Livestock Breeding and Genomics

Topics for Master Theses

Topics for Master Theses at Qualitas AG together with ETH are shown here.

Description

Methods for analysing livestock data, in particular for the estimation of breeding values: principles of selection index, introduction to BLUP, application of common models used, relationship matrix, methods for the estimation of variance components, basics of breeding programs. The material will be illustrated via exercises and assignments.

Information

Lecturer: Peter von Rohr
Date: Friday 9-12
Room: LFW C 11
Exam:
- Time: 09:15 - 11:15
- Room: LFW C 11

Exercise Platform

The exercise platform can be used to work on the exercises. The platform is available at: https://1-htz.quagzws.com/rstudio.

The username corresponds to the part of your e-mail address before the @-sign. The password is sent to you by a separate e-mail.

Questions

Questions can be asked during the lecture and during the exercise hour or via e-mail:

Peter von Rohr (peter.vonrohr at gmail.com)

Lecture Program

Week	Date	Topic
1	20.09	Introduction to Livestock Breeding and Genomics
2	27.09	Quantitative Genetics/Single Locus
3	04.10	Genetic Evaluation with Different Sources of Information
4	11.10	Genetic Covariance Between Relatives
5	18.10	Best Linear Unbiased Prediction - Univariate Analysis
6	25.10	Best Linear Unbiased Prediction - Multivariate Analysis
7	01.11	Models with Random Environmental Effects
8	08.11	Analysis of Longitudinal Data
9	15.11	Variance Components Estimation
10	22.11	Linkage Disequilibrium
11	29.11	Genomic Selection
12	06.12	Genom-Wide Association Studies
13	13.12	Questions, Test Exam
14	20.12	Exam

Material

Course material (notes and slides) and Exercises with Solutions can be downloaded from this section.

Course Notes

Week	Date	Topic
1	20.09	Introduction to Livestock Breeding and Genomics
2	27.09	Quantitative Genetics
3	04.10	Genetic Evaluation
4	11.10	BLUP
5	18.10	Genetic Covariance
6	25.10	Additional Aspects of BLUP
7	01.11	Multiple Traits
8	08.11
9	15.11	Variance and Inbreeding
10	22.11	Genomic Selection
11	29.11	Review on Selection Index Theory
12	06.12	Variance Components Estimation
13	13.12
14	20.12	Exam

Slides

Week	Date	Topic
1	20.09	Introduction to Livestock Breeding and Genomics
2	27.09	Quantitative Genetics, Part 2
3	04.10	Genetic Evaluation
4	11.10	BLUP
5	18.10	Genetic Covariance
6	25.10	Numerator Relationship Matrix, Inverse Numerator Relationship Matrix
7	01.11
8	08.11	Inbreeding
9	15.11	Variance and Inbreeding
10	22.11	Additional Aspects of BLUP
11	29.11	Multiple Traits
12	06.12	Genomic Selection
13	13.12
14	20.12	Exam

Exercises

Week	Date	Topic
1	20.09
2	27.09	Introduction to Linear Algebra and Livestock Breeding
3	04.10	Matrices and Quantitative Genetics
4	11.10	Single Locus Breeding Values
5	18.10	Own Performance and Repeated Records
6	25.10	Progeny Records and Sire Model
7	01.11	Numerator Relationship Matrix and Animal Model
8	08.11	Decomposition and Inverse Numerator Relationship Matrix
9	15.11	Inbreeding
10	22.11	Variance and Inbreeding
11	29.11	Accuracy and Decomposition of Predicted Breeding Values
12	06.12	Multivariate Analysis
13	13.12	Genomic Selection
14	20.12	Test Exam

Solution

Week	Date	Topic
1	20.09
2	27.09
3	04.10	Introduction to Linear Algebra and Livestock Breeding
4	11.10	Matrices and Quantitative Genetics
5	18.10	Single Locus Breeding Values
6	25.10	Own Performance and Repeated Records
7	01.11	Progeny Records and Sire Model
8	08.11	Numerator Relationship Matrix and Animal Model
9	15.11	Decomposition and Inverse Numerator Relationship Matrix
10	22.11	Inbreeding
11	29.11	Variance and Inbreeding
12	06.12	Accuracy and Decomposition of Predicted Breeding Values
13	13.12	Multivariate Analysis
14	20.12	Genomic Selection, Test Exam

More Material

Week	Date	Topic
1	20.09	Introduction to Linear Algebra, Introduction to R/RStudio, Questionnaire
2	27.09
3	04.10
4	11.10
5	18.10
6	25.10
7	01.11
8	08.11
9	15.11
10	22.11
11	29.11
12	06.12	Bibliography
13	13.12
14	20.12

Latest Changes: 2019-12-13 10:55:57 (peter)