Genetics Potential In Organic Fruit

Apple Breeding DNA


Editor’s Note: The author of this story, Kate Evans ([email protected]), is an associate professor/associate scientist at the Washington State University Tree Fruit Research and Extension Center, where she heads up the apple breeding program.

New technologies available to plant breeders are increasing the possibility of successful targeted selection for a range of characteristics, resulting in new varieties, some of which may have more potential for organic production over current varieties. DNA-assisted selection in traditional breeding programs can increase the efficiency of selection for robust disease or pest resistances while also enabling the breeder to select for good fruit quality.

Projects such as the European Union-funded DARE and HiDRAS resulted in advances in tools enabling the breeder to pre-select for resistance to apple scab and powdery mildew; other ongoing projects are developing similar tools linked to resistance to fire blight (Erwinia amylovora). While the RosBREED project is focused on fruit quality traits, the principal aim of the project is to enable breeders to implement the DNA-assisted technology, thus having a much greater impact on the production of new Rosaceae products in the U.S. Besides the application of new technologies in traditional breeding programs, there are further possibilities for advances in molecular biology and genetic modification to offer new breeding systems that are acceptable for organic agriculture for the development of new improved varieties.


Traditional fruit breeding and selection since the early part of the 20th century has led to the development of breeding lines and varieties, such as CrimsonCrisp, Topaz, and Rajka apples that are able to thrive in some organic production conditions. Many sources of resistance used are from related species and are frequently associated with poor fruit quality traits. In order to introduce these resistances and select against the poor quality traits, several generations of crossing and selection are required. In a tree crop such as apple where each generation usually takes at least five to six years seed to seed, introducing these new traits can easily take in excess of 50 years.

Huge advances have been made in DNA-based technologies in fruit from the first molecular marker maps to the full genome sequences. Such technologies enable breeders to target specific traits much more effectively than using traditional selection techniques, and can be used to produce varieties especially suited for organic production.

DNA-Assisted Selection

One of the first technologies to be developed was that of DNA-assisted (or “marker-assisted”) selection. Markers (or sequences of DNA associated with a trait of interest that can be easily identified in the laboratory) can be a gene itself or a linked marker, a non-coding sequence near to the gene(s) of interest. The development of molecular marker maps was essentially driven by the need to map traits of interest and co-locate flanking markers that could be used for selection at early stages within breeding programs.

DNA markers are not only useful for screening seedlings but can greatly improve the efficiency of a breeding program by enabling the breeder to design more efficient parental combinations following DNA-assisted parent selection. Many of the first markers identified in apple were linked to genes for resistance to pathogens and identified as part of the EU-funded DARE and HiDRAS projects; such markers should therefore be of great interest to organic producers.

Gene Pyramiding

Breeding lines have been developed for resistance genes, but to ensure the sustainability of these resistances, their use must be managed. Rapid generation cycling by pathogens in the orchard results in the risk that these single gene resistances are overcome. One strategy that breeders can use to create more durable resistance is gene pyramiding, where more than one gene for resistance to a particular pathogen are combined through a series of crosses between resistant parents carrying different genes.

Standard pathology screening used by breeders cannot differentiate between individuals that have a combination of genes and those that have only inherited one; by developing DNA markers that are linked to different resistance genes, breeders can identify the gene combinations and thus select individuals with more durable, sustainable resistance.

Fruit Quality Markers

Some progress has been made in identifying genes or markers linked to fruit quality. For an apple breeder who has to wait up to five or six years to see the most important traits, those of fruit quality, on a seedling due to the long juvenility period of apple, markers for fruit quality are essential. To date there are few published; however the two apple genes Md-ACS1 and Md-ACO1 from the ethylene pathway are useful indicators of potential storability and texture. The RosBREED project is poised to deliver a battery of new DNA-based markers linked to fruit quality not only for apple but also strawberry, peach, and sweet and tart cherry.

FasTrack Technology

As explained previously, introducing a resistance gene into apple while maintaining fruit quality using traditional breeding methods can take longer than a typical research career; consequently, breeders are always looking for opportunities to speed up the breeding process. European scientists have produced early flowering transgenic apple lines by over-expressing the BpMADS4 gene from silver birch. These will flower and produce fruit in less than one year and when combined with DNA-assisted selection are ideal for the introgression of genes of interest or the pyramiding of several genes of interest within a manageable amount of time.

Breeding lines have already been produced which combine two genes for scab resistance, and two genes for mildew resistance with a QTL for resistance to fire blight by crossing sources of resistance to the early flowering lines. These breeding lines will be crossed with high fruit quality cultivars for several generations to eliminate the unwanted traits from the resistance donors after which non-transgenic multi-resistant seedlings will be selected. Similar technology has also been used in plum breeding in the U.S. to introduce plum pox resistance; non-transgenic plums to be released as a result of this technology have recently been deregulated by USDA’s Animal and Plant Health Inspection Service (APHIS).

Opportunities Abound

New technologies are available to facilitate the selection of new varieties especially suited to organic production systems. The recently published genome sequences should enable the development of new DNA markers and the targeting of further genes. Opportunities from genetic modification should not be overlooked despite current regulatory issues. It should also be noted that tree fruit crops are typically propagated on a rootstock; the acceptability of a conventional scion with a genetically manipulated rootstock is less clear, but rootstocks such as the plum rootstock Stanley, with enhanced disease resistance to Phytophthora cinnamomi and the root-knot nematode Meloidogyne incognita, may well prove particularly useful for organic production.

Don’t Overlook GMOs

Although currently not accepted by most organic production guidelines, genetic modification should not be overlooked, as it offers perhaps the fastest, most efficient route to produce varieties better adapted to organic production. Mapping traits on a molecular map to identify flanking markers can also form the starting point to clone the genes, and once cloned, these genes can be transformed into other varieties using genetic modification. One scab resistance gene Rvi6 (Vf) has already been cloned and transformed into Gala. Artificially transferring a gene between organisms that could otherwise be conventionally bred, as with the scab-resistant Gala, is an example of cisgenics rather than transgenics, where a gene is artificially transferred between two organisms that could not otherwise be conventionally bred.

For a crop such as apple, where fruit is sold by variety name, successfully introducing a new variety produced through traditional breeding involves an expensive marketing and development campaign and considerable risk to the grower; one advantage of using technology such as cisgenics to introduce resistance is that the resulting variety is effectively unchanged for the consumer.

A further form of genetic modification that is being used currently in apple is transient gene silencing; targeted genes are “switched off” rather than new genes being added, as is the case with the new non-browning Arctic apples from Okanagan Specialty Fruits of Summerland, British Columbia.