diversity from wild ancestors, through

land races to the advanced varieties of modern agricultural monocultures? Such

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18 Biodiversity: N ew L eads f o r the Pharmaceutical and Agrochemical Industries

biodiversity audits have brought the dual benefits of highlighting the dangers of reliance

on a dramatically limited set of crop genotypes as well as identifying genes of value to

advanced agriculture that have been left behind in the wild gene pool by the bottle-neck of

dome~tication.~.

Clearly, the availability of a broad gene pool for crop species must be maintainedthrough appropriate ex situ and in situ strategies. New transgenic techniques’ mean that

the breadth of the available gene pool can now transcend not only species but, subject to

ethical and social considerations, even taxonomic phyla. By ensuring that the biodiversity

resources of our planet are sustained, the genetic wealth of, not only our crop plants, but

even other under-utilised or even undiscovered species, will be available to provide food

and other biological resources for future generations. The rapidly developing science of

genomics and the post-genomics sciences will provide new ways to catalogue and

sympathetically exploit our biodiversity heritage as well as helping us retain or even

recover a natural environment that is compatible with a high quality of human life.

2 THE ECONOMIC VALUE OF PLANT BIODIVERSITY

If we consider the role of plants in agriculture we find that, of the estimated 300,000 to

500,000 species of higher plants, only a very small minority are directly exploited as food.

Even if we take an extremely liberal view of what constitutes a food species we find that

only around 7,000 species (of an estimated total of approximately 30,000 edible species)

have ever been exploited as food by man. The situation is even more constrained if we

take an objective account of the true impact of these species. The generally held view is

that some 30 species are largely responsible for feeding the world. Wheat, rice and maize

provide more than half of all plant derived dietary energy input at a global level, though anumber of other species have a considerable impact at a regional or local basis.

Given the importance of such a relatively few species for world food supplies, the

maintenance of genetic diversity within these species is of crucial importance for global

food security. This diversity provides the basic resource for breeding programmes for the

development of cultivars that are resistant to current and future pest and pathogen strains

or are adapted to environmental stresses such as drought or salinity. A major problem

exists, however, in that there is no simple direct measure of relevant genetic diversity

within a crop species that is globally applicable. For example, in future we may require

genetic diversity for resistance to pest and pathogen strains that are yet to appear in

agriculture. How can we identify such diversity now to ensure that changes in land useand agricultural practice do not lead to the loss of relevant resistance genes?

One potential route to achieve this is to establish and maintain genetic resource

collections for all key crop species. Currently this operation is underway on a global scale

based on ex situ (i.e. based on farm or ‘wild’ reserve)

collections! The successful operation of such genetic conservation strategies is uniquely

dependent on international co-operation and agreements and is characterised by many

notable success stories.’ There are, however, many operational difficulties in practice. The

survival of genetic resource collections requires significant long-term investment. In

particular the maintenance of stored seed collections through cycles of regeneration and

the management of in situ reserves are both labour intensive and require to be undertaken

in the context of a lack of simple scale or baseline for genetic diversity. The major

difficulty is that we have no simple concept of how much diversity is enough. This is

partially the result of the complexity of plant genomes. A typical plant species may have

as many as 50,000 genes each with many possible allelic states. In practice, the only

absolute measure of genetic diversity for agriculturally relevant traits is based on the traits

(i.e. genebank) or in situ



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Natural Products -History, Diversity and Discovery 19

themselves, which for genetic resource collections requires direct evaluation in large scale

agronomic trials over many sites and seasons or screens against known races of pests and

pathogens. This difficulty has led to the adoption of a growing range of molecular

technologies to quantify or partition genetic diversity in crop plants. This approach has,

until relatively recently, been based on the exploitation of various classes of ‘neutral’genetic markers such as isozymes, RFLPs (Restriction Fragment Length Polynnorphisms),

AFLPs Amplified Fragment Length Polymorphisms) and SSRs” (Simple Sequence

Repeas lo These technologies are all based on gel electrophoresis and allow scientists

to quantify genetic diversity at a series of sample points in the genome. Their use, in

combination with the theories of population genetics, has led to the development of

improved strategies for both collection and maintenance of plant germplasm.

There is, however, still a significant problem in that such ‘neutral’ marker systems,

though giving value information about the overall genetic architecture of diversity, do not

allow us to gain detailed information about the actual genes that determine key traits.

Plant molecular biology has begun to make significant progress towards the

characterisation of agriculturally relevant enes in crop plants. This is particularly true in

the case of pest and disease resistance.’” Nevertheless, we have only begun the process

of identifying which of the 40 -50,000 genes in the plant are of primary importance in

crop improvement.

