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31326 Castanet Tolosan CEDEX - France

Dernière mise à jour : Mai 2018

Menu Logo Principal Institut Agro Rennes-Angers Angers University   IRHS

IRHS

Reconstructing and checking pedigrees

The knowledge of pedigree relationships between cultivars enables both to bring information about breeding history over the past centuries and to estimate heritabilities and genetic correlations of economically interesting traits in modern breeding programs.

The knowledge of pedigree relationships between cultivars enables both to bring information about breeding history over the past centuries and to estimate heritabilities and genetic correlations of economically interesting traits in modern breeding programs.

In apple as well as in pear, cultivars can be maintained in orchards or in collections over centuries thanks to grafting. Some extremely old cultivars are supposed to date back to the Middle Ages or even to the Roman antiquity.

Thanks to the collections of apple genetic resources maintained at IRHS and in several European partner collections, we were able to reconstruct parentages between old cultivars and reveal yet unknown parentages. In a first step, direct parent-offspring relationships involving more than 800 cultivars were identified using dense molecular marker data (genetic footprints derived from more than 250000 SNP (= single nucleotide polymorphism) markers spread over the whole genome) obtained for more than 1400 old or local (mostly European) apple cultivars (Fig1). Parents of emblematic cultivars such as 'Calville Blanc d'Hiver' (France), 'Transparente de Croncels' (France), 'Ribston Pippin' (UK) or 'White Transparent' (Baltic States) were identified (Fig2). The reconstructed pedigree encompassed at this stage seven generations. It shed light on the major and unexpected impact of two Renaissance cultivars of French and English origins, namely 'Reinette Franche' and 'Margil', and of one cultivar of Russian origin in the 1700s, 'Alexander'. These results coincide with the writings of the famous French pomologist André Leroy who wrote in 1873 that ‘Reinette Franche’ was the ‘mother of a considerable number of apple varieties’ and gave them its name (i.e. most of 'Reinette' cultivars). Older cultivars, from the Middle Ages or the Roman times, had no, or only single, identifiable offspring in the set of studied cultivars. All these results illustrate the history of ancient empirical selection and recent breeding of apple cultivars.

In a second step, we are taking part to a larger analysis, involving cultivars maintained in other collections (North and Eastern Europe, United States, …), in order to identify other parentage relationships and extend the large reconstructed pedigree. First we assessed the compatibility between molecular marker data obtained with two different SNP genotyping arrays, thus enabling to continue the analysis for a lower cost. Then, a method taking into account the SNP marker location was developed to allow the identification of more distant relationships than direct parent-offspring, on the basis of “shared haplotypes” (i.e., sharing of large DNA fragments inherited from a more distant or not identified common ancestor). Other methodological approaches under development, e.g. using marker data of triploid cultivars, will enable to further the pedigree analysis (i.e., inferring diploid parents of triploid cultivars, which are numerous in apple and pear). The obtained pedigree already opens up avenues to follow alleles at genes controlling economically interesting traits and thus accelerate the breeding of new cultivars using molecular markers.

Pedigree_Fig1

Fig1 : Example of the density of parentage relationships between (mostly) European cultivars. Each cultivar is represented by a dot while connecting lines in the network represent parent-offspring relationships. Most cultivars are represented by blue dots. ‘Reinette Franche’ is represented by a red dot, the English cultivar ‘Cox’s Orange Pippin’ by a green dot, and the Russian cultivars ‘Alexander’ and ‘Borowitsky’, by purple and orange dots, respectively.

Pedigre_Fig2

Fig2: Example of pedigree reconstructed using molecular markers

Associated publications

Muranty H., Denancé C., Feugey L., Crépin J.L., Barbier Y., Tartarini S., Ordidge M., Troggio M., Lateur M., Nybom H., Paprstein F., Laurens F., Durel C.E. (2020) Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm. BMC Plant Biology, doi: 10.1186/s12870-019-2171-6

N.P. Howard, M. Troggio, C.-E. Durel, H. Muranty, C. Denancé, L. Bianco, J. Tillman, E. van de Weg (2021) Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls. BMC Genomics 22:246. doi: 10.1186/s12864-021-07565-7

C.-E. Durel, H. Muranty, C. Denancé 2020 La généalogie des variétés de pommes (enfin) décryptée. Jardins de France n°659, 61-63 https://www.jardinsdefrance.org/la-genealogie-des-varietes-de-pommes-enfin-decrypee/