The Royal Society Report - Push-Pull

3.2.2 Phenotype analysis
Marker-assisted plant breeding places the emphasis on
DNA screening rather than on detailed analysis of the plant
phenotype. However, the breeding cycle is further
enhanced whenever plant phenotypes can be analysed
with higher resolution and greater precision than
previously. In this section we describe various
developments in phenotype analysis that can be combined
with MAS to enhance the identification of crop plants with
agronomically useful genes or combinations of genes.
3.2.2.1 Phenotyping platforms
It is now possible to screen many different plant genotypes
quickly and simultaneously for the traits expressed
(phenotype) using ‘phenotyping platforms’ (Finkel 2009) .
These systems involve the use of precisely defined
environmental conditions and sophisticated imaging and
other recording methods to monitor the growth and
development of crop plants (Xie et al. 2006; Rajendran
et al. 2009). When combined with high-resolution genetic
maps or with mutant collections in which a high proportion
of genes in a genome are disrupted, these platforms are a
very effective way of revealing sets of genes that influence
agronomically significant phenotypes. Trait data can often
be obtained automatically. For instance, root platforms
now allow dynamic characterisation of root system
architecture and sites of root water uptake in hundreds of
plants using non-invasive systems built on computer
tomography (de Dorlodot et al. 2007). Other systems make
it possible to introduce drought stress and measure
biomass, transpiration, leaf growth and architecture, root
growth and architecture and soil water uptake in many
plants in a single experiment.
These phenotyping platforms are sophisticated, resourceintensive
facilities and they are not appropriate for local
breeding institutions. However, they are an essential
component of the research infrastructure in leading
national and international research centres where they are
required for full exploitation of high-resolution genetic
maps and genome sequence data.
3.2.2.2 High throughput analysis of small molecules
Plants make an enormous diversity of small molecules,
which include mediators of communication between
plants, between microbes and between plants and
microbes. High throughput analysis (a technique which
allows the fast analysis of a large number of molecules in
parallel) based on mass spectrometry now allows these
small molecule populations to be better described (Schauer
& Fernie 2006). In some instances functions can be
assigned to these small molecules by combining mass
spectrometry output with expression profiling and
phenotype analysis. These high throughput approaches
have revolutionised our ability to analyze the natural
chemicals in plants and other organisms: it is no longer
necessary to devise separate assay methods for each type
of chemical because in a single sample it is now possible
to identify thousands of compounds.
Application of these methods now allows a chemical profile
of individual plants in the progeny of breeding crosses or
following particular crop management strategies. Individual
compounds or sets of compounds can then be used as
indicators of useful traits in the way that DNA markers are
used as described in Section 3.2.1.1. In large-scale
breeding programmes and trials of new crop management
practice it may be easier and more efficient to assay the
compounds rather than the traits when there are many
plant lines or crop treatments under investigation. In effect
this would be a ‘metabolic marker’ approach that could be
used together with, or instead of, DNA markers.
Recent work illustrates the potential of this approach: a set
of metabolites was identified that is associated with plant
acclimation to cold (Guy et al. 2008). This work was carried
out in the model species Arabidopsis but similar analyses
could be repeated in crops and applied to a variety of traits.
These assays would provide metabolic markers, for
example, of crucial stress-sensitive stages of development
of our major crops, eg grain abortion and early seed
growth under drought or other crucial traits. The
development of these methods is not as well advanced as
DNA MAS but they are likely to be an important
complementary approach over the next five years.
In the longer term new technologies for chemical
characterisation also link to the development of novel crop
protection chemicals. Many of the existing crop protection
chemicals are based on natural compounds found in
plants. Some herbicides are plant hormone derivatives and
compounds to protect from disease may be based on
chemicals in plants involved in signalling during disease
resistance. With the availability of high throughput
methods to characterise the chemical composition of crop
plants there is a long-term opportunity to identify novel
compounds that can be applied to crop plants sustainably.
3.2.2.3 Isotopic analysis for drought resistance or
high water use efficiency
In 1982 Farquhar and co-workers developed a method for
assessing water use efficiency of crops using the ratio of
the abundance of the natural isotopes of carbon, 13 C and
12
C (Farquhar et al. 1994). During diffusion and biochemical
fixation of CO 2 , the ratio 13 C/ 12 C is different from the
normal abundance in the atmosphere. The ratio depends
on the balance between diffusion into the leaf and
demand, so a measure of the ratio gives a measure of
water use efficiency. The approach has now been used to
investigate water use efficiency in many crops. In C3
plants, the technique has led directly to the selection of
improved crop varieties, most notably Q15 in wheat
(Condon et al. 2004). However, it is not suitable for
screening C4 plants such as maize.
3.2.2.4 Modelling
Progress in breeding for high and stable yields in crop plants
under many kinds of environmental stress would be greatly
speeded up if it were possible to predict the consequences
24 I October 2009 I Reaping the Benefits The Royal Society