Introduction to Plant Biotechnology

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Introduction to Plant Biotechnology

Richard B. Flavell

Ceres Inc., Malibu, CA, USA

INTRODUCTION

Mankind uses a wide range of plant species forfood, feed, fibre, energy, chemicals and drugs. The

exploitation of plants for the benefit of mankind(plant biotechnology) has been developed as partof evolution of societies throughout the world.Plant biotechnology, in its broadest sense, istherefore pervasive in every society and in someapplications is highly developed, having progressedvia a huge number of technical and intellectualadvances.

Plant breeding was practised in primitive formsin the early civilisations. Indeed, settlements weremadepossibleby thepurposefulgrowing of specificselected plants, i.e., agriculture for food, feed andfibre. These selected plants, land races, formed

the basis of agriculture for thousands of years.Most of the plants used directly to produceagricultural products today have been selected andbred specifically for the purpose from their wildrelatives. While slow progress in crop improvementvia selection occurred at many places in the worldthroughout history, it was the birth of the laws ofheredity and the science of genetics around 1900that turned plant breeding into a science-basedprogressive technology.

Todays most advanced plant breeding involvesthe improvement of plants by selection of themost favourable combinations of (all) the allelesin the species via knowledge-based proceduresand in some cases via the addition of new genesdesigned in the laboratory to confer specific prop-erties. It depends on the integration of genetics,

mathematics with statistics, chemistry, pathology,cytology, molecular biology and computationalbiology, together with considerable automation,data handling and analytical systems. It is themolecular biology, automation and data handlingthat have changed so much over the past 1020 years. These technical advances have beenespecially extraordinary and have set the stagefor developments that offer opportunities unparal-leled in the history of mans exploitation of plants.The two chapters in this introductory volumeprovide overviews of firstly, the theory and practiceof plant breeding, secondly, many of the appli-cations of plant biotechnology in the provisionof food, feed, fibre, chemicals, drugs and energyas part of, and in addition to, plant breeding.

The diversity in the plant kingdom is immense.

While a large number of species have been ex-ploited directly to sustain societies, the proportionused to provide food for most people is very small.Tree species are perennial sources of food such asfruits, as well as fibre for construction and paper,while medicines and drugs are extracted fromorgans of a very few species. The diversity in theplant kingdom is a big challenge for plant breedingand biotechnologyso many species needresearchand development to be deployed on them.

PLANT BREEDING

There are many products that illustrate thespectacular successes of plant breeding. For ex-ample, maize and wheat are essentially man-made

Handbook of Plant BiotechnologyEdited by Paul Christou and Harry Klee C 2003 John Wiley & Sons Ltd


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2 HANDBOOK OF PLANT BIOTECHNOLOGY

crops. Their ancestral wild forms are considerablyinferior for food production from many points ofview. Todays tomatoes and potatoes have beenbred from small toxic wild forms (e.g., Frary et al.,2000). The Green Revolution in wheat andrice was possible because of the recognition andincorporationof novel dwarfing mutant alleles intocultivators in the 1950s and 1960s.

Plant breeders base their goals and activitieson knowledge of the consumer and farmers to beserved, the environments in which the plants needto succeed and the biological and genetic featuresof the species. Yield in the various environmentsin which a crop is grown is a near-universalbreeding objective. To optimise yield, it has beennecessary to select for tolerance/resistance to pestsand diseases, to abiotic stresses such as drought,

salinity, heavy metals, cold or heat and a host ofother factors includingflowering time, seed quality,taste and industrial utilities. The genetic featuresof a species determine whether true breedinghomozygous cultivars or F1 hybrids are required.If true breeding homozygous cultivars are requiredthenthe breeding strategy has to involvecreation ofnew combinations of genes, selection of preferredphenotypes and then production of homozygouslines. The selection can be early or late in the pro-cess. Homozygosity can also be created early viachromosome doubling in haploids or late. For out-breeding species the cultivar can be an improved

population of genotypes or single or double crosshybrids. The various breeding strategies that arefollowed are based on a statistical understandingof quantitative genetics. Plant breeding and plantperformance are based on all the genes in aplant. Thus, they have a very complex basis. Thiscomplexity has been modelled by quantitativegeneticists (Mackay, 2001), butnow the complexityis being defined in physical and functional detailby genomics. Genomics is the term given tothe generation and study of large quantities ofdata comprising chromosomal DNA sequences,genes, the time and place of expression of thegenes, gene-phenotype associations, genetic andphysical maps and the details of genetic variation.

