Tools for genetic studies in polyploids

Yanlin Liao

Research output: Thesisinternal PhD, WU

Abstract

This thesis aims to develop and explore methods and tools to use a probabilistic method in studying the inheritance of polyploid crops and for creating linkage maps for polyploids. The pipeline in studying polyploid genetics is: i) genotyping, ii) genotype calling, iii) inheritance examination, and iv) linkage mapping. The layout of this thesis follows the pipeline of this experimental design.  

Currently, a SNP array is used commonly in genotyping polyploids. Compared with a SNP array, bait capture sequencing has higher flexibility and cost-efficiency. In Chapter II, we investigate the usability of bait capture technology in polyploids and compare the genotyping results with those using a SNP array in three model crops: potato, Alstroemeria, and Chrysanthemum.  

After genotyping, automated genotype calling is required before genetic analysis. Until now, many different genotype calling software packages are available, which use distinct algorithms. To evaluate different methods and find the most suitable genotype calling method, simulated data is required. Chapter III presents GenoSim, a simulation tool that can generate simulated sequence reads and SNP array data. Before we perform linkage analysis, understanding the inheritance of the plants can help choose a suitable model for linkage estimation.  

In previous studies, bi-allelic markers were used in understanding the inheritance of polyploids in a quantitative approach. Chapter IV describes methods using haplotypes in inheritance studies of polyploids; this approach could benefit from the high specificity of multi-allelic markers (the haplotypes) and maintain high coverage.  

Mapping is performed under the assumed inheritance of polyploid crops. Currently, discrete dosage estimates are used for linkage mapping in different software packages. However, in obtaining the discrete dosage, a threshold needs to be set and the use of this threshold results in missing data. Chapter V introduces a method that uses probabilistic genotypes rather than discrete genotypes in mapping.  

In Chapter III, haplotypes are used in inheritance analysis. Chapter VI presents mappire, a package to perform genetic mapping in polyploids with haplotypes.  

Building on the work of previous chapters, this thesis is rounded off with a general discussion in Chapter VII, where I discuss how these findings will impact future genetic research in polyploids and how they could be beneficial to crop breeding.  

Original languageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • Wageningen University
Supervisors/Advisors
  • Visser, Richard, Promotor
  • Maliepaard, Chris, Co-promotor
  • Bourke, Peter, Co-promotor
Award date28 Jun 2022
Place of PublicationWageningen
Publisher
Print ISBNs9789464472059
DOIs
Publication statusPublished - 2022

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