Designing breeding programmes
Information from the course leader
Welcome to “Designing Breeding Programmes” (HV0195) 2024
The course starts 10.00 Monday January 15 in lecture room Y, in the Ulls building at the Ultuna Campus, Uppsala http://www.slu.se/en/about-slu/locations/slu-uppsala/ .
Schedule and homepage
During the course we will use a “virtual course room” in Canvas that you will be able to access at (https://student.slu.se/en/studies/educational-systems/canvas-learning-platform/canvas-login/?). In Canvas you will find the first tasks to be done in the course, such as preparing for the Previous knowledge exercise and questions for the first Ethics lecture. Let me know (susanne.eriksson@slu.se) if you cannot access Canvas, and need to get the information via email.
Registration
You need to register for the course and can self-register. To be able to do the registration you need to have activated your student IT account (see check list below). If the self-registration does not work during the week before the course starts (e.g. because you who have been accepted conditionally (villkorlig antagning) please contact us-husdjur@slu.se.
Other information
It is important that you participate in compulsory parts marked in bold in the time table such as the compulsory course start. In case you cannot participate due to valid reasons, please let me know as soon as possible (susanne.eriksson@slu.se).
Please inform the education administrator (us-husdjur@slu.se) in case you do not intend to take the course.
As a new student at SLU you find a useful check list here: https://student.slu.se/en/studies/new-student/.
It is possible that we will use Zoom at some occasion: https://student.slu.se/en/sw-news/2020/3/new-tool-for-e-meetings-for-slu-students/. In case you would need to access some programs on the student computers via “My desktop” you can find information about it at https://student.slu.se/en/study-support/it-support/support/my-desktop/. To access some of the SLU servers/articles/tools from home you may need to log in via VPN (https://student.slu.se/en/study-support/it-support/support/access-to-databases-requires-vpn/). In case you have problems to use or access the SLU online tools you will need to ask the IT-service for help at the start of the course (https://student.slu.se/en/study-support/it-support/).
If you have further questions regarding the course, please contact:
susanne.eriksson@slu.se (course leader) or us-husdjur@slu.se (education administrator).
We are looking forward to meeting you and hope that you will find the course interesting!
Kind regards, Susanne
Course evaluation
The course evaluation is now closed
HV0195-30019 - Course evaluation report
Once the evaluation is closed, the course coordinator and student representative have 1 month to draft their comments. The comments will be published in the evaluation report.
Additional course evaluations for HV0195
Academic year 2022/2023
Designing breeding programmes (HV0195-30140)
2023-01-16 - 2023-03-21
Academic year 2021/2022
Designing breeding programmes (HV0195-30001)
2022-01-17 - 2022-03-23
Syllabus and other information
Syllabus
HV0195 Designing breeding programmes, 15.0 Credits
Utformning av avelsprogramSubjects
Agricultural Science Animal Science Animal science Agricultural scienceEducation cycle
Master’s levelModules
| Title | Credits | Code |
|---|---|---|
| Discussions | 1.0 | 0102 |
| Exercises | 3.0 | 0103 |
| Project | 3.0 | 0104 |
| Written exam | 8.0 | 0105 |
Advanced study in the main field
Second cycle, has only first-cycle course/s as entry requirementsMaster’s level (A1N)
Grading scale
The grade requirements within the course grading system are set out in specific criteria. These criteria must be available by the course start at the latest.
Language
EnglishPrior knowledge
180 credits at first cycle level7 credits genetics/animal breeding
7,5 credits statistics
English 6
Objectives
The course gives the student advanced knowledge in practical animal breeding and good contact with geneticists.
On completion of the course, the student should be able to:
describe how breeding organisations work and explain why the breeding programmes of today are designed the way they are,
estimate genetic parameters, breeding values and genetic progress,
design breeding programmes for domestic animals of different species, in various environments and production systems,
assess animal breeding programmes with regard to different sustainability aspects and suggest concrete measures to improve these programmes,
critically review scientific literature in animal breeding.
