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ASCI 431/831 Advanced Animal Breeding

Spring 2018

Instructors

Name: Ron Lewis
Office: A218i Animal Science Building
Email: ron.lewis@unl.edu

Name: Gota Morota
Office: A218f Animal Science Building
Email: morota@unl.edu

Time and Location

Tues./Thurs. 2:00-3:30pm
Animal Science Building, Room A221

Office Hours

The instructors will hold office hours as specified on the course Canvas site.

Prerequisites

ASCI 330 (Animal Breeding), or its equivalent, is the prerequisites for this course. Please do not enroll in ASCI 431/831 until you have successfully completed that prerequisite course.

Materials

There is no textbook required for this course. Due to the nature of the course, handouts prepared by the instructors and guest lectures, and reading assignments from the scientific literature, web-based materials and reports will be used to illustrate principles, demonstrate applications, and focus lectures on practical outcomes of advanced breeding programs.

Learning Objectives

The objective of this course is to provide students with the necessary knowledge, exposure to research results, and explanation of breeding applications to critically evaluate strengths, weaknesses and expected outcomes of present and potential animal breeding strategies. Upon successful completion of this course, students will be able to:

Demonstrate an understanding of the state-of-the-art applications of animal breeding and quantitative genetics (including their benefits and limitations) to the genetic improvement of livestock within the United States and elsewhere in the world.
Demonstrate an ability to locate and interpret research results, and recognize the applications of such research to livestock breeding programs.
Demonstrate an understanding of sources of variation in performance of animals, and the methods used to control or adjust for this variation.
Predict responses to selection for a broad array of selection situations, including the use of molecular markers.
Predict average performance of crossbred populations and mean industry values for breeding systems using crosses of several different breeds.
Plan future breeding program strategies contingent upon the goals that are established.

Syllabus

[PDF]

Schedule

Lectures will be delivered using a whiteboard and presentation slides.

1/9 (T): Overview of course; Review of basic statistics
1/11 (R): Review of basic statistics; Introduction to R [GitHub]
1/16 (T): Introduction to R; Review of allele and genotypic frequencies
1/18 (R): Review of allele and genotypic frequencies in R; Numerator relationship [HTML]
1/23 (T): Numerator relationship
1/25 (R): Class discussion; Numerator relationship in R [P][HTML]
1/30 (T): Class discussion; Analysis of variance (ANOVA) - repeatability
2/1 (R): Computing A and its inverse; Hardy-Weinberg equilibrium test [Slides][HTML][HTML]
2/6 (T): Analysis of variance (ANOVA) - repeatability and heritability
2/8 (R): No class due to WCGALP
2/13 (T): No class due to WCGALP
2/15 (R): No class due to WCGALP
2/20 (T): Estimating repeatability and heritability using ANOVA in R [HTML]
2/22 (R): Class discussion; Predicting response to selection [P]
2/27 (T): Midterm exam in-class
3/1 (R): Predicting response to selection; ICC R package [HTML]
3/6 (T): Pedigree-based BLUP [HTML]
3/8 (R): Genome-based BLUP [HTML]
3/13 (T): Mixed model equations (MME) [HTML]
3/15 (R): SNP-BLUP [HTML]
3/20 (T): Spring break
3/22 (R): Spring break
3/27 (T): Class discussion; MME class example [P]
3/29 (R): MME class example
4/3 (T): Economic selection indices for multiple traits
4/5 (R): Class discussion; Economic selection indices for multiple traits [P]
4/10 (T): Economic selection indices for multiple traits
4/12 (R): Class discussion; Economic selection indices for multiple traits[P]
4/17 (T): Deterministic formulas for genomic prediction [HTML]
4/19 (R): Student presentations
4/24 (T): Guest lecture - Dr. Dan Moser (Angus Genetics Inc.)
4/26 (R): Student presentations
5/3 (R): Final exam - 3:30 to 5:30 p.m.