Know more

Intro

The study is based on the analysis of seven mutants from the Gala variety, selected for their contrasted color and pattern phenotypes. Two main goals:

1. to set up a standardized phenotyping workflow for apple fruit color
2. to detect putative genetic/epigenetic differences between the reference Gala and its mutants thanks to the last released Gala genome sequence and to re-sequencing ofGala mutants.  

Description

Since 1995, the Plant Variety Rights System in Europe is implemented and administered by the Community Plant Variety Office (CPVO), which is a decentralized European agency. Its mission is to provide protection with an intellectual property right for new plant varieties. In fruits the system is based on the exam of DUS (Distinction, Uniformity, Stability) traits. Geves (Groupe d'étude et de contrôle des variétés et des semences) is in charge of this experiment for all plant species in France. Geves has delegated to the VadiPom team the realization of these DUS tests for pome fruit species. VadiPom manages the most important DUS reference collection among the five European institutes performing DUS on pome fruits.

Two main types of varieties are found in apple: those resulting from hybridization and those resulting from mutation. These mutants are present and marketed in all the major varieties (Gala, Red Delicious, Golden Delicious, Jonagold, … ); they can differ from the original variety by few characteristics, in particular the tree habit but commercially the most important trait affected by mutation is the apple skin color: the more colored mutants ensure growers a higher income; there is thus, in all the major groups of apple varieties a race towards intensities and percentages of coloration increasingly strong. 

The current DUS tests, based exclusively on phenotypic observations, easily distinguish the new varieties resulting from hybridization.  But, the small differences between mutants of the same variety make DUS tests very complicated.

The objective of the "Imoddus-apple mutant" project is therefore to answer this issue by developing and testing phenotypic and molecular tools (genetic and epigenetic). It was carried out on 7 mutants of the Gala variety. 

Thanks to recent researches, especially the discovery of new high-quality apple genomes and subsequent resequencing, we now have potential genetic tools to look for slight genetic variations between mutants. Furthermore, in recent years it has become increasingly clear that epigenetics plays a very important role in the regulation of gene expression. Therefore, it is very likely that apple mutants aren't true genetic mutants (DNA alleles), but epigenetic mutants (epialleles, differing in DNA methylation patterns thus affecting gene expression). Such epialleles would not differ from the parental line in the DNA sequence, but only in DNA methylation patterns. Such a differential methylation process of the genes involved in fruit coloration is assumed to be responsible for many other apple mutants. 

In the same recent period, the development of new sensors and machine learning approaches have  led the way to new  phenotyping tools In order to increase the efficiency and reliability of DUS testing of apple mutants. 

Results

Phenotyping is managed in collaboration with ImHorPhen. It aimed at developing a static 3D computer mockup derived from point cloud data, for automatized apple phenotyping. A prototype of a sorting machine has been set up. First samples have been successfully phenotyped in spring 2020, and first results are expected for 2021. Genetic and epigenetics approaches are underway in the frame of the PhD thesis of W Wang (2017-2020) in collaboration with the Valema team, ETHZ and Agroscope (Switzerland). First results show that both genetic and epigenetic factors can explain differences among colored mutants. In parallel, Valema developed “BiSePS” (Bisulfite Sequencing processing software), a tool to analyse DNA methylation differences among individuals through Whole Genome Bisulfite Sequencing.