GENOMICS

Genomics has developed from technology devel-opments in molecular biology especially in genediscovery and characterisation technologies whose

development lies outside the plant kingdom. Theprocess of gene purification via cloning came frombacterial genetics and the ability to splice novelDNA into replicating plasmids and to select andpropagate the rare plasmid containing the desiredgene. Efficient, high throughput sequencing ofcomplete plant genomes, expressed sequence tags(ESTs) and full-length cDNAs, followed major in-novationsin automated sequencers and computingand ways of assembling and analysing the hugeamounts of sequence data. This biotechnologyresearch is now underpinned by a diverse arrayof industries supplying reagents and equipment.Entrepreneurs and venture capital investmentshave developed many such industries.

The extraordinary technical developments inplant molecular genetics, over the past 20 years,

culminated at the end of 2000 in determination ofalmost all the complete nucleotide sequence of thenuclear genome of the plant Arabidopsis thaliana(Arabidopsis Genome Initiative, 2000). So, for thefirst time in the history of plant biology it waspossible to start analysing the genetic content ofa species, predict all the genes to discover thefunctions of each of them and start the long haulof discovering how the set of 30 000 to 70 000genes provides the developmental complexity oftheorganism andits differences from other species.The complete sequences of two rice genomeswere reported in 2002 (Goff et al., 2002; Yu

et al., 2002) and several more complete plantgenome sequences will emerge in the next fewyears(Chandler and Brendel, 2002; VanderBosch andStacey, 2003). New information indicates that thegenomes contain not only well-known kinds ofgenes but many sources of transcribed RNA thatare involved in the post-transcriptional controlof mRNA levels and thereby in regulating plantdevelopment (Kidner and Martienssen, 2003).

In the model species Arabidopsis and rice, pro-grammes are very advancedto obtain mutations inevery genefor gaining knowledgeabouttheir func-tion. In addition, in species favourable for transfor-mation, genetic variants are being created by thedesign, construction and insertion of novel copiesof each gene, expressed differently or encoding anovel protein variant. This also provides in vivoknowledge on the role of each gene and protein.

It has been known for over three decadesthat chromosomes contain many families ofhighly repeated sequences. Some are organised in


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INTRODUCTION TO PLANT BIOTECHNOLOGY 3

large arrays, especially around centromeres andtelomeres. The molecular biology of centromereand telomere functions dependent upon thesearrays is now becoming known. Other families ofrepeats have evolved from transposable elementsthat spread through chromosomes of populationseither via movement of the DNA element itselfor via transcription intermediates. The movementof such elements leads to considerable struc-tural diversity of chromosomes during evolutionand many mutations affecting gene function.These mutations lead to silencing, down- or up-regulation of gene expression.

The sequencing and mapping of these elementsand genes along plant chromosomes, within andbetween species, is revealing the molecular basisof variation that has evolved during species

divergence, that breeders have been working with(Tenaillon et al., 2001) and the haplotypes thathave been selected to create successful crops (Chinget al., 2002). These comparisons are opening upthe powerful subject of comparative genomics.The most noteworthy discovery of comparative QA1genomics for plant biotechnology to date is thefinding that during the divergence of grasses,the order of genes along large chromosomalsegments has been conserved (Gale and Devos,1998). This conservation has occurred despitethe accumulation and deletion of large quantitiesof repeated sequences and transposable elements

between the genes. The practical significanceof thisconservation is that from the complete sequence ofthe rice genome, the position of related genes canbe predicted in the chromosomes of maize, wheat,barley, millet, sugarcane and all other grasses,once the related chromosome segments have beenaligned. This has greatly helped the productionof genetic maps of all these species and hence,breeding strategies.

Knowledge of gene sequences allows proteinproduct sequences to be predicted. Comparativeprotein analysis across the kingdom is helping topredict the functions of closely related proteinsfrom any other organism once the function of aprotein is discovered in one organism.

While the function of individual proteins can beassessed from in vitro studies or from comparativestudies across the kingdom, the in vivo function ina plant needs to be assessed via genetics, assumingthat there is genetic variation for the gene orvariations can be created. Genetic analysis of a

few crop plants and some tree species is becomingwell developed. Such analyses have provided thechromosomal location of quantitative trait loci(QTLs) that contribute to key characteristics ofplant size, shape, yield, chemical composition,disease resistance and tolerance to biotic stresses,etc. The analyses were painstaking till the last10 years or so, because they were dependent onother phenotypically expressed genetic markerswhich are present on the same chromosome toassay linkage. With the deployment of restrictionenzymes, PCR and DNA sequencing, variantscan now be discovered rapidly for almost anychromosome sequence and hence detailed mapscan now be readily constructed for any species.All genomes appear to contain a huge numberof arrays of repeating nucleotides due to frequent

