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Rights: The University of Waikato
Published 9 June 2011

DNA markers are short sequences of DNA that can provide information about the genetic make-up of an individual organism (such as an apple seedling). Breeders use information from markers to streamline the breeding process. Here, Andy Allan and Richard Espley describe how marker-assisted selection can make apple breeding more efficient, and how the apple genome sequence is making it easier to develop new markers.

Teaching points
Marker-based approaches use genetic information to understand more about individual apple plants. An alternative conception is that these approaches are similar to transgenics, in which the genome of a plant is directly modified in the laboratory. Students can explore the key similarities and differences between marker-assisted breeding and transgenics with a variety of resources.

This resurces below have further information:

Students could go online to research the different forms that a marker can take such as single nucleotide polymorphisms (SNPs) and microsatellites.


Richard Espley (Plant & Food Research)
A marker is literally something that marks out a particular gene, and that gene will translate into a particular trait. So we have a map for the apple genome that is full of these markers, and these markers tell us which copy or which version of a gene is present, for example, in a seedling population. So these markers may be able to predict what the likely performance of a tree or a fruit is going to be.

Andy Allan (Plant & Food Research)
It’s like identifying a criminal in a forensic scene of the crime. Instead, we are identifying an apple tree which has all the characteristics that we really like. So producing a marker will allow us to take DNA of the population of apples and say which one of those trees will produce an apple that has red flesh.

So you will have a whole lot of seedlings in the ground, and if you take the DNA of those thousands of little seedlings and find the 1 tree that has the right allele for red flesh, you can get rid of all the others if you like and grow that 1 tree more quickly, hothouse it, so you have saved a few years. You've also saved a lot of space in growing trees that actually don't have the genes, the alleles that you are really interested in. Within our breeding programmes, we already use markers for pathogen resistance – a very important grower-related issue – and we've got a marker for red flesh, and with the genome and its availability we will be able to produce thousands of other markers for particular characteristics that we really love.

Now we have 57,000 genes that we can design markers to, the process becomes a lot more challenging technology wise, but a lot more informative.