There is more to learn from
‘bad plants’ in breeding programmes than one might think.
New research into Aradopsis (thale cress) shows that many
genotypic variations cannot be seen in the appearance of the
plant – the phenotype – because the effects of the variation
gradually die out. In addition to this buffering, scientists
have proven the existence of crucial clusters of genes. As
mutations in one of these so-called hotspots have a direct
effect on the plant’s performance, phenotyping of plants
using techniques like metabolomics, proteomics and in vivo
imaging, is the future.
The DNA of two Arabidopsis
lines, one from the Cape Verde Islands and one from Poland,
differs in no less than 500,000 locations. Scientists from
Wageningen and Groningen discovered, however, that the
appearance and molecular differences between the offspring
of a cross-breed of these lines could be traced back to just
six hotspots – important clusters in the DNA. The remaining
differences were on stand-by.
“The further 'the distance'
between a process and the DNA, the less variation there is,”
says Joost Keurentjes, scientist from the Genetics and the
Plant Physiology group at Wageningen University. “The
variations gradually die out and lose their function.”
Additionally, DNA analyses showed that this dying out occurs
in all phases between the genotype and the eventual
phenotype.
Buffering probably develops
because plants contain proteins that protect co-proteins.
One of these chaperones is called the heat shock protein. If
one of these proteins is switched off (such as HSP90), a
greater degree of variation develops within the phenotype.
“These guards apparently mask the variations in the protein,
and proteins that are slightly changed continue to function
in the same way. The chaperone is turned off in stress, i.e.
a shift away from ideal conditions.” According to
Keurentjes, buffering variations is in accordance with
‘Darwinian logic’. “If all genetic variations were
immediately expressed a plant would be doomed as its
surroundings remain pretty much the same. It is in different
circumstances that differences emerge. This mechanism allows
an organism to accumulate mutations during favourable
conditions that only become effective once the conditions
change.”
Chain reaction
The hotspots causing the phenotypic differences discovered
by Keurentjes and his colleagues are the vulnerable spots in
plant systems. “While most mutations have no effect on a
plant’s performance, changes in a few critical spots can
cause a chain reaction.” The hotspots depend on plant stage,
genetic background and the environment in which the plants
grow. In the studied cross-breed, a blue light receptor that
influences flowering time was situated in a hotspot, for
example. Moreover, a great deal could be traced back to the
erecta locus: When mutations occur in this spot on the
chromosome, it is not just the plant itself that is smaller
but all elements. “This affects various processes such as
cell and plant size,” adds Keurentjes. “A mutation can
result in a completely different plant.” A third hotspot is
known to be important to the metabolic system, determining
aspects such as energy management and, therefore, day and
night rhythm.
This is the first time that
the existence of hotspots and gene buffering has been so
clearly shown, underlines Wageningen University Professor of
Plant Breeding Richard Visser. “Although it was already
known that characteristics can be linked, this knowledge
opens up the possibilities of actually using this fact.” It
shows that it is possible to search more specifically for
pieces of DNA that are involved in multiple plant processes,
and that it is important to be alert when cross-breeding a
characteristic determined within one of these hotspots. “It
is costly to map all hotspots of all plants,” adds Visser.
“However, we are taking a similar approach using tomatoes,
which we are studying for fruit and flavour at the Centre
for Biosystems Genomics. It would be interesting to find the
hotspot for flavour.”
The right direction
According to Visser, research into thale cress also
shows that breeders should be focussing more on the bad
plants in their programmes. “Around 95 percent of all plants
are discarded in the first round. As a result breeders are
throwing away information that could have helped steering
the process towards a better variety.”
Visser also sees
possibilities in searching for plants that provide a peak
yield under good and less optimal conditions, whereby wild
varieties should definitely be included. “The future lies in
phenotyping as many different genotypes or varieties as
possible. We are also working on that, using varieties from
around the world of crops such as potato and barley. The
modern measuring methods are so accurate that you could say
that the historical phenotyping will have to be entirely
redone.”
Joost Keurentjes’ research
was financed by the Netherlands Organisation for Scientific
Research (NWO) and the Centre for BioSystems Genomics
(CBSG).
Yvonne de Hilster
Literature:
System-wide molecular evidence for phenotypic buffering in
Arabidopsis Jingyuan Fu, Joost J.B. Keurentjes, Harro Bouwmeester,
Twan America, Francel W.A. Verstappen, Jane L. Ward, Michael
H. Beale, Ric C.H. de Vos, Martijn Dijkstra, Richard A.
Scheltema, Frank Johannes, Maarten Koornneef, Dick
Vreugdenhil, Rainer Breitling and Ritsert C. Jansen.
Nature Genetics 41, 166-167 (2009)
