Characterization of the genetic diversity

Characterization of the genetic diversity

In France, apple and pear old cultivars are conserved by numerous actors and represent a diversity reservoir that must be characterized from both phenotypic and genotypic point of view in order to better manage it and exploit its potential, specifically in a climate change context. We have been contributing for many years to the characterization of these genetic resources using microsatellite markers (SSR), and more recently SNPs, in collaboration with the VaDiPom team in charge of apple and pear genetic resources management.

First, we coordinated the CorePom project, funded by the French Foundation for Biodiversity Research (FRB), which enabled the characterization of the whole INRAE collection and numerous other collections in France, including those managed by the "Croqueurs de pommes®" association, the “Centre Végétal Régional d’Aquitaine” (CVRA), the “Centre Régional de Ressources Génétiques” (CRRG) of the Nord-Pas-de-Calais region, the "Mordus de la pomme" association, and many other associations and local authorities (Fig1). We are continuing this work of genetic characterization in the frame of agreements with the Union Pomologique de France and the Croqueurs de pommes®.

Diversity_fig1

At the French scale, more than 6000 apple and 2000 pear accessions were genotyped with a minimum of 16 SSR markers, which represents a considerable amount of work in referencing and comparing old and local cultivars on a national level. Many genetic redundancies were observed within and between collections, and unique cultivars specific to each collection could be identified. Many naming errors were also corrected. The management of these genetic resources is thus greatly facilitated, even if genetic markers do not (yet) make it possible to distinguish 'sports' within a set of accessions sharing the same SSR profile. A unique genotype code number ('MUNQ' code for 'Malus UNiQue genotype code' and ‘PUNQ’ for 'Pyrus UNiQue genotype code') is proposed, and regularly incremented by our team, for each group of accessions sharing the same SSR profile, which makes it possible to easily compare accessions between collections. For apple, this MUNQ code has been extended to the European scale during the European FruitBreedomics project, and even to the international scale with the USDA (USA) collection for example. The same has been done for pear in the framework of the ECPGR Pomefruit_C&E project and another collaboration with USA. To do this, it was often necessary to set up a procedure to harmonize the SSR genotypic data available for these foreign collections with those of the French collections. Our team thus played a pioneering and major role in the comparison of apple and pear genetic resources conserved at the European/international scale. The MUNQ and PUNQ codes are increasingly used by germplasm managers who are starting to insert them into their databases. An increasing part of the MUNQ data is made public via the following regularly updated dataset: https://data.inrae.fr/dataset.xhtml?persistentId=doi:10.15454/HKGMAS

The available SSR data also made it possible to analyze the extent and structure of the apple genetic diversity present in the germplasm collections (similar work in progress for pear). At the French scale, there is no significant geographical structure, but we were able to show a structure between old dessert and cider cultivars and with recent cultivars (Fig2). At the European scale extended to Russia, we were able to show a rather weak structure, showing the importance of the flow of plant material (grafts in particular) between European countries over the centuries. However, a North-East/South and West structure was clearly identified (Fig3).

Diversity_fig2
Diversity_fig3

Modification date: 20 December 2023 | Publication date: 01 September 2021 | By: ResPom