1

ASSIGNMENT ON:

GENETICS AND MODERN

AGRICULTURE

SUBMITTED BY : AKHILA A B NAIR

P2015002
1st MSc ZOOLOGY
FATIMA MATA NATIONAL COLLEGE,
KOLLAM
SUBMITTED TO : DR. SARLIN P J
ASSISTANT PROFESSOR
FATIMA MATA NATIONAL COLLEGE,
KOLLAM
SUBMITTED ON : 09/09/2021
 2

SL.NO TITLE PAGE NO.

1 INTRODUCTION 4
2 APPLICATIONS OF 5-6
NEW GENETICS IN
FOOD AND
AGRICULTURE
3 AGROBACTERIUM 6
MEDIATED GENE
TRANSFER IN PLANTS
4 COMMERCIAL 7
CULTIVATION OF
TRANSGENIC CROPS
5 EMERGING 8
SCIENTIFIC
DISCOVERIES FOR
ADDRESSING
COMPLEX TRAITS

6 THE FUNCTION AND 9-12

REGULATION OF
PLANT GENES—
GENOME-WIDE
ANALYSES
PROVIDING A FIRM
FOUNDATION FOR
THE NEW GENETICS
IN CROP
IMPROVEMENT
7 13
IMPROVING THE
ESSENTIAL AMINO
ACID BALANCE IN
PLANT PROTEINS
USED FOR FOOD
AND FEED
 3

8 ENGINEERING THE 14-15

METHIONINE
BIOSYNTHETIC PATHWAY
IN PLANTS

9 EXPRESSION OF 15-16
METHYONINE RICH
PROTEINS IN GM PLANTS

10 MANIPULATING SEED 16-18

FATTY ACIDS FOR HUMAN
NUTRIRION AND FOR
INDUSTRY

11 DISCOVERY AND USAGE 19-21

OF GENES FOR
IMPROVED DISEASE
RESISTANCE IN CROP
PLANTS

12 CONCLUSION 22-24

13 REFERENCE 25
 4

INTRODUCTION

The current tools of enquiry into the structure and operation of the
plant genome have provided us withan understanding of plant
development and function far beyond the state of knowledge that
we hadpreviously. We know about key genetic controls repressing
or stimulating the cascades of geneexpression that move a plant
through stages in its life cycle, facilitating the morphogenesis of
vegetative and reproductive tissues and organs. The new
technologies are enabling the identification of key geneactivity
responses to the range of biotic and abiotic challenges experienced
by plants. In the past, plant breeders produced new varieties with
changes in the phases of development, modifications of plant
architecture and improved levels of tolerance and resistance to
environmental and biotic challenges by identifying the required
phenotypes in a few plants among the large numbers of plants in a
breeding population. Now our increased knowledge and powerful
gene sequence-based diagnostics provide plant breeders with more
precise selection objectives and assays to operate in rationally
planned crop
improvement programmes. We can expect yield potential to
increase and harvested product quality portfolios to better fit an
increasing diversity of market requirements. The new genetics will
connect agriculture to sectors beyond the food, feed and fibre
industries; agri-businesswill contribute to public health and will
provide high-value products to the pharmaceutical industry as well
as to industries previously based on petroleum feedstocks and
chemical modification processes.
 5

APPLICATIONS OF NEW GENETICS IN FOOD AND

AGRICULTURE
Applications of modern genetics are being used to
improve the efficiency and sustainability of agricultural practices
today. For example, recent discoveries have led to:

• Better understanding of how plants function, and how

they respond to the environment.
• More targeted selection objectives in breeding programmes
to improve the performance and productivity of crops, trees,
livestock and fish, and post - harvest quality of food .
• Use of molecular markers for smarter breeding, by
enabling early generation selection for key traits, thus
reducing the need for extensive field selection.
• Molecular tools for the characterization, conservation and
use of genetic resources.
• New molecular diagnostics, to assist in the improved diagnosis
and management of parasites, pests and pathogens.
• New vaccines to protect livestock and fish against lethal
diseases.

