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Apple trees in blossom. © INRA, NIORE Jacqueline

Apple: a very high quality genome obtained

An international consortium led by INRA and involving research scientists in France, Italy, Germany, the Netherlands and South Africa, has been able to obtain a very high quality apple genome by combining the most recent DNA sequencing technologies with classic mapping methods. Their findings provide scientists an unprecedented view of the composition and evolution of a tree genome, and offers new perspectives for the creation of new varieties, notably in order to reduce pesticide use. These results are published in Nature Genetics on 5 June 2017.

Updated on 01/12/2018
Published on 06/06/2017

Apples are one of the most widely consumed fruits in the world, and 84.6 million tonnes of apples are produced each year. In order to enable the more efficient selection of new apple varieties, it is essential to gain access to a high quality genome. This will permit the genetic and epigenetic studies that are essential to identifying the key genes involved, for example, in fruit size and colour or disease resistance.

  
Based on a genetic map with a high density of markers, it was possible to assemble the genome in 17 pseudo-molecules representing the 17 chromosomes of the apple. With a total size of 649.3 Mb assembled in 280 fragments, this genome comprises 42,140 genes.  

Diagram showing the 17 chromosomes of the apple. Coloured links between the chromosomes indicate duplicated regions.. © INRA, Nicolas Daccord
Diagram showing the 17 chromosomes of the apple. Coloured links between the chromosomes indicate duplicated regions. © INRA, Nicolas Daccord

   

Rearrangements identified in the apple genome as going back 21 million years

This new genome has, for example, enabled scientists to identify important rearrangements that occurred in the apple genome about 21 million years ago. These changes may have been due to the emergence of the Tian Shan mountain range in Kazakhstan, the region where the apple originated. These geological and environmental events may have contributed to the contrasted evolution of the common ancestor of the apple and pear.

    

Epigenetic studies to understand fruit development

Using this very high quality genome, the scientists were able to conduct epigenetic studies focused on the transmission of information independently of the DNA sequence. This allowed them to demonstrate that epigenetic markers can influence fruit development through the differential expression of genes.

From left to right: a  'Golden Delicious' fruit, a #13 doubled haploid fruit whose genome was sequenced, and a #18 doubled haploid fruit identical to #13. The difference in fruit size between the two doubled-haploids is probably due to epigenetic differences identified as affecting key genes involved in fruit development.. © INRA, Jean-Marc Celton
From left to right: a 'Golden Delicious' fruit, a #13 doubled haploid fruit whose genome was sequenced, and a #18 doubled haploid fruit identical to #13. The difference in fruit size between the two doubled-haploids is probably due to epigenetic differences identified as affecting key genes involved in fruit development. © INRA, Jean-Marc Celton

  
This genome is an essential tool for the entire community working on apple breeding, and more generally in order to acquire knowledge on genome evolution and regulation. It will also facilitate an acceleration of the creation of new and more resistant varieties that will reduce the use of pesticides, improve apple quality or adapt these varieties to environmental constraints and climate change.

  

Find out more

Website on the apple genome: https://iris.angers.inra.fr/gddh13/
Twitter: @AppleGenome

Contact(s)
Scientific contact(s):

  • Etienne Bucher (33 (0)2 41 22 56 99) Research Institute for Horticulture and Seeds (Joint INRA – AgroCampus Ouest – Université d’Angers Research Unit)
Press Relations:
INRA News Office (33 (0)1 42 75 91 86)
Associated Division(s):
Plant Biology and Breeding
Associated Centre(s):
Angers-Nantes

Reference

Nicolas Daccord, Jean-Marc Celton, Gareth Linsmith, Claude Becker, Nathalie Choisne, Elio Schijlen, Henri van de Geest, Luca Bianco, Diego Micheletti, Riccardo Velasco, Erica Adele Di Pierro, Jérôme Gouzy, D Jasper G Rees, Philippe Guérif, Hélène Muranty, Charles-Eric Durel, François Laurens, Yves Lespinasse, Sylvain Gaillard, Sébastien Aubourg, Hadi Quesneville, Detlef Weigel, Eric van de Weg, Michela Troggio and Etienne Bucher, High quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nature Genetics (2017) doi:10.1038/ng.3886