errors in replication,deletion and expansion viaunequal crossing over (Tautz, 1989). These min-isatellites provide prolific and easy-to-measurepolymorphisms and have revolutionised the ge-netic mapping of genomes. Complete genomesequencing and genetic mapping, i.e. expandingknowledge about chromosome segments thatcontain genetic variants affecting vital charactersleadsusintoaneraofin vivo genefunction analysis.High-throughput analyses of single nucleotidepolymorphisms are also being brought on line toallow rapid analyses of haplotypes and mutationslinked to QTLs (Rafalski, 2002).

The combination of genomics, genetics andplant breeding is leading to an understanding ofthe genes (alleles) involved in specifying valuableattributes in crop species. The availability ofmolecular markers covering the entire genome of acrop is driving molecular marker-assisted breedingto make plant breeding more efficient. Theprinciples and practice of efficient plant breeding,incorporating high-throughput genomics are nowestablished. There is now a need to establishthese procedures in more corporate and publicsector breeding programmes and for more crops.Reductions in cost coming from new innovationand more efficient deployment should greatly helpmore widespread use of marker-assisted breeding.

TISSUE CULTURE

The culture of plant organs and cells is importantin many areas of plant biotechnology. In plant


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(cereal) breeding, haploid cells in anthers areroutinely cultured for chromosome doubling, andthen regenerated to produce doubled haploidhomozygous plants (Forster and Thomas, 2003).In the process of creating transgenic plants,transformed cells are proliferated in culture beforebeing induced to differentiate again into roots,shoots and whole plants.

The biochemistry of cells in culture is signifi-cantly different from that in differentiated cells andthis has been exploited for looking for metabolitesthat are formed rarely in whole plants. Certainplant species and tissues can be induced to formsingle cell, or a few cell, cultures very rapidlyand these are used in fermenters to facilitatethe controlled, contained production of valuablemolecules in the cells. While this technology

has held much promise, it is being displaced inemphasis as transgenic plants are providing newways of modifying pathways and boosting yieldsof desired metabolites. In some cases cells can becultured in fermenters and then be provoked toform somatic embryos by hormone manipulation.The massive production of such embryos facilitatesthe clonal production of large numbers of identicalseedlings (Guha and Maheswari, 1964).

Some species, including some agriculturallyimportant species can be propagated asexually.Clonal propagation offers a way of multiplyingcomplex genotypes (e.g., hybrids) and this has

a major place in many industries, e.g., forestry,potato production, horticulture (e.g., strawberries)and floriculture.

TRANSGENIC PLANTS

In 1982, the first fertile transgenic plants werecreated and in the following decade or so, over 100plant species were transformed worldwide. Today,twomain procedures are usedfor introducing novelgenes into plants. The most widely used procedureis that evolved in the soil-borne bacterium,Agrobacterium tumefaciens, to transfer a specificsegment of one of its plasmids into plant cells.The other is biolisticsthe shooting of DNAinto cells. Following both methods, transformedcells are selected in culture and regenerated intowhole plants. Both procedures result in one, orfrequently more than one, copy of the novelgene being integrated into the plant chromosome.

Although frequently the genes behave as regularMendelian genes, they can be affected by theenvironment in which they reside and also becomeepigenetically modified with methyl groups. Thiscan alter their activity. Thus, it is important thatmany transformants are made and sifted to findindividuals in which the gene behaves stably asrequired in plant breeding and commerce.

The commercial plantings of transgenic cropstoday include soybean, corn, canola, cotton andpapaya. Acreages have increased each year sincetheir introduction in 1996. They have been greatestin the USA where they were first produced butare now being adopted in all continents includingdeveloping countries, but not in the EU. Thesoybeans have been engineered to be resistantto the herbicide glyphosate, easing weed control,

while the cotton and corn cultivars carry a novelgene that encodes a protein that is toxic tospecific insect larvae, thus protecting the cropsfrom damage by these pests. This protectionprovides considerable financial savings due to thereduced use of insecticides, which are also a healthhazard. The introduction of these transgenic cropcultivars on this scale is the most rapid adoption ofcultivars ever and is witness to the extraordinaryimprovements that can be made using carefullyselected transgenes.

Before transgenic products can be releasedinto commerce they need to be deregulated

by government agencies or their allowed usedefined. The process of gaining the informationrequired by the government agencies can be verytime consuming and relatively expensive. Thismakes the cost of developing transgenic productsfor commerce greater than for non-transgenics.Thus, it is currently recognised that transgenicagricultural products need to be substantiallybetter than existing cultivars before they becomefinancially worthwhile to the producer.