Such applications, which are already making substantial

contributions to agriculture in both industrial and developing
countries, use information derived from modern genetics
and new molecular techniques. ( For examples, see: CGIAR
2 0 0 0a; IFPRI 2001; ISNAR 2002b; ICSU 2002; Agricultural
Biotechnology Country Case Studies, Persley and MacIntyre,
2001; Serageldin and Persley, 2003).
New scientific discoveries in modern genetics, and particularly gene
technology, also provide options for the targeted introduction of
transgenic strains that are genetically modified for one or more traits.
 6

Transgenic strains are produced by means of recombinant DNA

technologies (genetechnol ogies ) that enable the movement of genes
between species that do not normally cross in nature. Although
transgenic strains of various species of crop s, trees, livestock and fish
have been developed experimentally, only transgenic crop varieties are
in widespread commercial use in agriculture today.

AGROBACTERIUM-MEDIATED GENE TRANSFER IN PLANTS

In plants, the process of genetic engineering was driven by

the discovery that a common soil borne bacterium and plantpathogen,
Agrobacterium tumifaciens, had a means by
which it naturally transferred some of its own bacterial DNA
into targeted plant cells, and this transfer and integration of
bacterial DNA into the plant cells then caused the plant cells
to produce new compounds for the bacterium to use. It is this
naturally occurring transformation process that provided the
scientific basis for genetic engineering in plants. A recent report by the
French Academiedes Sciences (2002) highlights the importance of this
fundamental discovery about Agrobacterium, as the basis for genetic
engineering in plants.
Agrobacter ium is now being used as a biological transfer agent to
move one or more genes from bacteria to plants, from plant to plant,
and theoretically from any other organism into plants. For example,
insect resistant plants contain toxin - producing genes from the
bacterium, Bacillus thuringensis (Bt) introduced into cotton, corn and
other crops.Herbicide tolerant soybean contains genes isolated from
soil - borne bacteria. A modified strain of Agrobacterium tumifaciensis
also being used for the biological control of crown gall disease, the first
 7

genetically modified organism to be released into the environment for

commercial use( Ke r r, 1991).

COMMERCIAL CULTIVATION OF
TRANSGENIC CROPS

The first transgenic plants were produced experimentally

in 1983, by means of Agrobacterium-mediated gene transfer.
The commercial cultivation of transgenic crops began in
1995. By 2002, there were approximately 58.6 million
hectares of genetically modified crops growing in sixte e n
co un tr i es (ISAAA 2002b ) . These crops are mainly soybean ,corn,
cotton and oil seed rape (canola), with resistance to certain insects and
/or herbicide tolerance ( Figure 2.1). Many
other crop/trait combinations are under investigation

Broadly, the first wave of genetically modified crops,

which are in commercial use, address production traits; the
second wave, which are mainly under development, address
quality and/or nutritional traits; and the third wave address
complex stress response traits and novel products able to be
produced in plants. The scientific basis of dealing with each
of these groups of traits is increasingly complex (ICSU 2002).
Several socio-economic studies have assessed the benefits
derived from specific applications of genetically modified crops and
other applications of modern genetics in agriculture.
For example, the benefits derived from Bt cotton are
documented in several countries, including Australia, China,
South Africa and the USA (e.g. ISAAA 2002a; Pray et al. 2002,
Pardey et al. 2002).
 8

EMERGING SCIENTIFIC DISCOVERIES FOR

ADDRESSING COMPLEX TRAITS

Most characteristics of food are controlled by more than

one gene. Thus taste, aroma, colour, nutritional composition
and other aspects of food quality are the result of complex
biochemical reactions within the plant before and after harvest.
Emerging scientific developments are enabling complex
traits that are controlled by multiple genes to be addressed,
with the intention of developing new products of potential value for
food and agriculture, human health and the environment. The
attractiveness of the new targets is tempered by the fact that they are
technically difficult, requiring the expression and control of several
genes, which are often involved in different biochemical pathways. The
scientific basis of these developments in genomics, proteomics and
metabolomics and related areas is reviewed in a companion ICSU
publication on Biotechnology and Sustainable Agriculture (ICSU 2002).
These emerging scientific possibilities also pose new challenges
in the assessments of the risks and benefits of potential
new products to human health, biodiversity and the environment.
Some of the potential products are meant for food or
feed use, while others are intended for use as pharmaceuticals,and
others as compounds for industrial uses. Some will require inter specific
transfer and control of multiple genes. Other will rely on switching on
/or off and better regulating genes that are already present in the
organism but not usually expressed. New scientific developments also
offer potential means to overcome some of the risks in the cultivation
 9

