Sequencing the apple genome
The genome sequence of the Golden Delicious apple was published in 2010. It sheds light on the history of the apple and should make apple breeding faster and more accurate.
What’s in a genome?
Sequencing DNA
Sequencing machines can work out which DNA base is present at each position in a DNA fragment because each one is labelled with a different fluorescent molecule (shown as black, blue, green and red on the graph).
A genome is the complete set of DNA that’s carried in each cell of an organism. It contains all the organism’s genes, as well as other sections of DNA that regulate gene activity and chromosome structure. There’s also a lot of DNA that has no known function at all.
‘Sequencing the genome’ means working out the exact order in which DNA bases (A, G, C and T) occur in an organism’s DNA.
The sequencing project: New Zealand’s role
The apple genome was a collaborative effort between Italy, the USA, Belgium, France and New Zealand. Golden Delicious is a key apple variety in Italy, which is why it was chosen for sequencing. New Zealand scientists provided access to Golden Delicious trees, expertise in bioinformatics and a lot of hard work!
Find out more about the work undertaken by New Zealand scientists on mapping the apple genome.
The apple genome: lots of genes
The scientists who sequenced the apple genome made several unexpected findings. For one, it had a huge number of genes (approximately 57,000). This was more genes than had yet been found in a plant genome and twice as many as in the human genome. The apple genome also contained an unusually large number of transposons – short chunks of DNA that can ‘jump around’ within the genome sequence.
What the apple genome can tell us
The genome sequence of the Golden Delicious apple was published in 2010. Scientists at Plant & Food Research, including Andy Allan, contributed to the project. Here, Andy describes how the apple genome will increase the speed of apple breeding programmes, and what the genome can tell us about the apple’s history.
An Asian ancestor for apple
The apple genome sequence confirmed that the central Asian apple Malus sieversii is the ancestor of the modern apple – not the European apple Malus sylvestris, which has previously been proposed as an ancestor. Researchers worked this out by comparing the DNA sequence at many places within the Golden Delicious genome with the same place in the DNA of wild apple species. They showed that Malus sieversii DNA had the most similarity to Golden Delicious at these sites.
This finding fits well with our current understanding of how the apple became domesticated. It is thought that Silk Route traders and their animals ate wild apples from Kazakhstan, helping them spread east to Europe and west to China. Programmes of domestication were then begun in these areas and eventually developed into selective breeding programmes.
For further information read the article The germplasm collection: a library of apples.
The apple genome sequence and breeding
The apple genome sequence should make the apple breeding process considerably faster and more accurate. Because it tells us the location and sequence of every gene in the apple, it will enable the design of many more DNA markers for desirable traits. In turn, this should improve marker-assisted selection and genomic selection – 2 breeding techniques that rely on DNA markers.
DNA markers and apple breeding
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 resources below have further information:
Making a transgenic plant (interactive)
Students could go online to research the different forms that a marker can take such as single nucleotide polymorphisms (SNPs) and microsatellites.
The article Genetic information and apple breeding provides additional information.
It’s also likely that the genome of individual apple seedlings will be sequenced routinely in the future, when the cost of sequencing is less. Eventually, this might provide an alternative to marker-dependent breeding techniques.
The genome sequence also provides insight into how existing apples function. As the genomes of other apple cultivars are sequenced, it will help researchers understand the basis of important apple characteristics like flavour, texture and disease resistance.
Useful links
Read the original research paper that reported the apple genome sequence (published in the journal Nature Genetics).
These short videos give a step-by-step account of how a genome is sequenced (with specific reference to the human genome).
This article from PHYS.ORG explores the history of the apple from its wild origins.