3 THE IMPACT OF THE NEW ‘OMICS’TECHNOLOGIES

The new science of genomics and the imminent availability of the complete sequence of

the Arabidopsis and rice genomes are changing the way we approach many genetic

problems in crop plants. Together with the growing collections of ESTs (or ExpressedSequence Tags) for most of the world’s major crop species this whole genome level

sequence will underpin new high-throughput technologies in crop diversity analysis and

improvement. A particularly valuable feature is the commonality of these new ‘omics’

technologies across all living organisms. This enables agriculture to benefit from

technology advances that are been driven by the large-scale investment associated with

molecular medicine and drug discovery.

Already in the field of medical genetics a significant investment has been made in the

large scale sequence analysis necessary to develop a large number of markers based on

Single Nucleotide Polymorphisms or SNP’s.13 These are based on the alternative

occurrence of a two or more nucleotides at a particular position of the DNA sequence andcan be readily adapted to the generation of DNA genotyping ‘chips’. Though the

development of this technology requires a high initial level of investment the range of

potential applications of the resulting genotyping chips, based on many thousands of

SNPs, is enormous, e.g they offer the prospect of rapidly screening for an extremely wide

range of human genetic disorders. There are already programmes underway in both the

public and private sectors to develop this technology in the most commercially valuable

crop species such as maize. The availability of SNP-based genotyping chips is likely to

have enormous impact on both the inventory and exploitation of genetic diversity, offering

the prospect of fast-track molecular breeding with dramatically improved efficiency.14’ 5

New high throughput technologies will also enable us to obtain a much clearer

understanding of the molecular basis of phenotype. i.e. they will enable us to characterise

the molecular basis of such traits as yield, quality and disease resistance. Already

significant progress has been made in the development of technologies to simultaneously

monitor the ex ression patterns of many thousands of genes using expression

microarrays.16, These are based on the immobilisation of many thousands of



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20 Biodiversity: New L eads fo r the Pharmaceutical and Agrochemical Industries

oligonucleotides or cloned cDNAs in gridded arrays. High throughput methods are also

becoming available for the characterisation of most of the proteins in a given tissue

sample, using a combination of 2D gel analysis for separation and techniques such as

matrix-assisted laser desorption ionisation - time-of-flight (MALDI-TOF) mass

spectrometry followed by comparison with a reference database.*-*’

Though technologically more demanding because of the range of chemical entities that

must be analy sed, technologies are also becoming available for high-throughput

characterisation of the full range of metabolites that are found within living cells?1 These

techniques utilise an array of spectroscopy-based techniques e.g. pyrolysis mass

spectrometry, Fourier-transform infrared spectroscopy and dispersive Raman

spectroscopy. Their integration with DNA, RNA and protein analysis methods will

provide a comprehensive framework for the characterisation of living tissues and the

quantification of molecular biodiversity.

The development and utilisation of these new high-throughput technologies, however,

requires an increasing1 sophisticated data management and analysis infrastructureas well

as new software tools2 Increasingly, with the rapid advance in molecular technologies,

the Bioinformatics component has become the rate-limiting factor. The scale of the data

avalanche can be seen from the continued exponential growth in the available DNA and

protein sequence in public repositories. The latest, March 2000, release of the EMBL

DNA database contains some 23 Gbtyes of data (http://www.ebi.ac.uk) and we are only

beginning to contemplate the problems of archiving and exploiting microarray data.

The rapid progress of the full repertoire of ‘omics’ technologies, provided they can be

utilised in a ‘cost effective’ manner, offers the prospect of the development of a

sophisticated scientific framework to efficiently exploit the genetic diversity that is

available in crops plants and their relatives in the agriculture of the New Millenium. This

exploitation can be undertaken within the gene pool of crop species through well-established conventional r0utes.2~Alternatively, an array of molecular techniques are now

available for gene transfer to plants?4 effectively removing any taxonomic restriction on

the genepool that is available for a given crop species. Such transgenic approaches may

also be utilised to engineer novel pathways to obtain new products from ~lants.2~

These new ‘omics’ technologies will also enable us to efficiently identify ‘novel’

compounds of value to both the Agrochemical and Pharmaceutical industries. It is of

crucial importance that the data that results from high throughput analyses of the genome,

transcriptome, proteome and metabolome of crop plants and their relatives is archived in

an appropriately structured and indexed manner. This will enable it to be fully integrated

and data-mined over an extensive period as our ability to formulate increasinglysophisticated queries on these data sets develops.

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