of genetically modified crops and other living modified organisms (for

eg:by limiting gene flow to related and/or wild species).
 10

THE FUNCTION AND REGULATION OF PLANT

GENES—GENOME-WIDE ANALYSES PROVIDING
A FIRM FOUNDATION FOR THE NEW GENETICS
IN CROP IMPROVEMENT
The ways in which plants develop and respond to the environment in
order to produce an optimal yield of food or fibre is the result of the
controlled expression of the approximately 30 000 genes that are present
in the genome of all plants. The role of genomics is to define the
function of these genes, determine how they are regulated and how their
gene products interact. These findings can then be applied to crop
improvement.
The genome of Arabidopsis thaliana, a dicot (or broad-leafed species)
related to the Brassicas (like canola and cabbage), and the genome of
rice, a monocot, have been completely sequenced (The Arabidopsis
Genome Initiative 2000; Goff et al. 2002). Sequencing of the genomes
of a number of other species—maize, lotus, Medicago truncatula,
poplar, grape and tomato—is underway
(www.ncbi.nlm.nih.gov/genomics). The two sequenced genomes serve
as basic references for all crop plants—Arabidopsis for the dicots and
rice for the cereals. The gene content of these two widely divergent
species is remarkably similar and it is probable that further genome
sequencing will reinforce the similarity of gene content across all the
flowering plants. The similarity of gene make-up of the genome of
different species is not necessarily mirrored by the way in which these
genes are regulated or by the interaction of their products in regulatory
networks; these properties can differ markedly. It is this difference in
patterns of gene expression that differentiate species. Genes that specify
secondary metabolites or particular attributes, such as structural
properties, have evolved from a common pool of genes. Gene
duplication, such as occurs in polyploidy, and acquisition of separate
functions or separate patterns of expression by each of the duplicated
genes has been a frequent avenue for providing variation to be acted on
by natural selection (Adams & Wendel 2005).
 11

Genomics can assist in identifying which genes are involved in

specifying particular characteristics of a plant. The first step in
identifying the function of a gene is to compare its nucleotide or amino
acid sequence with all of the sequences in databases derived from the
genomes of other organisms. A function may be assigned through
similarity to other genes with known function, hence genomes can have
usefulness across species or even across kingdoms in allowing us to
specify function. Genome-wide mutagenesis using transposable
elements such as Ac/Ds, Tos17 (an endogenous retrotransposon of rice)
or T-DNA insertions has resulted in the production of populations
consisting of many lines, where each line contains an insert in a single
gene. Since the DNA sequence of the insert is known, it is simple to
determine which gene has been disrupted by cloning the flanking
sequence. There is a set of Arabidopsis lines containing inserts in
approximately 80% of the genes and, in rice, a similar proportion are
tagged; these lines are freely available
(www.arabidopsis.org/abrc/ecker_frank.jsp and Hirochika et al. 2004).
These tagged lines can be made homozygous and their phenotypes
determined to associate a gene with a specific phenotype. The tagged
genes can then become candidates for crop improvement either as
DNA markers or directly in transgenic breeding.
Interruption of gene activity can also be generated by RNAi, a
supplementary form of mutagenesis, by which a construct introduced
into a plant gives rise to a double-stranded RNA that activates a
sequence-specific degradation mechanism that disrupts the mRNA of the
gene target which may produce a phenotype (Wang & Waterhouse
2002). The advantages of RNAi for functional genomics are that RNA
constructs targeted to a gene act in a dominant manner, and a gene in
any background (e.g. a mutant background) can be targeted. Recently,
synthetic microRNAs have also been used for gene silencing.
MicroRNAs play a role in the control of genes involved in plant
development and stress response so the new technology provides an
additional option for silencing. Because microRNAs are shorter (21 nt)
 12

compared with the 200–300 bp usually targeted by RNAi, conserved

regions in gene families can be targeted, silencing multiple genes
simultaneously (Alvarez et al. 2006; Schwab et al. 2006).
An essential aspect of applying genomics to crop improvement is that
there must be the ability to use high-throughput technologies to screen
for changes in phenotype. Phenotyping can involve automated growth
measurements and imaging under various environmental stress
conditions. It should also involve field-based screening as characters that
appear useful in the glasshouse are sometimes not maintained in the
field. Such high-throughput strategies have formed the basis for a
number of international consortia to characterize mutations or silenced
lines in specific classes of Arabidopsis genes (e.g. Agrikola, to identify
the functions of specific types of transcription factor genes (Hilson et al.
200

