Towards a Joint International Database: Alignment of SSR Marker Data for European Collections of Cherry Germplasm.

Matthew Ordidge,Christina Kägi,Stephanie Mariette,Daniela Giovannini,Edward Venison,Annalisa Marchese,Markus Kellerhals,Suzanne Litthauer,Felicidad Fernandez-Fernandez,Hilde Nybom,Monika Höfer,Marine Blouin-Delmas

doi:10.3390/plants10061243

Abstract

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.

Highlights

In 41 out of 53 samples theoretically replicated between the two phases of Great Britain (GB) data, a consistent alignment factor could be identified (Supplementary Table S1)
Thirty-two further samples from the first phase of analysis, which had been deemed to represent duplicates in the collection to those used for comparison, were in general agreement with the locusor allele-range-specific alignment factors
For the locus EMPaS02, an allele-range-specific alignment factor was deemed necessary, with alleles of 146 bp and 148 bp being adjusted by 4 bp and the remainder of alleles adjusted by 3 bp based on the majority of examples

Summary

Introduction

The importance of conserving genetic diversity of agricultural crops is widely accepted and over 7000 accessions of sweet cherry are currently listed within the global Genesys database [1]; over 6500 are included within EURISCO, the European Search Catalogue for Plant Genetic Resources [2]. Providing access to data has been a priority of the European Cooperative program for Plant Genetic Resources (ECPGR) Prunus working group since its establishment [3]. Sweet cherry is a challenging crop to distinguish at a morphological level and genetic markers offer significant value in efforts to compare between genebank holdings. The AEGIS (A European Genebank Integrated System) initiative [5] to develop a better co-ordinated European collection within ECPGR would benefit substantially from the ability to align and compare DNA marker data produced in different countries

Objectives

Methods

Results

Discussion

Conclusion