Project properties
Title Distinguishing disomic and tetrasomic inheritance in peanut
Group Plant Breeding, Laboratory of
Project type thesis
Credits 36-39
Supervisor(s) Chris Maliepaard and Yanlin Liao
Examiner(s) Yanlin Liao and Chris Maliepaard
Contact info chris.maliepaard@wur.nl yanlin.liao@wur.nl
Begin date 2023/07/01
End date 2026/07/01
Description Because peanut is an allotetraploid crop, it is usually considered as a diploid in genetic analysis because it follows fully disomic inheritance, meaning that chromosomes from the same subgenome pair and can recombine, whereas homoeologous chromosomes, across subgenomes, do not pair and recombine. However, studies by Pandey et al. (2017) and Bertioli et al. (2019) have indicated the presence of tetrasomic recombination in peanut. By genotyping peanut as a tetraploid instead of a diploid, it is possible to investigate the potential for tetrasomic inheritance by examining marker segregation and preferential pairing parameters from Identity By Descent (IBD) probabilities. A Multi-parent Advanced Generation Inter-Cross (MAGIC) population has been created from eight homozygous parents, which can be used not only for Quantitative Trait Loci (QTL) analysis but also for studying inheritance patterns. Additionally, with the MAGIC population's structure, it is possible to determine the regions of tetrasomic recombination in each cross. It is possible that a simulation study will be needed to study the behaviour of markers and traits under different modes of inheritance, possibly on the same chromosome.
Used skills This is a topic that does not involve phenotyping in field or greenhouse or lab work, but only development of suitable data analysis scripts (in R, preferably) using the genotyping data from the MAGIC peanut population, and carrying out these analyses, interpretation of the results and finding leads for subsequent research. This project is a collaboration with the Henan Academy of Agricultural Sciences, the data for this project is from this institute. The project is carried out in Wageningen.
In this topic, the student will carry out genetic analyses of molecular markers to find out more about the pairing behaviour of chromosomes and the inheritance patterns in peanut. The student will need to think about methods that allow distinguishing tetrasomic inheritance from disomic inheritance and quantifying the evidence for these inheritance modes. If different patterns are found, the student will visualize these differences according to genome positions and strength of the evidence. If time allows, a QTL analysis in this MAGIC population will be carried out, using information about the inheritance patterns
Requirements knowledge of R and skills to write R scripts are required for this topic. The MSc thesis student will also need a good understanding of statistical methods and quantitative genetics (linkage mapping, QTL analysis, GWAS studies) for this topic. The student must have an interest in further developing R scripting skills and statistical analysis skills. Courses: R for statistics; modern statistics for the life sciences; data science for genetics and plant breeding.