A second resource that complements and extends genome sequences is

gene arrays (microarrays), which consist of large numbers of
oligonucleotides or cDNAs arrayed on slides. For the sequenced
genomes all predicted genes can be included on the arrays. The arrays
can then be hybridized to RNA extracted from a particular tissue or
developmental stage from a mutant, or from a plant subjected to
environmental or disease stress to determine which genes are
preferentially expressed compared with expression in control wild-type
plants. The basic principle underlying microarrays is that if a gene is
expressed under certain conditions, it may play a role in that condition,
for example, genes induced by salt may provide protection in saline
conditions. For genomes that are not sequenced, expressed sequence tags
(ESTs) or anonymous cDNAs can be arrayed and hybridized in the same
way and candidate genes sequenced later. Using microarrays, genes with
expression patterns similar to those of known genes can be chosen
giving a greater choice of target, e.g. under anaerobic conditions genes
can be chosen with a similar expression response pattern to alcohol
dehydrogenase suggesting a similar involvement in the anaerobic
response. Data from many thousands of Arabidopsis microarray
experiments have been gathered together in the Genevestigator database
 13

(www.genevestigator.ethz.ch/) where data from different mutants,

different stages of development or different stresses are all gathered
together for public access. A reduction in the cost of sequencing has also
fostered the development of high-throughput sequencing of expressed
genes in cDNA libraries as an indicator of gene expression levels. Only
short stretches of sequence are required to match an EST to its gene
sequence, so massively parallel signature sequencing strategies provide a
good starting point for determining the expression levels of a particular
gene in the particular tissues or conditions of treatment of the plants
from which the libraries are made. These tools provide a ready
knowledge of where and when any particular gene is expressed. The
conservation of many genes and biological processes between species
means that expression patterns are also likely to be conserved, thus
interrogating the Arabidopsis expression databases with a gene sequence
from another plant can also provide some useful information in defining
the functional roles of that gene (e.g. Zhang et al. 2004).
 14

IMPROVING THE ESSENTIAL AMINO ACID

BALANCE IN PLANT PROTEINS USED FOR
FOOD AND FEED
Seeds are major sources of dietary protein for large vegetarian
populations around the world and intensively farmed animals. However,
the protein in seeds can have a skewed amino acid composition due to
the high abundance of a limited number of individual seed storage
proteins. Of the 20 protein amino acids, 10 are classified as ‘essential’
because they cannot be synthesized by animals, and consequently must
be obtained from the diet. Insufficiency of certain essential amino acids
can be a cause of malnutrition in countries that are dependent on a diet
of low diversity and can limit the efficiency of animal production.
Legume and cereal grains are particularly important for human and
animal nutrition, but their seed protein is deficient in the essential amino
acids methionine and lysine, respectively (Tabe & Higgins 1998; Amir
& Galili 2003). These deficiencies can be offset to some extent by
combining the two types of seeds, but animal feeds are still
supplemented with synthetic amino acids for optimal nutrition (Habben
& Larkins 1995). In developing countries, up to 90% of food intake can
be derived from a single crop species, so amino acid balance of
individual seeds becomes a critical consideration also for human
nutrition.In recent years, both genetic modification and plant breeding
with induced or natural mutants have achieved important successes in
modifying amino acid composition of cereals and legumes. This section
is focused on modification of mainly grain legumes to improve their
content of the essential, sulphur-containing amino acid, methionine.
Three approaches have been used: genetic modification to increase
methionine biosynthesis; genetic modification to increase methionine
storage in protein; and selection of mutants with increased methionine.
 15

