The Royal Society Report - Push-Pull

Genes or combinations of genes affecting crop production
can be easily identified using genomics. In genetic
improvement strategies these genes can be targeted in
breeding programmes or they can be transferred into crops
by GM as described in more detail below. However, it should
be stressed that the information from genomic studies is
also important for the science that underpins changes in
crop management. The information about genes, proteins
and metabolites in crop plants allows strategies for crop
management to be developed that maximise agronomic
performance of crops in a sustainable way.
New methodologies for determining DNA sequences are
orders of magnitude more efficient than the methods used
for the first generation of genome sequences from model
organisms and man. There are several versions of these
new methods and it is likely that others will emerge in the
near future. Sequencing a genome is currently being
transformed from a multimillion pound project into one
costing less than one million pounds for a completely new
genome and a few thousand pounds for an individual of a
species for which a full genome is already available.
Generating the DNA sequence data is now straightforward
and cheap: the computational analysis and annotation of
the sequence is the most expensive and time-consuming
part of a genome project.
Genome sequencing methods were first applied to the
model plant species Arabidopsis and we now have
complete genome sequence data of Arabidopsis thaliana,
rice, maize, sorghum, soya bean, poplar, grapevine and
papaya. With the introduction of the new sequencing
technology it is likely that ongoing genome projects for
wheat, potato, tomato, sunflower, apple, pear, peach,
strawberry and other crops can be accelerated. 5 Other
crop genome sequences could be completed in relatively
short times and it will be possible to generate data from
several varieties of previously sequenced crops.
3.2.1.2 Marker technology
Plant breeding is a well established method for improving
the performance of crop plants by making defined crosses
between genetically distinct parents, screening progeny
for desired trait combinations and selecting preferred
individuals with better combinations of characteristics that
can then be bulked and developed into lines and varieties.
The procedures for screening progeny for desired traits are
often the most challenging stages in conventional plant
breeding because many plant lines have to be tested for
phenotypes that may be difficult to assay. Disease resistance,
for example, can normally be identified only after extensive
testing of multiple plants in each line for susceptibility.
Similarly, yield enhancements cannot be identified by
collecting the products from a single plant; the products
from several plants need to be combined and measured
accurately in replicated tests. The advances described below
allow these screening procedures to be streamlined.
5 See http://www.Phytozome.net.
Breeders and geneticists can often show that defined traits
are conferred by specific genes, or are associated with
quantitative trait loci (QTL)—stretches of DNA strongly
associated with the gene for a particular trait. These traits
are often difficult to measure, requiring laborious and
incompletely reliable assessment methods. It therefore
makes breeding easier if instead of measuring the trait, a
molecular DNA genetic marker linked to the QTL can be
monitored in progeny. This method is cheaper and more
reliable. In addition, undesirable traits are often genetically
linked to desired traits. This is known as linkage drag. DNA
markers help identify rare plants in a breeding program in
which the desired trait is retained but deleterious traits are
left behind. This is referred to as marker-assisted selection
(MAS). DNA marker technology has evolved through
several stages. In its most advanced form, it is based on a
genome sequence and generates dense genetic maps in
which the markers are very close to, or may actually
represent, the gene of interest. More complex applications
of MAS involve selection for traits affected by multiple
genetic loci.
An example of the application of MAS is in the development
of submergence-tolerant rice. In rice, the major genetic
determinants of flooding tolerance have been identified and,
using this information, MAS has been employed to develop
flooding tolerant varieties (Hattori et al. 2009; Singh et al.
2009; Voesenek & Bailey-Serres 2009). Many other
examples of MAS suggest that this approach will be
increasingly important in breeding as genome sequence
data become available for more crop plants.
3.2.1.3 Genetic modification
Traditional and marker-assisted plant breeding involve the
introduction of novel traits into crops by crossing as
described above. The crosses might involve different
genotypes of the crop or they might involve the crop and a
related species (interspecific crosses). Progeny of the
crosses are selected for traits of interest using DNA
markers. Traditional plant breeding is slow, taking 10 years
or more for a breeding cycle. Furthermore, breeding of
some crops which are not propagated by seed, such as
potato and banana, is extremely difficult. In molecular GM,
novel genes are introduced, either individually or in small
groups, into a crop plant. The genes inserted may either be
from the same species (this is known as cisgenics) or from
another species (transgenics). These methods circumvent
the crossing cycle associated with conventional genetic
improvement and in cisgenic approaches they allow
transfer of genes within a species but without the
complication of linkage drag.
GM-based methods are used widely as a routine tool in
research and they have greatly facilitated major advances
in plant biology over the last 25 years. They are particularly
important in the ongoing task of assigning function to each
of the 10,000 to 20,000 genes which have been identified
in each species and in elucidating the cellular mechanisms
in plant biology. The application of GM techniques in crop
plants, however, has been controversial. In the USA,
22 I October 2009 I Reaping the Benefits The Royal Society