Governments have drawn up the guidelinesfor allowing the release of transgenic plants(genetically modified organisms, GMOs) into theenvironment and into food/feed chains, basedupon many criteria. The reasons for treatingthem as distinct from non-GMO products arebased on the assumptions that it is possible tocreate products by foreign gene insertion thatare toxic to people or the environment, andthat gene flow from transgenic crops to wildrelatives and non-transgenic crops via pollination


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may have consequences that are unwanted inthe short- or long-term. Different societies andgovernments differ in their views on the accept-ability of GMOs in food and local environments.This is currently causing considerable confusionfor the international food/feed producers, foodprocessing industries and consumers. For the pastfew years there has been a moratorium on thegrowing of such products in the EU. While theUSA,Argentina, Australia, Canada and China, forexample, have embraced specific transgenic plants,the EU and other countries are being extremelycautious. The EU has decreed that all productsfrom transgenic plants are labelled as such. Theconsequential effects of the EU stance on worldtrade issues are large. The EU decision to label theproducts of GMOs is leading to the requirement to

identify the existence of transgenes in all productsand trace the transgenes from seed to product. Therequired assay systems that need to be deployedat many steps in the chain are providing newopportunities for biotechnology companies thatprovide such detection kits and services.

MACROMOLECULES AS RAW MATERIALSAND HIGH VALUE PRODUCTS

The principal molecules in plant organs harvestedfor food, animal feed or industrial uses are

carbohydrates, proteins and oils but there are alsoa host of other molecules in lower concentration.Plant biotechnology research has focused on thesevaluable molecules not only for their value inthe food and feed industries but also for the hugerange of other industries that incorporate thesemolecules into their products. Sometimes the cropscontaining these molecules are produced specifi-cally for the industry in question and sometimesthey are bought as commodity byproducts of theagricultural/food/feed processing industries.

Starches in grains are composed of amyloseand amylopectin chains of varying lengths andbranches. The properties of the starch are deter-mined, in part, by the chain lengths and degrees ofamylose branching. Manipulation of the levels andkinds of the enzymes involved in starch biosynthe-sis create starches with different properties suitablefor different industrial purposes. This has been avery active field of R&D, especially in corn andpotatoes, the major sources of industrial starch.

Theoils from oilseeds areused widelyin industryand are also a major source of oils for foodproducts and cooking. The length of the carbonchain and the extent of unsaturation in the oilare key parameters in determining the propertiesof the oils. Reductions in C18 polyunsaturatesin consumed products are desirable for healthreasons. By adding different oil biosynthesisenzymes, or reducing the levels of existing ones,major changes in the fattyacid profile canbe made.For example, by adding a thioesterase from thebay tree to canola, it was possible to increase theconcentration of lauric acid from 0 to 40% of thetotal fatty acidsin seeds. Manipulationof fatty acidprofiles has been a significant R&D activity.

DHA (docosahexenoic acid) and EPA (eicos-apentenoic acid) are fatty acids that enhance

human health. They are present in fish andmicroalgae but absent in plants. The transfer ofthe genes from fish and microalgae into an oilseedplant to make an alternative, cheap source ofthese fatty acids for human consumption is anattractive proposition. Many chemicals derivedfrom petroleum are used in adhesives, paints,detergents, lubricants, nylon, cosmetics, etc. Theopportunities of producing specific desirable formsin plants via agriculture increases with the abilityto design transgenics.

It may become economically worthwhile makingplastics such as PHA (polyhydroxyalkanoate) and

PLAs (polylactides) in plants by adding the rele-vant microbial genes that direct synthesis of thesepolymers. Many products are now nutritionallyenhanced by the addition of vitamins and antioxi-dants. By adding or manipulating genes encodingthe relevant biosynthesis pathways it should bepossible to create plants that are nutritionallyenhanced endogenously and so be considered asfunctional foods or nutraceuticals. The mostwell-known example today is perhaps golden rice,that contains genes encoding three enzymes thatlead to accumulation of provitamin A, a moleculethat can relieve blindness in children whose majordiet is rice based.