ENGINEERING THE METHIONINE

BIOSYNTHETIC PATHWAY IN PLANTS
Sulphur is taken up from the soil in the oxidized form of sulphate and is
subsequently reduced in the plastids of plant cells, then incorporated into
an amino acid backbone derived from serine via the action of the
enzyme serine acetyltransferase. The product of this reaction is cysteine,
the first stable reduced sulphur metabolite in the cell, and a substrate for
many other biochemical pathways. Methionine is derived from cysteine
by the sequential action of three enzymes, the first of which,
cystathionine γ-synthase (CGS), combines O-phosphohomoserine from
the aspartate amino acid pathway and cysteine (Leustek & Saito 1999).
There are numerous reports in the literature of genetic manipulation of
the activities of the enzymes of reductive sulphur assimilation and
sulphur amino acid biosynthesis (reviewed by Amir & Tabe (2006)).
Some dramatic increases in free cysteine and methionine have been
observed in the leaves of the GM plants, sometimes at specific growth
stages. However, free amino acids are much less abundant in planta than
protein-bound amino acids. Consequently, in the few cases where total
amino acid composition was analysed, these manipulations had
relatively minor effects on total methionine concentration. For example,
constitutive expression of a CGS enzyme from A. thaliana in GM
tobacco or GM alfalfa increased free methionine in the leaves, but had
no significant effect on protein-bound methionine (Hacham et al.
2002; Bagga et al. 2005). On the other hand, in a rare exception to this
generalization, expression of a mutated form of CGS in GM tobacco
resulted in not only a large increase in free methionine in the leaves, but
also a twofold increase in protein-bound methionine compared with
controls. The high-methionine GM plants showed a severe, abnormal
phenotype (Hacham et al. 2002). In summary, in most studies,
increasing flux through the methionine biosynthetic pathway seems to
have produced little increase in the methionine content of endogenous
plant protein.Photosynthetic source leaves are assumed to be the major
sites of sulphur assimilation in plants; however, it has been demonstrated
that the pathway of reductive sulphur assimilation is active in
 16

developing soya bean seeds (Sexton & Shibles 1999) and that sulphur
amino acid biosynthesis occurs in developing embryos in the grain
legume, Lupinus angustifolius (Tabe & Droux 2001). Thus sulphur
assimilation in the developing seed itself appears to be an important
source of sulphur amino acids for legume seed storage protein synthesis.
Recently, manipulation of the cysteine biosynthetic pathway in
developing lupin seeds was shown to result in large increases in free
cysteine, although free methionine and total sulphur amino acid levels
were not increased (L. Tabe, unpublished data).

EXPRESSION OF METHIONINE-RICH PROTEINS

IN GM PLANTS
Expression of an added gene for a methionine-rich protein or
‘methionine sink’ has been a successful GM strategy for modifying plant
methionine content. This approach has been mainly used to improve the
amino acid balance of legume seed protein, which can contain less than
half the methionine required for optimal animal nutrition. Early attempts
to increase the content of methionine in seeds by transgenic expression
of genes for endogenous storage proteins mutated to add extra
methionine residues were unsuccessful (e.g. Hoffman et al. 1988). A
better strategy was the creation of a synthetic gene encoding an artificial
protein rich in essential amino acids. Expression of a synthetic protein
containing 31% lysine and 20% methionine residues in GM tobacco
seeds under the control of a seed-specific promoter increased the total
methionine concentration by 30% in the mature seeds (Keeler et al.
1997). A comparable result in a grain legume would give significant
improvement in the nutritive value of the seed protein.
Methionine sink manipulation has most commonly in involved
transgenic expression of naturally occurring, methionine-rich plant
proteins. Sulphur-rich proteins that have been expressed in GM dicots
include 2S seed albumins from sunflower, Brazil nut and sesame,
 17

proteins that contain up to 18% methionine residues (Altenbach et al.

1989; Kortt et al. 1991; Tai et al. 1999a,b). This strategy has mainly
been applied to the grain legumes owing to their low-intrinsic
methionine concentrations; however, seeds of other species such as
maize and canola have also been modified, not because they lack
methionine themselves, but as a means of providing additional protein
methionine in animal feed formulations containing grain legumes. For
example, sulphur-rich zeins containing up to 28% methionine residues
have been overexpressed in GM maize (Chui & Falco 1995).

