Jun 7, 2017
Tool for developing new sustainable apple varieties published

An international team of scientists, among whom researchers from Wageningen University & Research Centre published the week of June 5 a high quality genome sequence of apple in the journal Nature Genetics. The publication of the genome allows faster and more targeted new apple varieties to develop with disease resistances, improved product properties and improved fruit quality. The results thus support a more sustainable production of apples, both from an environmental and a financial point of view.

The genome has been investigated by an international consortium of research institutes from France, Italy, Germany, the Netherlands and South Africa. The high quality of the genome data, which contains more than 42 thousand suspected genes, has been obtained using the latest sequencing techniques that generate long DNA sequences with a highly specific apple breed and with the most informative genetic linking card in apple that Has been developed in earlier research.

The genome sequence offers new insights into the organization of the apple genome. All 93 percent of the 42,000 suspected genes are validated by RNA sequencing. This knowledge is useful for identifying genes that drive an interesting trait and for the development of DNA-based diagnostic tests that will enable faster breeding of new breeds.

The use of a so-called dihaploid apple breed was crucial for the success of this study. The apple is a cross pollinator, so its genome is heterozygote. In addition, the apple is the result of hybridization between two different species, which interfere with full genome duplication. As a result, each regular apple breed can have four variants of each DNA sequence. The dihaploid breed used in this study is special because it can only have two variants of each sequence. As a result, the genome of this breed is much less complicated, so that a very high quality genome sequence could be generated.

Among other things, it has become very clear about the duplication patterns between the 17 chromosomes of apple, making it easier to find gene copies with a similar function. Furthermore, so-called ‘repetitive areas’ are composed. These unidentified areas in the Apple genome may play a role in regulating gene expression. Finally, a new type of repetitive sequence was found that could be specific to centrometers. This discovery can provide new insights on chromosome division and replication.

The research was coordinated by Etienne Bucher of INRA-Angers (France). Researchers of Wageningen University & Research have contributed in particular to large-scale DNA analysis (genomic sequencing), the development and application of bioinformatics, and the granting of access to an unprecedented genetic map of apple.

Wageningen University & Research develops new apple varieties. Thus, the famous races Elstar and Santana have been developed and the recently launched Natyra. Because Santana’ and Natyra are resistant to diseases, these varieties are suitable for organic farming. ‘Santana’ has a special characteristic that the apples are suitable for consumption by most people with mild apple allergy.

Wageningen will use the new insights into the DNA of the apple in the targeted breeding of new breeds, especially aimed at sustainability.

This new genome sequence has been made possible thanks to some financial support from the European Commission and some national granting agencies.

Source: Wageningen University University and Research Centre

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