A high quality genome sequence of apple is published in Nature Genetics by an international team of scientists from France, Italy, Germany, the Netherlands and South Africa. The publication of the sequence facilitates faster and more targeted breeding of new apple varieties with increased disease resistance and better fruit quality.
The genome sequence gives new insights into the organization of the apple genome. Already 93 percent of the 42,000 putative genes have been validated through RNA sequencing. This knowledge is useful for the identification of genes that control a trait of interest and for the development of DNA-based diagnostic tests that can accelerate breeding of new varieties.
The use of a so-called dihaploid apple variety was critical for the success of this study. Apple is an outcrossing species, making its genome heterozygous. Also, apple originated from a hybridization between two different species, which 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 complexity reduction, which made it possible to generate a very high quality genome sequence.
The new insights in the apple genome include a clear view on the duplication patterns among the 17 chromosomes of apple. This facilitates the identification of gene copies with similar function.А new type of repeat sequence was found that may be specific for centromeres, which may lead to new insights in chromosome division and replication.
High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development, Nature Genetics (2017). nature.com/articles/doi:10.1038/ng.3886