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

Ordidge, Matthew and Litthauer, Suzanne and Venison, Edward and Blouin-Delmas, Marine and Fernandez-Fernandez, Felicidad and Höfer, Monika and Kägi, Christina and Kellerhals, Markus and Marchese, Annalisa and Mariette, Stephanie and Nybom, Hilde and Giovannini, Daniela (2021). Towards a Joint International Database: Alignment of SSR Marker Data for European Collections of Cherry Germplasm. Plants. 10 , 1243
[Research article]

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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.

Authors/Creators:Ordidge, Matthew and Litthauer, Suzanne and Venison, Edward and Blouin-Delmas, Marine and Fernandez-Fernandez, Felicidad and Höfer, Monika and Kägi, Christina and Kellerhals, Markus and Marchese, Annalisa and Mariette, Stephanie and Nybom, Hilde and Giovannini, Daniela
Title:Towards a Joint International Database: Alignment of SSR Marker Data for European Collections of Cherry Germplasm
Series Name/Journal:Plants
Year of publishing :2021
Volume:10
Article number:1243
Number of Pages:18
Publisher:MDPI
Associated Programs and Other Stakeholders:Z - SLU - Library > Odla mera
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 404 Agricultural Biotechnology > Genetics and Breeding
Keywords:Prunus avium, sweet cherry, SSR, microsatellite, germplasm, genetic resource
URN:NBN:urn:nbn:se:slu:epsilon-p-112780
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-112780
Additional ID:
Type of IDID
DOI10.3390/plants10061243
Web of Science (WoS)000666448800001
ID Code:24856
Faculty:LTV - Fakulteten för landskapsarkitektur, trädgårds- och växtproduktionsvetenskap
Department:(LTJ, LTV) > Department of Plant Breeding (from 130101)
Deposited By: SLUpub Connector
Deposited On:14 Jul 2021 09:26
Metadata Last Modified:15 Jul 2021 04:03

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