Introductory genetics
1
Introduction
2
A brief introduction to AlphaSimR
2.1
Introduction
2.2
Creating founder haplotypes
2.3
Setting simulation parameters
2.3.1
Adding traits to a breeding simulation
3
Recombination
3.1
Introduction
3.2
Create parent generation
3.3
Make a full-sib family
3.4
Haplotypes of the parent generation
3.5
Haplotypes of the offspring generation
3.6
Assigning parental haplotypes to offspring haplotypes
4
Populations
4.1
Introduction
4.2
Create a test population
4.3
Observe gene frequencies
4.4
Observing SNP haplotype frequencies
5
Physical mapping of genomes
5.1
Introduction
6
Understanding additive traits
6.1
Introduction
6.2
Simulating a population to explore additive traits
6.3
Breeding, genetic, and phenotypic value
6.4
Heritability of additive traits
6.5
Individual QTL effects
6.6
Genome wide association of additive traits
6.7
QTL mapping
7
Simulating a tilapia like genome
7.1
Introduction
Published with bookdown
Introductory genetics through tilapia breeding simulations
Chapter 5
Physical mapping of genomes
5.1
Introduction