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Sequence of apple genome reveals unexpected results

29 Aug 2010

Analysis of the complete DNA sequence of apple suggests that a major step in evolution of the fruit was caused by a catastrophic environmental event, possibly the same one that killed the dinosaurs.

An international consortium, including scientists at Plant & Food Research, has sequenced the more than 600 million base pairs of DNA which make up the apple genome. This sequence will open the way to understanding characteristics of importance to consumers, such as crispness, juiciness and flavour, or to producers, such as harvest time.

The sequencing has revealed that large lengths of apple chromosomes are copied in other chromosomes. This duplication would explain why the apple, and closely related pear, genomes have 17 chromosomes, while all other plants in the Rosaceae family (including peach, raspberry and strawberry) have between 7 and 9 chromosomes. Many of the genes in these duplicated areas are related to fruit development and this larger number compared with other fruit may have enabled the distinctive features seen in apple.

Evolutionary analysis tracked this whole genome duplication (WGD) event to around 60 million years ago. It is thought to be a genetic survival response to an event that caused mass extinctions of other species, including the dinosaurs. Other well adapted plant species, such as poplar, have been shown to have undergone a similar evolutionary response at the same time.

The research is published in the prestigious journal Nature Genetics.

Apple is the fourth most economically important fruit crop worldwide, accounting for $395 million of New Zealand’s export income. The sequencing of the genome will assist scientists in identifying the genetic controls of characteristics that consumers desire in new varieties of apples, such as texture, taste and colour. Genetic markers developed from these key genes will be used to screen thousands of apple seedlings in conventional breeding programmes to pre-select those with the right combination of traits for commercial success.

“Understanding how important characteristics in plants are controlled is vital in reducing the time to breed successful commercial cultivars,” says Dr Roger Hellens, Science Group Leader (Genomics) at Plant & Food Research. “Now we have the sequence of the apple genome, we will be able to identify the genes which control the characters that our sensory scientists have identified as most desired by consumers – crispness, juiciness and flavour.”

Plant & Food Research scientist, Dr Sue Gardiner, said analysing the apple genome sequence produced some unexpected results.

“It seems that at some point, around 50 to 65 million years ago, the apple ancestor separated from its Rosaceae cousins on the evolutionary pathway. By duplicating almost all of its genome, apples now have very different fruit characteristics to related plants, such as peaches, raspberries, and strawberries. The timeframe for this evolutionary change coincides with similar events in other plants and mass extinctions of some species, including the dinosaurs. This suggests that a major environmental event forced certain species, including apple, to evolve for survival.”

The apple genome project included scientists from 13 institutions in five countries – Italy, the USA, Belgium, France and New Zealand. The lead organisation, Instituto Agrario di San Michele all’Adige (IASMA), was funded by the provincial council of Trentino, Italy, with additional support from other organisations and funding bodies. Plant & Food Research, the New Zealand collaborator, provided access to a breeding population of 600 apple trees, used to help order sections of DNA sequence on the 17 chromosomes.  The whole genome sequence, together with a detailed genetic map constructed from the Plant & Food population, will be used to advance the Plant & Food Research apple breeding programme, which has previously developed the commercially successful JAZZ brand cultivar.

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