The objective of our study was the alignment of microsatellite or simple sequence repeat (SSR) marker data across germplasm collections of cherry within Europe. Through the European Cooperative program for Plant Genetic Resources ECPGR, a number of European germplasm collections had previously been analysed using standard sets of SSR loci. However, until now these datasets remained unaligned. We used a combination of standard reference genotypes and ad-hoc selections to compile a central dataset representing as many alleles as possible from national datasets produced in France, Great Britain, Germany, Italy, Sweden and Switzerland. Through the comparison of alleles called in data from replicated samples we were able to create a series of alignment factors, supported across 448 different allele calls, that allowed us to align a dataset of 2241 SSR profiles from six countries. The proportion of allele comparisons that were either in agreement with the alignment factor or confounded by null alleles ranged from 67% to 100% and this was further improved by the inclusion of a series of allele-specific adjustments. The aligned dataset allowed us to identify groups of previously unknown matching accessions and to identify and resolve a number of errors in the prior datasets. The combined and aligned dataset represents a significant step forward in the co-ordinated management of field collections of cherry in Europe.

Fresh berries are a popular and important component of the human diet. The demand for high-quality berries and sustainable production methods is increasing globally, challenging breeders to develop modern berry cultivars that fulfill all desired characteristics. Since 1994, research projects have characterized genetic resources, developed modern tools for high-throughput screening, and published data in publicly available repositories. However, the key findings of different disciplines are rarely linked together and only a limited range of traits and genotypes has been investigated. The Horizon2020 project BreedingValue will address these challenges by studying a broader panel of strawberry, raspberry and blueberry genotypes in detail, in order to recover the lost genetic diversity that has limited the aroma and flavor intensity of recent cultivars. We will combine metabolic analysis with sensory panel tests and surveys to identify the key components of taste, flavor and aroma in berries across Europe, leading to a high-resolution map of quality requirements for future berry cultivars. Traits linked to berry yields and the effect of environmental stress will be investigated using modern image analysis methods and modeling. We will also use genetic analysis to determine the genetic basis of complex traits for the development and optimization of modern breeding technologies such as molecular marker arrays, genomic selection and genome wide association studies. Finally, the results, raw data and metadata will be made publicly available on the open platform Germinate in order to meet FAIR data principles and provide the basis for sustainable research in the future.

Simple sequence repeat (SSR) microsatellite markers have been extensively used to identify duplication and analyse genetic diversity in germplasm collections of apple. Here, we present findings from the use of a standard set of SSR loci in the managed repropagation of a significant international germplasm collection: the UK National Fruit Collection (NFC). A subset of eight SSR loci was deemed sufficient to distinguish all apart from the clonal relatives across a sample of 1995 accessions, with a single exception being one pair of full siblings. In total, 99% of accessions were able to be confirmed present and correct after the replacement of trees initially identified to be incorrectly propagated. In parallel to the curation of the collection itself, through an initiative led by the UK local apple enthusiast community, 3373 SSR profiles for apples held in local collections were compared to the NFC holdings. Overall, in both sets of material, diversity remained high with average gene diversity values of 0.800 and 0.812 in the NFC holdings and local collections, respectively. Accessions in local collections were not found to differ in their overall coverage of genetic diversity to that of the NFC collection (FST = 0.0035) although significant numbers of locally valued, and genetically distinguishable individuals were identified, some of which may represent ‘lost’ cultivars.

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