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Apple genome sequence helpful to breeding new apple varieties

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A high-quality genome sequence of apple has been published in Nature Genetics by an international team of scientists, including researchers from Wageningen University & Research in the Netherlands. The sequence facilitates faster and more targeted breeding of new apple varieties with increased disease resistance, improved production traits, and better fruit quality. This supports more sustainable apple production, both from an environmental and a financial perspective.

The genome sequence was assembled by an international consortium of research institutions from France, Italy, Germany, the Netherlands and South Africa. The high quality of the genome data, indicating over 42,000 putative genes, is the result of the use of latest sequencing technologies that generate long stretches of DNA sequences, a very specific apple variety, and the most informative genetic linkage map for apple developed in earlier research.

The sequence gives new insights into the organisation of the apple genome. Already 93% of the genes have been validated through RNA sequencing. This knowledge is useful for the identification of genes that control a trait of specific interest and for the development of DNA-based diagnostic tests that can accelerate the breeding of new varieties.

The use of a so-called di-haploid apple variety was critical to the success of this study. Apple is an out-crossing species, making its genome heterozygous. Also, apples originated from a hybridization between two different species that was coupled with a whole genome duplication. As a result, each regular apple variety has up to four variants for each of its DNA sequences. The di-haploid variety used in this study is special as it has only up to two variants of every sequence. This leads to a dramatic reduction in complexity that made it possible to generate a very high-quality genome sequence.

The new insights into the apple genome include a clear view of the duplication patterns among the 17 apple chromosomes. This facilitates the identification of gene copies with similar function. Next, so called ‘repetitive regions’ have been assembled. These, thus far, uncharacterized regions of the apple genome may be involved in regulating gene expression. Finally, a new type of repeat sequence was found that may be specific for centromeres, which may lead to new insights in chromosome division and replication.

The research was coordinated by Etienne Bucher of INRA-Angers. Researchers from Wageningen University & Research contributed to the genome sequencing, mapping and assembly, applying their experience and skills in bioinformatics and by giving early access to a high-quality genetic linkage map of apple.

Wageningen University & Research also develops new apple varieties that have included Elstar, Santana and the recently released Natyra. The latter two are suited for organic production as these varieties have disease resistance. Additionally, Santana can be consumed by most individuals with a mild apple allergy. Wageningen will use the new insights into the DNA of the apple in the targeted breeding of new varieties.

This new genome sequence was made possible by financial support from the European Commission and some national granting agencies.

Image: Apple with apple scab. Credit: Wageningen University

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