PhD position in apple breeding (Wageningen, Netherlands)

PhD position in apple breeding (Wageningen, Netherlands)
Fecha límite
9 febrero 2012

Información general en:


CF3_12 - Apple breeding in the omics era: genetic mapping, transcriptome sequencing, and isolation of resistance genes to Nectria canker

ADVISORS: Henk J Schouten and Miguel Soriano, Wageningen UR (The Netherlands) - Michela Troggio, FEM, San Michele all'Adige (Italy)


Problem: Apple canker, caused by the fungal pathogen Nectria galligena , can kill branches and trees and therefore may lead to tremendous damage and losses in apple orchards, especially in wet climates. Also it may cause rotting during storage of the apples. The disease can be controlled to some extend by manual pruning and fungicides, but in view of human health, cost reduction and the environment it is better to prevent the disease through natural host resistance. Apple cultivars differ in their susceptibility. Several cultivars, such as Jonathan, Santana, Golden Delicious and Clozeau, have a reasonable level of resistance.

Aim of the project: The aim of the project is genetically mapping the resistance in Golden Delicious and isolation of underlying resistance genes. It will be done by combining the genetic mapping with the analysis of the transcriptome in diseased and healthy tissue of resistant and susceptible progeny. The project will result into molecular markers linked to resistance, and identification of candidate resistance genes. These results will be applied to marker assisted breeding for resistance to Nectria and for isolation of a causal resistance gene for application of cisgenesis.

Starting position:

Three F1 populations. One has Golden Delicious as a parent. These populations had extensively been evaluated for two components of Nectria resistance, i.e. number of infections per tree and expansion of the necrosis after infection;
Golden Delicious has been sequenced;
SNP-arrays for segregating populations of Golden Delicious have been developed;
A large additional segregating populations of Golden Delicious is present for genetic fine-mapping (~3000 seeds)

Approach in the project:

DNA will be isolated from the three F1 populations that have been screened for resistance, starting with the Golden Delicious x Discovery population. The others have second priority;

SNP markers will be scored for these populations, using the SNP-arrays;

By combining the marker information and the resistance data, the resistance components will be mapped genetically (QTL mapping);

The strongest, most promising QTL from Golden Delicious from the first population will be studied in more detail. For that purpose, the large segregating populations will be used additionally. Plants with recombinations in the QTL region will be tested for resistance, and more markers will be added for fine mapping;

Expression of candidate genes will be studied in healthy and diseased tissue for different genotypes. The transcriptome of these genotypes will be sequenced;

In the narrowed down QTL region, candidate genes will be selected, using the whole genome sequence of Golden Delicious, and the expression data;

Candidate genes will be isolated and transferred to the susceptible cultivar ‘Gala’ for evaluation of the effect of these genes on resistance.

Required title: Laurea/MSc in Biology, Genetics, Biotechnology, Agronomy, acceptable for matriculation in the PhD school of the Wageningen University

Languages: English language well-written and fluently spoken


Construction of linkage maps using SNP markers;
QTL mapping;
Disease tests for Nectria resistance;
Transcriptome analysis of resistant and susceptible apple genotypes, using next generation sequencing;
Identification of candidate resistance genes by combining data from transcriptomes and whole genome sequence of apple;
Writing at least 4 articles in peer review journals.
Skills: Enthusiasm for research and strong motivation for pursuing a PhD; team work spirit, but also capacity to work independently; strong commitment to group activity in terms of publications and ideas; willingness to learn and optimize new techniques; good communication skills


Henk J. Schouten and Miguel Soriano (WUR) work on isolation of resistance genes in apple and development of cisgenic apple cultivars.

Michela Troggio (FEM) is expert in the field of structural and comparative genomics in Rosaceous crops, high-throughput sequencing and application of SNP platforms.

Eric van de Weg will be advisor in this project too. He has experience for many years in genetic mapping of traits in apple, such such as resistance to Nectria canker.


Wageningen University, The Netherlands.


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