MANIPULATING SEED FATTY ACIDS FOR

HUMAN NUTRITION AND FOR INDUSTRY
Crop and livestock production systems are the mainstay of the many
essential nutrients that support human life, health and well-being. As
more is being learnt about the specific role of key nutrients in human
nutrition, it is also becoming apparent that the supply of some nutrients
is compromised and in some cases may not be sustainable into the future
from current resources. The most notable of these potential shortfalls
relate to the long chain polyunsaturated fatty acids (LC-PUFA) of the
omega-3 (ω3) class, such as eicosapentaenoic acid (EPA, 20 : 5Δ5,8,11,14,17)
and docosahexaenoic acid (DHA, 22 : 6Δ4,7,10,13,16,19), that are found
predominantly in fish and other seafood. Inadequate levels of EPA and
DHA are typical in Western-style diets that are low in seafood and have
been associated with increased incidence of cardiovascular disease,
cancer, stroke, diabetes, inflammatory disease, neuropsychiatric
disorders and many other conditions prevalent in Western societies
(Simopoulos 2003). Consequently, nutritionists and health authorities
now regularly recommend significant increases in consumption of fish
and other seafood rich in EPA and DHA. However, it is now widely
acknowledged that global fisheries are fully exploited, with many on the
verge of collapse (Myers & Worm 2003), and they may be inadequate to
sustain even current levels of fish consumption. Fish farming and other
forms of aquaculture are rapidly expanding and can help to overcome
 18

the declining catch from wild fisheries, but many aquaculture systems
rely heavily on wild fisheries for feeds and are actually net consumers,
not producers, of ω3 LC-PUFA (Naylor et al. 2000; Pauly et al. 2002).
This situation means that existing marine-based sources of ω3 LC-PUFA
are unlikely to be sufficient to sustain current levels and anticipated
future increases in human needs.
Fortuitously, the advent of genetic engineering technologies is now
providing a solution to this dilemma through the development of
transgenic plants equipped with the ability to synthesize ω3 LC-PUFA.
This is being achieved by the transfer of genes encoding the EPA and
DHA biosynthetic pathways from marine microalgae and other micro-
organisms into agricultural crops, in particular oilseed crops. All higher
plants have the ability to synthesize the main C18-PUFA, linoleic acid
(LA, 18 : 2Δ9,12) and α-linolenic acid (ALA, 18 : 3Δ9,12,15), and some can
also synthesize γ-linolenic acid (GLA, 18 : 3Δ6,9,12) and stearidonic acid
(SDA, 18 : 4Δ6,9,12,15). However, higher plants are unable to further
elongate and desaturate these ω3 C18-PUFA to produce ω3 LC-PUFA
that are characteristic of the marine microalgae that are the ultimate
source of EPA and DHA found in fishes. Synthesis of ω3 LC-PUFA in
higher plants therefore requires the introduction of genes encoding all of
the biosynthetic enzymes required to convert ALA into EPA and DHA.
Substantial parallel gene discovery efforts conducted over the last 10
years in a range of LC-PUFA-synthesizing organisms have resulted in
the cloning of genes for all of the fatty acid desaturase and elongase
enzymes involved in the aerobic pathway for LC-PUFA synthesis and
have been reviewed in detail (Sayanova & Napier 2004). Recently,
significant progress has been reported in expressing these pathways
transgenically in seeds with the achievement of substantial levels of
EPA (20% of total fatty acids) in soya bean seed oil (Kinney et al. 2004)
and later the synthesis of low levels of DHA (1–2% of total fatty acids)
in A. thaliana (Robert et al. 2005) and Brassica juncea (Wu et al. 2005).
These studies used different combinations of LC-PUFA biosynthetic
genes from a variety of organisms and revealed the considerable
complexity associated with introduction of this multi-step fatty acid
 19

biosynthetic pathway into higher plants (Singh et al. 2005). It is

probable that additional or alternative metabolic manipulations will be
required in order to achieve significantly higher levels of DHA synthesis
and accumulation in transgenic seed oils. However, it is now clearly
apparent that seeds can be engineered to produce the range of ω3 LC-
PUFA required in the human diet and potentially in concentrations that
should be nutritionally effective. Crop plants engineered in this way will
ultimately provide the affordable, renewable and sustainable sources of
ω3 LC-PUFA that are urgently needed to overcome the inadequate and
potentially unsustainable supply from traditional marine sources.
 20

DISCOVERY AND USAGE OF GENES FOR

IMPROVED DISEASE RESISTANCE IN CROP
PLANTS
The use of disease-resistant crop cultivars provides an effective method
of controlling a large number of diseases. However, continuous breeding
efforts are required to counter evolution or migration of new pathogen
strains. One stumbling block continues to be the lack of agreement
regionally between breeders as to the most effective deployment of
valuable R genes to prevent their stepwise erosion by pathogen
evolution. Plant molecular biology is and will make increasing
contributions to resistance breeding by making resistance breeding more
effective and more efficient, especially through the use of markers for
breeding and providing resistance genotypes for varieties to improve
decision making about their deployment.

