Beyond plant genomes: which perspectives
Apple DNA sequences (around 13 billion sequenced nucleotides) were produced during 2007 and 2008, and in 2009 researchers assembled and reconstructed the gene content and order into the 17 apple chromosomes. The sequences equal a 17-fold coverage of the apple genome with over 82% of the genome assembled in the chromosomes and over 90% of the genes anchored to a precise position in the chromosomes.
Sequencing activity was performed using advanced technologies which demonstrated a growth rate unexpected until few years ago. In a decade, high throughput facilities moved from thousands of nucleotides per day to billions per hours, requiring an adequate growth of the related bioinformatics, not always able to keep similar speed, becoming then the real bottle neck.
Sequencing of the apple genome has allowed new discoveries to be made and increased our knowledge of the apple plant and its history. In particular:
- the cultivated apple was domesticated 3-4000 years ago from a recent wild progenitor, Malus sieversii, a species that is still widespread in the forests across Kazakhstan and China;
- the apple genome underwent duplication around 50 million years ago, bringing the number of chromosomes from 9 in the old American progenitor to the current 17;
- it has the highest number of genes, 57 thousand, of any plant genome studied to date. Of these, the publication identifies the complete set of 992 genes responsible for disease resistance, a potentially useful arsenal for genetic improvement;
- a list of three million genome positions (molecular markers) is available, which may serve as an orientation reference within the genome and to discover the functions of its genes;
- several families of genes which may be correlated with the development of the pome, the botanical name for the fruit of apple and its close relatives (e.g. pear, medlar), have been identified.
The data obtained will allow new varieties of apple to be developed more quickly than with conventional genetic improvement methods, resulting in plants with self-defence mechanisms against diseases and insects and which produce healthier and tastier fruits. The aim is to construct apple varieties requiring fewer agro-technical interventions, leading to more sustainable fruit cultivation, a research line that the Agricultural Institute of San Michele all’Adige has been following for several years. Sequencing of the apple genome has increased a thousand-fold our knowledge of this important agricultural plant, in particular its nutritional properties, environmental impact, exploration of biodiversity, philogenetic and evolutionary studies.
