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Domestication of Apple: Pedigrees, Inbreeding and Selection for Specific Genomic Regions

Carlsbergfondets internationaliseringsstipendier

What

The overall objective is to describe the genetic relationships, and selection for specific genomic regions in North European and world-wide important apple cultivars. It provides crucial knowledge for future improvement of cultivated apple. Using high-density genome-wide SNP markers, we aim for identifying genomic regions in apple that have been conserved for several generations during apple breeding, and are critical for successful apple cultivars. We will uncover the set of genes that each individual has inherited from each parent (haplotype), and reveal the degree of inbreeding in major apple cultivars. The findings will provide crucial knowledge for future improvement of apple cultivars. The overall impact of the study is to increase the genetic diversity utilized in apple production.

Why

To feed a growing global population and meet future climate changes there is an urgent demand for new plant cultivars. New cultivars arise from breeding that exploits the genetic variation kept in gene bank collections. However, traditional breeding in apple is time consuming and unpredictable. Genomics-based breeding allows speeding up and focusing the breeding process, but depends on genomic knowledge of the breeding material kept in gene bank collections. Lack of basic genetic information on gene bank accessions is a major obstacle for the potential utilization of germplasm resources. In addition, the narrow genetic diversity among major apple cultivars poses a serious threat for inbreeding in future generations, and lacking ability to adapt to future climate changes.

How

We will use state-of-the-art technologies by three overall approaches: 1) Generating genome-wide genotype data for about 200 Danish apple cultivars using the robust 20k Infinium SNP array. 2) Compare this data with existing data for more than 1,000 important apple cultivars originating from all over the world, where genotype data is already available at the host institution. 3) Re-construction of extinct genotypes for detailed pedigree reconstruction, which is now possible thanks to recent haplotyping software. This allows at once QTL discovery, examination for genomic hot spots of selection intensity and unprecedented insight into the genomic composition of any apple individual.

SSR

There is a strong need for apple cultivars with improved genomic traits. This is to develop new cultivars with resistance to various pests and diseases in order to reduce the vast amount of pesticides used in apple production. New genotypes with adaptation to current climate changes are needed as well as highly productive cultivars adapted marginal climate zones such as in the Nordic Region. Recent focus on natural colorants and aromas as alternatives to artificial additives in the food industry has furthermore created a need for cultivars with new traits in addition to ever-changing customer demands. New plant cultivars have the potential to increase productivity under changing climate to feed a growing global population.