Genetic information and apple breeding

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. Scientists and organisations need to get approval to conduct any research involving genetically modified plants.

Approvals come with strict conditions. The research trees must be grown in closed facilities. Plant & Food Research have a purpose-built containment facility for this work. It is a large glasshouse built for growing trees. The glasshouse sits on a concrete block that houses an engine for circulating air because, unlike a standard glasshouse, this one has no windows to enable heating, cooling and airflow.

Pollination is done by hand as no bees or other pollinating insects can be used.

People must put on protective clothing when entering the space and remove it when exiting. This ensures no plant material is accidentally carried out into the environment.

All material leaving the facility is autoclaved before disposal – this includes things like plant prunings or soil and used protective clothing.

No food or drink is allowed to be consumed in the facility – this makes things very interesting when the scientists want to assess some of the apple traits like taste!

After two years of unsuccessful attempts to get approvals to taste test the apples in New Zealand, Dr Andy Allen and a science team had to travel to America where eating fresh genetically modified foods is allowed. To get the apples from the containment facility to the airport Andy’s team had to clear several regulatory hurdles. The apples had the core and seeds removed and were triple bagged for the journey.