Plant proteins in cereal seeds that are used asmajor sources of animal feed are often low inessential amino acids such as lysine, methion-ine and cysteine. Biotechnological manipulationshave led to increase in these essential aminoacids. The pharmaceutical industry also focuseson producing antibodies and antigens that are


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proteins (Chargelegue et al., 2001; Cramer et al.,1998). These may be produced cost effectivelyin animal or microbial cells. However, where theamounts required are extremely high, plants maybe much more economically suitable productionvehicles (Ma et al., 1995). There is therefore nowa lot of activity in producing large quantities oftherapeutic proteins in transgenic plants. Associ-ated with these initiatives is discussion about thedesirability of producing pharmacologically activemolecules in crop plants also used for food/feed.The probability that mistakes will happen inkeeping the seed lots separate is too high, someargue.

Transgenic plants may be good productionvehicles for industrial enzymes and other proteinsnot known to be pharmacologically active (Hood

et al., 1999). Thus, several companies are insertinggenes for enzymes into plants, growing andharvesting the plants and purifying the requiredenzyme. This is a growth opportunity in plantbiotechnology. The promise of massive productionof specific proteins in plants has given rise toa plethora of ingenious promoters, expressionvectors and ways of exploring amplification ofgene templates via viral vectors in order to boostproduction of the desired proteins.

METABOLITES

Many important ingredients in food and feed aremetabolites. Plant biotechnology is increasinglyfocusing on defining the genes and enzymesresponsible for the production of thesemetabolites,and in particular, how production is regulated.Many flavonoids, terpenes, alkaloids and vitaminsare made in only specialised cells or in response tobiotic or abiotic stresses and so understanding andmanipulating the complex pathways of secondarymetabolism is an exciting opportunity. Alreadymany of the genes specifying pathways have beencharacterised and specific plants making largeramounts of nutritionally important metabolitessuch as lycopene and vitamin E have been created.

Many of these secondary metabolites also haveeffects as antagonists or agonists on other cellularmolecules. They can thus be a source of fungicides,insecticides or herbicides in agriculture if they killor inhibit growth of the target organisms but notthe crop. Thus, the agrochemical industries have

sought extensively to find such potentially valuableagrochemicals from plants. Where the secondarymetabolites agonise or antagonise targets in man,they can be a source of drugs, e.g., aspirin,taxol, codeine and vincristine. Thus many phar-maceutical and small biotechnology companieshave undertaken large screening programmesinvolving tens of thousand of species lookingfor plant metabolites that interact with knowntarget molecules or processes in animal cells orin bacteria or fungi that are harmful to humans.The discovery of a valuable new drug is rare.This is because of many reasons. One of themis that many of the plant tissues used in thescreens have not been optimised for the levels ofsecondary metabolites likely to serve as drugs.Here is an opportunity for plant biotechnology

to serve the pharmaceutical industry better. Also,even when a potential drug has been characterised,producing enough of it from natural sources maybe problematic or prohibitively expensive. Heregenetic or environmental manipulation of themetabolic pathway to produce much more of thedesired product can be extremely valuable.

CLOSING PERSPECTIVE

Plant biotechnology, like all aspects of the lifesciences, has changed very rapidly over the past

20 years. The new ways of analysing genes,molecules and processes constitute new platforms,together with established plant breeding systems,for discovery, product design and making novelproducts. These products will be improved sourcesof food, feed, fibre, energy, chemicals or drugs.The knowledge of the ways plants develop theirarchitecture, survive abiotic and biotic stresses,utilise fertiliser, water and CO2, and make complexsecondary metabolites and macromolecules willincrease much more rapidly than over previousdecades. Most importantly the genes and allelesthat programme these attributes will becomeknown rapidly from the combination of genomics,genetics and plant breeding for the speciesintensively studied. The poorly understood specieswill remain a challenge, butcomparative moleculargenetics will enable them to be investigated muchmore rapidly than before.

There is a new vast array of genes and promotersavailable from genome sequencing in all kingdoms.


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This toolbox provides a limitless number ofoptions to explore the improvement of plants forcommercial and social benefits via the addition oftransgenes.

From standpoint of the research one canexpect that the properties of plants will changeconsiderably over the coming decades, giventhe new opportunities to reprogramme themgenetically. However, which products will emergedepends on which forms are economically andenvironmentally sound and socially acceptable. QA2The accompanying chapters summarise much ofthe technologies, progress and future perspectivesfor plant biotechnology. They illustrate that theprinciples of the new plant biotechnology are nowwell established, butof course, the technologies willcontinue to change due to innovations and new

examples will come andgo as options areevaluatedscientifically, economically and socially.

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QUERIES TO THE AUTHOR

QA1. Please check whether the meaning of this sentence is retained after editing.QA2. Please provide names of all authors for this reference. (Goff SA et al. (2002))QA3. Please provide names of all authors for this reference. (Yu J et al. (2002))

Introduction to Plant Biotechnology

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