(a) DNA markers for breeding

Our efforts have been mainly targeted at rust, nematode diseases of

cereals and barley yellow dwarf virus, and molecular markers have been
developed for improved breeding efficiency. Effective genetic resistance
in wheat for cereal cyst nematodes is currently provided by
the Cre1 and Cre3 genes. Breeding new resistant varieties has, however,
been hindered by the slow and laborious nature of the plant bioassay for
nematode resistance. DNA markers have now been identified for both
resistance genes based on cloned genes of the nucleotide binding site–
leucine rich repeat disease resistance gene class (deMajnik et al. 2003).
These genes co-segregate with the Cre1 and Cre3 resistance genes and
although there is no direct evidence to indicate that the cloned genes
themselves control nematode resistance, they have provided excellent
 21

sources for development of simple, rapid and accurate PCR-based

markers that are currently being used by wheat breeders.
Wheat breeding has relied heavily on genetic resistance to rust disease to
control stem, stripe and leaf rust. Breeding efforts have been particularly
successful for stem rust using major genes for resistance and DNA
markers for resistance are being increasingly used. In areas where stem
rust resistance has been a major breeding objective, success has been
achieved mainly by using varieties carrying several different stem rust
resistance genes, diversity of resistance genotypes and discouragement
of the cultivation of susceptible varieties. DNA markers are now being
used increasingly for these breeding efforts. DNA markers need to be
simple to use and also applicable to as wide a range of breeders
germplasm as possible. For example, while some markers can be useful
for genetic mapping of resistance genes in particular crosses, they are
frequently not useful in all breeder lines where they fail to detect
polymorphisms between resistance gene donors and susceptible
recurrent parents. Consequently, there can be a long development stage
between marker identification and application that involves fine-tuning
to produce a robust marker across a range of useful genotypes.
Many wheat varieties carry the durable stem rust resistance gene Sr2 that
is effective in providing partial resistance against all strains of stem rust
at the adult stage of growth. PCR-based DNA markers have now been
developed for marker-assisted breeding using the Sr2 gene
(Spielmeyer et al. 2003), and have provided an entry point to finely map
this gene for future molecular cloning (Kota et al. 2006) with the aim of
understanding the molecular basis of an adult plant, durable, non-strain-
specific resistance gene. Several other stem rust resistance gene markers
have been developed and are described below. Good progress is being
made in developing a PCR-based marker for the durable adult plant leaf
and stripe rust gene pair Lr34–Yr18.
 22

(b) DNA Markers useful for gene stacking

Pyramids or gene stacks of multiple stem rust resistance genes in a
single variety can provide durable resistance. Traditionally, R gene
pyramids are achieved using sequential bioassays with rust strains
capable of differentiating those different resistance genes. This
becomes more difficult for breeders if each of the genes used
provide resistance to all available pathogen strains. This is where
DNA markers will make a big contribution to providing simple tests
for the presence of specific R genes. For stem rust, markers
for Sr38, Sr24, Sr26, SrR and Sr31 have now been developed (Seah et
al. 2001; Mago et al. 2005a,b). The latter four genes provide
resistance to all stem rust strains currently found in Australia and
the markers for Sr24 and Sr26 that provide resistance to the
proliferating strain Ug99 now found in Africa will have global
applications.

