Genetic analysis in plant conservation research
What is genetic analysis?
Genetic analysis is the study of genes, the fundamental physical units of heredity in living organisms. Genes are composed of DNA and control the development and control of the organism.
Why do we study the genes of plants?
Grinding a plant leaf in
liquid nitrogen to then extract
DNA from it
Genetic analysis provides a valuable tool for increasing our understanding of Western Australian wildflowers.
A plant's genes provide a picture of the plant's unique individual biological makeup. This picture provides one way of comparing genetic differences and similarities
- between individual plants of a species,
- between different populations of the same plant species,
- between one plant species and another.
A plant's genes also provide us with an insight into the extended family history of the plant. It helps to document the environmental forces that shaped a species across time and the ways in which plants (and the population to which they belong) have adapted to these forces to survive in a specific region.
An understanding of the genetic makeup of plants, and the forces that have shaped populations of species, can lead to more effective management strategies for a species and the threats its may face.
Why is genetic diversity important?
Western Australia has nearly 12, 000 plant species. This diversity in species has been recognised as one of the great wonders of the natural world, and the South West of WA has been classified as a biodiversity hotspot.
This diversity reflects the complex array of genetic variation between plant species, and within species themselves. It is a result of millions of years of evolution, the selection and adaptation by individual plants and species to the environments in which they live.
These evolutionary adaptation mechanisms have occurred over long periods of time through changes or mutations in the basic genetic material of plants. Mutations that result in useful features, or that do not disadvantage the organism, get passed on in reproduction, generating differences in populations and species over time.
Loss of the genetic diversity impedes the species ability to adapt to the challenges posed by environmental change (new diseases, pests, parasites, pollution, climate cycles and global climate change). Without adequate genetic diversity, plant species may ultimately face the risk of extinction.
How does genetic analysis help to increase our understanding of WA plants?
Genetic analysis helps to increase our understanding of WA plants in the following ways:
- Increasing our understanding the biology of plant species
Genetic analysis allows us to further understand the biology of important processes in plant development. These processes include the ways in which plants reproduce and adapt to changing environments. Genetic analysis also allows us to identify traits that are valuable for the long term survival of a species - for example, locating the genes that control resistance to dieback or the genes that enable plants to survive in salinity affected areas.
- Enabling us to assess the genetic health of plant species
An accurate estimate of the level and distribution of genetic diversity within a species is an important element in designing conservation programs. By identifying the degree of genetic variation in populations, we can:
- Identify populations at risk -
Identifying populations at risk involves identifying those populations with insufficient diversity to adapt to changing environmental conditions. Once identified, these populations can be actively managed.
- Define management units within species -
Populations within species may be sufficiently different that they deserve management as separate units. For example, in a species where most of the genetic variation occurs as differences between populations, it would be better to conserve a number of populations throughout its range.
- Study the effect of habitat fragmentation on genetic diversity -
Habitat fragmentation occurs when native vegetation is cleared, dividing continuous habitat into fragments. The species within these fragments, or habitat islands, often have little genetic contact with other populations in other fragments. Without this contact, there is a greater degree of inbreeding within populations and a decline in genetic diversity.
- Resolving taxonomic uncertainties
While many plants may have the same visible characteristics, their genetic makeup may be significantly different. Thus apparently widespread and low-risk species may in reality comprise a multiple distinct taxa, some of which may be rare or endangered. Genetic analysis can also identify hybrids, the offspring of two different species that have sometimes been classified as distinct species.
- Building our knowledge about the evolutionary history of plant species
Not all groups of plants have the same degree of genetic diversity. Some plants come from recent evolutionary lines and are genetically very similar. Others evolved from more ancient lines and are genetically far more diverse. By concentrating on identifying and conserving ancient lines, we ensure that we conserve populations with a high degree of genetic variation. This variation ensures the evolutionary potential of species.
Examining the evolutionary lines of our plants also provides information on how plants have responded to historical environmental change over millions of years. Western Australia has few geographic features but has experienced significant historic climate change leading to complex patterns of genetic diversity. In Western Australia many species are also quite restricted and occur in localised areas that may be large distances apart. This means that they have been separated for long periods of time, and are genetically distinct even though they may still belong to the same species. Identifying areas of genetic richness is important for conserving the evolutionary potential needed for ongoing adaptation (e.g. due to climate change), and managing distinct genetic groups within species.
