Information about apple genetics is helping breeders at Plant & Food Research in New Zealand to breed new apple cultivars faster and more efficiently.
Selectively breeding new apple cultivars
In New Zealand, new apple cultivars are developed through selective breeding. This is the same technique that humans have used for thousands of years to breed plants and animals with desirable characteristics. However, breeders now have access to genetic information from apples that can make the breeding process faster and more efficient.
Breeders at Plant & Food Research (PFR) are using 2 genetic approaches – marker-assisted selection and genomic selection – to help select apples for breeding. Both techniques make use of DNA markers, and both can give breeders information about the apples that a seedling will produce. The article Breeding a new apple cultivar has further information.
Markers provide genetic information about a seedling
Researchers at PFR and elsewhere have identified a large number of DNA markers at defined locations within the apple genome. These short sequences of DNA act as signposts – they can give researchers information about functional DNA sequences nearby.
Markers can provide information about which allele(s) of a gene a seedling probably carries. For instance, there is a marker for red flesh, which is very closely linked to the gene shown by PFR scientists to control apple flesh colour. Scientists can use the marker to tell which allele(s) of the gene a seedling probably carries and therefore whether it will produce red-fleshed apples. PFR scientists also use markers to check whether seedlings have disease-resistance alleles.
Some markers are known to be associated with complex traits (such as apple firmness), which are usually controlled by several genes. However, the genetic basis of complex traits is not yet well understood. The article Discovering what controls apple flesh colour has further information.
Two approaches to using markers
Breeders at PFR are using DNA markers in 2 ways to streamline breeding.
Marker-assisted selection uses a small number of markers to check whether a seedling will produce apples with a particular trait, such as red flesh. This means that seedlings without that trait can be discarded at an early stage, making breeding more efficient.
Genomic selection looks simultaneously at thousands of markers that are spread across the apple genome. Breeders can estimate which markers affect which traits by looking at the pattern of markers in a ‘training population’ of plants (whose traits have been closely analysed). They then analyse markers in a new seedling population and predict which seedlings will be the best parents for the next round of breeding. This is measured as a genomic breeding value.
Genomic selection can speed up the breeding process, because parents can be selected at an early stage. It is currently being developed at PFR as a possible alternative to traditional trait-based selection.
Both approaches have benefited from the publication of the apple genome sequence, which makes it easier to design new markers and increases understanding of markers that are already in use.
Find out more about Sequencing the apple genome.
How do the 2 approaches fit together?
Marker-assisted selection and genomic selection give breeders different sets of information. This table compares the 2 approaches:
Marker-assisted selection | Genomic selection |
| Identifies which seedlings have a particular trait (such as red flesh or disease resistance) | Estimates the overall value of individual seedlings as parents (breeding value) |
| Uses 1 or a few markers | Uses thousands of markers spread across the entire genome |
| Best suited to traits affected by a single gene (monogenic traits) or a couple of genes | Can provide information about complex traits (such as crispness) |
| Works best when the genetic basis of the trait is well understood | The genetic basis of the traits assessed need not be well understood |
| The marker(s) are known to associate with a specific gene | The relationship between markers and specific genes may not be understood |
| Makes the breeding process more efficient | Can speed up the breeding process |
Marker-assisted selection and genomic selection can be complementary, especially when breeding apples with a specific trait, such as red flesh. Breeders could first use marker-assisted selection to ensure they keep only seedlings that will produce red-fleshed apples. They could then use genomic selection to work out which of those seedlings have the highest breeding values for important complex traits.
Transgenics can provide information about gene function
Creating transgenic plants in the laboratory is a powerful way to learn about the function of individual genes. The information from these studies is important for making marker-based selection and genomic selection more accurate. Strict regulations are in place in New Zealand to ensure that material from transgenic plants is never released into the environment. The Environmental Proection authority (EPA) is the government organisation responsible for these regulations in New Zealand.