(c) DNA Markers for ‘value adding’ to alien resistance

sources
Many of the currently effective stem rust resistance genes are derived
from wheat relatives and many have negative dough characteristics that
are physically linked to the same chromosome region as the resistance
genes. They are consequently not suitable for use in high-quality bread
wheats. For several of these R gene sources, the flanking alien chromatin
regions have been reduced by recombination in ph1b mutant background
(Lukaszewski 2000). DNA markers are also being used to detect
recombinants carrying the R gene, but with reduced alien flanking DNA
(Rogowsky et al. 1991). Retained DNA markers are being used for the
deployment of the modified sources of Sr31, SrR and Sr26 to produce
near-isogenic lines for assessment of yield and quality effects and
introduction as pyramids into adapted cultivars
 23

CONCLUSION
The topics discussed in this paper present a set of examples of the ways
in which genetic modification to the biological software of our major
food and fibre production plants will continue to enhance the yield and
sustainability of agricultural systems. DNA technology is now routinely
used in plant improvement programmes with DNA sequence markers
enhancing both the speed and the power of selection schemes. Our
rapidly increasing knowledge of the functioning of crop genomes has
already provided enhanced performance in conventional breeding
programmes and although transgenic crops have not been welcomed in
all parts of the world, they have already gained significant approval
levels as judged by their use in approximately 4% of the production area
globally and that area has been increasing substantially in each of the
last 7 years.
These transgenic crops, including a fibre crop, cotton and the food and
feed crops maize, soya bean and canola, have all been accepted in the
various countries of the world in which they are grown and have entered
successfully into markets. This represents a significant growth
incorporation of transgenic modifications into breeding systems.
The understanding of the molecular bases of plant processes that we
have gained from the advances in genomics and our increasing
knowledge of gene regulation are opening up a new generation of
breeding advances, both through transgenic breeding and conventional
breeding. One of the advantages in many crops is that once precise
breeding objectives have been defined by research that has used all the
power of the new technologies, then breeders are able to use new
diagnostic tools to achieve the desired objectives through conventional
breeding programmes. This is providing a bridging period of
improvement in plant breeding while our societies move towards general
acceptance of transgenic tools in plant improvement programmes for our
food, feed and fibre crops.
 24

The examples in the paper range over improved environmental

responses and improved protection against pests and pathogens together
with improved nutritional value of crop products. There are likely to be
many other possibilities for tailoring our crop species in the future. For
example, breeders in the past have been able to adjust the architecture of
plants to fit agricultural systems; breeding tomatoes for a single
mechanical harvesting procedure is a dramatic example of plant
architecture modification to suit a modern agricultural practice. We can
expect these modifications to be more extensive than we have seen so
far. The modifications may deal with the type of inflorescence,
phyllotaxis, the way in which leaves respond to light in spatial and
temporal modes, and there is a lot to be gained in modification of root
systems to suit particular soils and their water and nutrient availabilities.
We will also profit from modification of internal architecture, the
anatomy of plant tissues; for example, the ratio of palisade and spongy
mesophyll leaf cells and the geometry of tissues in the root system are
areas in which we can expect telling alterations.
Some of the examples we have discussed in the paper have specifically
referred to challenges in Australian agriculture systems, but the points
emphasized have general applicability to cropping systems around the
world. In the case of transgenic cotton in Australia, one of the most
important features is that behind the successful introduction and
acceptance of the transgenic crop was the coordinate and packaged
introduction of the new genetic make-up of the crop along with the new
and mandatory ways of agronomic management. These were seen to be
of extreme importance in introducing the value of the new technology to
farmers. Farmers realized that it would be a huge loss if we were to
waste this new powerful technology in the way that we wasted many of
the advantages of the new pesticides in the recent past.
A reasonable conclusion is that genetic modification of crops, which has
been so powerful and so rewarding in terms of yield and management of
many of the major production species over the past few decades, will
hold enormous potential in all of the crop species we deal with. We have
 25

an increasing knowledge and power to modulate the development and

functional operation of crop plants so as to provide optimal performance
in our agricultural production system environments.
Agricultural performance rests on the interactions of genetics,
management and the environment. We have not always fully coped with
these interactions, and production levels in many parts of the world have
been less reliable than we might have hoped for. In many cases, the
health status of the natural resources in the production areas have
suffered and there has been great concern by society as to the damage
agricultural systems sometimes inflict on surrounding non-agricultural
environments. But although the environmental challenges have been
increasing in recent years, and continue to increase as a result of climate
change and other factors operating on production systems, we can be
confident that the new genetics is providing an increased ability to adjust
the biological software of our principal production species. We can
expect, in a variety of production environments to have the genetic
modifications, coupled with appropriate management regimes, to result
in an increased efficiency and sustainability of agri-business.
 26

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