- Determining the best populations for re-introduction or translocation for conservation purposes.
Genetic analysis is a key tool used to ensure the genetic fitness of plants to be used for conservation purposes. Populations that are reintroduced or translocated must have enough genetic variation to adapt to their new environment and the potential to adapt to future environmental changes. They must also be sourced from within the gene pool of the area to which they are located, to ensure that their genetic makeup does not significantly alter the genetic composition of the area.
What is DNA (deoxyribonucleic acid)?
The differences between various plants and animals come from the
different pieces of deoxyribonucleic acid (DNA) that they possess. DNA
is the basis of life. Built of complex chains of sugars and phosphates,
DNA makes up the genes that reside in the nucleus of every cell of
every living organism. It contains all the information that dictates
the design and creation of the substance, in the form of different
proteins that forms that organism. DNA is the blueprint of the life
that carries it, the life which then projects it into the next
generation.
DNA is passed on from parents to offspring in different combinations,
which are generated during reproduction. This ability to recombine,
inherent in reproduction, leads to a vast array of different
combinations, or genotypes. This is the basis of the differences that
we can see between individuals of a species, between different
populations of the same species and between one species and another.
Methods for genetic analysis
Genetic analysis of a plant
Analysis of a plant species' DNA and
proteins will show the amount and patterns of its diversity. Analysis
of proteins involves taking some seedlings or leaves of a plant and
grinding them in a buffer to release the proteins. The mixture is then
placed onto a medium, a gel, through which an electric current is
passed. The current separates the proteins according to their different
electrical charges. The gels are then stained to show different
proteins, allowing the differences between individual plants to be
clearly seen. These differences in proteins can be directly related
back to the coding gene.
Analysis of DNA requires DNA to be extracted from the plant. Some plant
tissue, usually leaves, is ground into a fine powder and mixed in a
buffer. The cells in the mixture are broken down by chemical action,
and the contents are released. The DNA is then separated and purified
from other cell contents.
The DNA can be analysed by one of a number of techniques. One method is
to use a 'probe', which is a small piece of DNA, to investigate what
that bit of DNA is like in different individuals. Using a lot of probes
gives information about lots of bits of the DNA. Another method, known
as 'polymerase chain reaction' (PCR), involves using two very small
pieces of DNA, called 'primers', which bind to the DNA, sandwiching it
and, through the action of an enzyme, amplifying it. After
amplification, the differences between the sandwiched bits of DNA can
be seen on a gel.
One advantage of the PCR method is that it uses only a very small
amount of DNA (five millionths of one gram), so that it can be used on
small herbarium specimens or on plants that only have a few small
leaves. DNA analysis can be more extensive than protein analysis,
because the DNA available to be analysed is virtually unlimited, while
there are a limited number of proteins, and in some plants only a few
proteins can be sufficiently resolved.
Polymerase chain reaction analysis (PCR)
Just as the analysis of DNA
has revolutionised genetic research, the PCR method has revolutionised
DNA analysis. It is now possible to get analysable DNA from fossils,
museum specimens, and dried plant specimens which may be hundreds of
years old.
PCR is a technique which is used to amplify (make lots of copies of) a
piece of DNA. DNA is made of two strands. These are held together by
bonds which can be broken by heating to 94ºC.
When cooled to 55ºC the
separated strands bind to the 'primers', two small bits of DNA which
were used to flank the bit of DNA to be amplified.
The temperature is
then raised to 72ºC, allowing an enzyme called 'Taq polymerase' can
make a new strand of DNA to match the original one.
At the end of one
cycle of heating to 94ºC, cooling, and heating to 72ºC, there are four
strands of DNA, two sets of two, instead of the original two strands.
During the next cycle of heating the primers attach again and the
process is repeated. A single piece of DNA would not be visible, but
after 30 or 40 of these heating cycles, the numerous copies of the
piece of DNA are clearly seen when run on a gel and stained.
Major DEC projects that use genetic analysis
Many of our flora projects have a significant genetic analysis component. Our major genetic projects are:
DEC staff papers on genetic analysis
- Bibliography searching on "genes" as key word
- Bibliography searching on "genetics" as key word
Further resources
Contact information
Margaret Byrne
Principal Research Scientist
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