SNP genotyping array

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Table of contents

Introduction
Disentangling diversity patterns due to demography or natural selection in Pinus pinaster transcription factors involved in wood formation
Introduction
Materials and Methods
Population sampling and DNA extraction
Candidate gene selection and sequencing
Sequence processing and polymorphic sites detection
Diversity, molecular differentiation and recombination rate estimates
Extent of linkage disequilibrium
Neutrality tests under the standard neutral model
Simulations of demographic scenarii
Results
Nucleotide diversity
Population differentiation
Recombination and LD
Neutrality testing
Assessment of alternative demographic models
Discussion
Low levels of nucleotide diversity in transcription factors
Power of neutrality tests
Impact of demographic history on diversity patterns in the Atlantic maritime pine population
Detection of selection signals in transcription factors?
Conclusion and perspectives
References
Supplementary Materials
Developing a SNP genotyping array for Pinus pinaster: comparison between in vitro and in silico detected SNPs
Introduction
Methods
Plant material
SNP discovery
SNP selection for array construction
SNP genotyping array
Measuring the error rate using pedigree data
Results
SNP detection and construction of the SNP array
Reproducibility and overall success rate of the SNP assay
SNP success rate according to a priori SNP functionality score
Comparison of allele frequency estimated by sequencing and genotyping
Measuring genotyping error rate with pedigree data
Discussion
Data summary
Conversion rates of in vitro- and in silico-SNPs for Pinus pinaster
Genotyping error rate
Conclusion and perspectives
References
Supplementary Materials
Genetic parameters of growth and wood chemical-properties in Pinus pinaster
Introduction
Material and Methods
Plant material
Data measurement
Statistical models for genetic parameter estimation
Results
Near infrared spectroscopy calibrations
Genetic parameters
Genetic correlations
Discussion
General considerations
Rapid wood-quality assessment techniques
Genetic effects and heritabilities
Perspectives for breeding applications
References
Association mapping for growth and wood chemical-properties in the Pinus pinaster Aquitaine breeding population
Introduction
Materials and Methods
Plant material
Phenotypic data
Genotypic data
Population structure
Statistical models
Multiple-testing corrections
Results
Population structure
Selection of markers for association tests
Statistical tests
Discussion
Population structure and familial relatedness
One-stage versus two-stage association mapping approaches
Power, allele frequency and sample size
Significant associations: which genes, which traits?
Conclusion and perspectives
References
General discussion and perspectives
Principal results obtained in this thesis
The candidate-gene approach in conifers
Power of association studies
Conclusion