New Insight into the History of Domesticated Apple: Secondary Contribution of the European Wild Apple to the Genome of Cultivated Varieties

The apple is the most common and culturally important fruit crop of temperate areas. The elucidation of its origin and domestication history is therefore of great interest. The wild Central Asian species Malus sieversii has previously been identified as the main contributor to the genome of the cultivated apple (Malus domestica), on the basis of morphological, molecular, and historical evidence. The possible contribution of other wild species present along the Silk Route running from Asia to Western Europe remains a matter of debate, particularly with respect to the contribution of the European wild apple. We used microsatellite markers and an unprecedented large sampling of five Malus species throughout Eurasia (839 accessions from China to Spain) to show that multiple species have contributed to the genetic makeup of domesticated apples. The wild European crabapple M. sylvestris, in particular, was a major secondary contributor. Bidirectional gene flow between the domesticated apple and the European crabapple resulted in the current M. domestica being genetically more closely related to this species than to its Central Asian progenitor, M. sieversii. We found no evidence of a domestication bottleneck or clonal population structure in apples, despite the use of vegetative propagation by grafting. We show that the evolution of domesticated apples occurred over a long time period and involved more than one wild species. Our results support the view that self-incompatibility, a long lifespan, and cultural practices such as selection from open-pollinated seeds have facilitated introgression from wild relatives and the maintenance of genetic variation during domestication. This combination of processes may account for the diversification of several long-lived perennial crops, yielding domestication patterns different from those observed for annual species

Comparative analysis of the duplication degree and genetic relationships between three apple collections located in the pyrenean region

One of the possibilities to improve the management of germplasm collections is to identify the redundancies that inevitably appear within and between collections. For this purpose, an accurate identification of the preserved accessions is an indispensable requisite. In terms of identification, traditional methods based on morphological and agronomic traits are less effective than molecular markers due to the fact that they can be highly influenced by environmental factors. The aim of this study was to quantify the duplication degree among three apple collections located in the Spanish and French Pyrenean region, using a common set of 14 SSR markers, as well as to assess the genetic relationships between the accessions held in the three collections. Only 17 genotypes (≈5% of the identified ones) were present in both Spanish and French collections. Two duplicates groups, nine (putative) synonyms and nine homonyms were identified. Remarkable differences in allelic variability and allelic frequencies distribution were found between the material preserved in Spanish and French collections, but the duplication and overlap highlighted the interest of coordinated international studies aiming at optimizing the management of germplasm collections

Genome wide association study of two phenology traits (flowering time and maturity date) in apple

The aim of Genome Wide Association Studies (GWAS) is to identify markers in tight linkage disequilibrium with loci controlling quantitative trait variation. These markers can then be used in marker-assisted selection (MAS) in fruit crops such as apple. The GWAS approach involves both phenotyping of a large population of mostly unrelated individuals for the traits of interest, and genotyping at high marker density. In the EU-FP7 project FruitBreedomics, almost 1,200 European diploid dessert apple accessions (old and/or local cultivars) from six germplasm collections were genotyped with the Affymetrix Axiom_Apple480K array (487,000 SNPs). Phenotypic data on a large number of traits have been gathered during the project. Here we focus on flowering period and harvesting date. Knowledge of the genetic control of these traits is necessary to develop cultivars that can face the challenges imposed by global climate change and to target cultivar development as a function of a prolonged vegetation period in the production regions. Different models were tested, including control for effects of population structure and relatedness between cultivars. The full model, controlling for both structure and relatedness, was shown to be the most appropriate to avoid spurious marker-trait associations. When analyzing data over all collections, one significant marker-trait association was obtained for each trait, on chromosomes 9 and 3, for flowering period and harvesting date, respectively. Thereby, genomic locations previously identified in bi-parental populations could now be confirmed for a genetically diverse germplasm

Genome Wide Association Study of two phenology traits (flowering time and maturity date) in apple

International audienc

Deciphering the genetic determinism of flowering/harvest period and several fruit sensory quality traits in apple by a Genome-Wide Association approach

National audienc

La graphiose de l'orme Exemples d'impact en France, bases scientifiques de la lutte, perspectives des recherches francaises

Available at INIST (FR), Document Supply Service, under shelf-number : RP 185 (2919) / INIST-CNRS - Institut de l'Information Scientifique et TechniqueSIGLEFRFranc