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Genome to phenome mapping in apple using historical data


Apple is one of the world’s most valuable fruit crops, but its large size and long juvenile phase prior to producing fruit make breeding new cultivars time consuming and expensive. Marker-assisted selection (MAS) can significantly decrease the time required for breeding new apple cultivars by allowing plants with a desired trait to be selected at the seed or seedling stage. However, MAS requires the discovery of genetic markers that predict traits of interest to breeders.

Hand reaching for apple

In the July 2016 issue of The Plant Genome, researchers scanned the genomes of 689 apple varieties for genetic makers and evaluated the ability of these markers to predict variation in 36 traits collected over 13 years from the USDA apple germplasm collection in Geneva, NY. Most traits were poorly predicted using genetic markers and are likely too strongly influenced by the environment to be candidates for MAS. However, the researchers discovered a novel association between the transcription factor NAC18.1 and harvest date and fruit firmness. A single nucleotide change was identified in this gene that may be causal and could be leveraged by apple breeders using MAS.

With the continued improvement of phenotyping technologies as well as the future prospect of whole-genome sequencing, genome-wide association mapping of diverse collections of apples promises to enable the more widespread adoption of marker-assisted selection and improve the efficiency of apple improvement.

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