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Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm

Muranty, Helene and Denance, Caroline and Feugey, Laurence and Crepin, Jean-Luc and Barbier, Yves and Tartarini, Stefano and Ordidge, Matthew and Troggio, Michela and Lateur, Marc and Nybom, Hilde and Paprstein, Frantisek and Laurens, Francois and Durel, Charles-Eric (2020). Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm. BMC Plant Biology. 20 , 1-18
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Abstract

Background Apple (Malus x domestica Borkh.) is one of the most important fruit tree crops of temperate areas, with great economic and cultural value. Apple cultivars can be maintained for centuries in plant collections through grafting, and some are thought to date as far back as Roman times. Molecular markers provide a means to reconstruct pedigrees and thus shed light on the recent history of migration and trade of biological materials. The objective of the present study was to identify relationships within a set of over 1400 mostly old apple cultivars using whole-genome SNP data (similar to 253 K SNPs) in order to reconstruct pedigrees. Results Using simple exclusion tests, based on counting the number of Mendelian errors, more than one thousand parent-offspring relations and 295 complete parent-offspring families were identified. Additionally, a grandparent couple was identified for the missing parental side of 26 parent-offspring pairings. Among the 407 parent-offspring relations without a second identified parent, 327 could be oriented because one of the individuals was an offspring in a complete family or by using historical data on parentage or date of recording. Parents of emblematic cultivars such as 'Ribston Pippin', 'White Transparent' and 'Braeburn' were identified. The overall pedigree combining all the identified relationships encompassed seven generations and revealed a major impact of two Renaissance cultivars of French and English origin, namely 'Reinette Franche' and 'Margil', and one North-Eastern Europe cultivar from the 1700s, 'Alexander'. On the contrary, several older cultivars, from the Middle Ages or the Roman times, had no, or only single, identifiable offspring in the set of studied accessions. Frequent crosses between cultivars originating from different European regions were identified, especially from the nineteenth century onwards. Conclusions The availability of over 1400 apple genotypes, previously filtered for genetic uniqueness and providing a broad representation of European germplasm, has been instrumental for the success of this large pedigree reconstruction. It enlightens the history of empirical selection and recent breeding of apple cultivars in Europe and provides insights to speed-up future breeding and selection.

Authors/Creators:Muranty, Helene and Denance, Caroline and Feugey, Laurence and Crepin, Jean-Luc and Barbier, Yves and Tartarini, Stefano and Ordidge, Matthew and Troggio, Michela and Lateur, Marc and Nybom, Hilde and Paprstein, Frantisek and Laurens, Francois and Durel, Charles-Eric
Title:Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm
Year of publishing :2020
Volume:20
Page range:1-18
Number of Pages:18
Publisher:BMC
Associated Programs and Other Stakeholders:Z - SLU - Libray > Odla mera
ISSN:1471-2229
Language:English
Publication Type:Journal article
Refereed:Yes
Article category:Scientific peer reviewed
Version:Published version
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 404 Agricultural Biotechnology > Genetics and Breeding
Keywords:Malus domestica, Genotyping, Parentage analysis, Parent-offspring, Founders, Germplasm collection, Empirical selection, Modern breeding
URN:NBN:urn:nbn:se:slu:epsilon-p-104559
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-104559
Additional ID:
Type of IDID
DOI10.1186/s12870-019-2171-6
Web of Science (WoS)000513182000002
ID Code:16716
Faculty:LTV - Fakulteten för landskapsarkitektur, trädgårds- och växtproduktionsvetenskap
Department:(LTJ, LTV) > Department of Plant Breeding (from 130101)
Deposited By: SLUpub Connector
Deposited On:04 Mar 2020 10:49
Metadata Last Modified:05 Mar 2020 05:02

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