Content
The course is characterised by a strong applicability to breeding programmes used in practise. The course gives an overview of the application of the sustainability concept in animal breeding. Examples of lecture topics are breeding objectives, economic weights and genetic evaluation, genomic selection and genetic diversity.
The students strengthen their knowledge through group discussions of scientific literature linked to the lectures. In a project that is carried out in groups, the students work with an assessment of a realistic breeding program. The project includes an ethical discussion of the breeding program.
The student trains various skills in statistics during the course, to use at examination and in future work. The student trains parameter estimation, genetic evaluation and estimation of genetic progress in computer exercises. Results of the computer exercises are also used in the project.
Apart from in the written and the oral examination, compulsory components occur within e. g. exercises, group assignments, and discussions.
Grading form
The grade requirements within the course grading system are set out in specific criteria. These criteria must be available by the course start at the latest.Formats and requirements for examination
Passed written and oral examination. Passed participation in compulsory course modules.
If a student has failed an examination, the examiner has the right to issue supplementary assignments. This applies if it is possible and there are grounds to do so.
The examiner can provide an adapted assessment to students entitled to study support for students with disabilities following a decision by the university. Examiners may also issue an adapted examination or provide an alternative way for the students to take the exam.
If this syllabus is withdrawn, SLU may introduce transitional provisions for examining students admitted based on this syllabus and who have not yet passed the course.
For the assessment of an independent project (degree project), the examiner may also allow a student to add supplemental information after the deadline for submission. Read more in the Education Planning and Administration Handbook.
Other information
The right to participate in teaching and/or supervision only applies for the course instance the student was admitted to and registered on.
If there are special reasons, students are entitled to participate in components with compulsory attendance when the course is given again. Read more in the Education Planning and Administration Handbook.
Additional information
The course assumes prior knowledge in basic animal breeding and genetics.Responsible department
Department of Animal Breeding and Genetics
Cooperating departments:
Further information
Litterature list
LITERATURE LIST, DESIGNING BREEDING PROGRAMMES HV0195
Some additional reading will be provided to you during the course, mainly optional articles that will be posted in our virtual classroom Canvas, that you will get access to at the start of the course.
BACKGROUND KNOWLEDGE
(for those that need an update this is strongly recommended to read before or early during the course)
Kor Oldenbroek and Liesbeth van der Waaij, 2015. Textbook Animal Breeding and Genetics for BSc students. Centre for Genetic Resources The Netherlands and Animal Breeding and Genomics Centre, 2015. Groen Kennisnet: https://wiki.groenkennisnet.nl/display/TAB/Textbook+Animal+Breeding+and+Genetics
BREEDING GOAL, ECONOMIC WEIGHTS
Groen A.F., Steine, T., Collea, J-J., Pedersen, J., Pribyl, J., Reinsch, N. 1997. Economic values in dairy cattle breeding, with special reference to functional traits. Report of an EAAP-working group. Livestock Production Science 49, 1-21. Canvas
Wolfova, M., Wolf, J. 2013. Strategies for defining traits when calculating economic values for livestock breeding: a review. Animal 7:9, pp 1401–1413. Canvas Canvas
Compendium and statistical methods (Strongly recommended to read early during the course)
Compendium: Genetic evaluation (36 pp) with Appendix. Canvas
Compendium: Selection and genetic change (22 pp), with Appendix. Canvas
Compendium: Statistical methods in animal breeding (35 p). Canvas
Zuur A.F., Ieno, E.N., Elphick, C.S. 2010. A protocol for data exploration to avoid common statistical problems. Methods in Ecology & Evolution 2010, 3–14. Canvas
CROSSBREEDING
Sørensen, M.K., Norberg, E., Pedersen, J. and Christensen, L.G. 2008. Invited Review: Crossbreeding in Dairy Cattle: A Danish Perspective. J. Dairy Sci., 91:4116-4128. Canvas
Clasen, J.B., Kargo, M. Østergaard, S., Fikse, W.F., Rydhmer, L., Strandberg, E. 2021. Genetic consequences of terminal crossbreeding, genomic test, sexed semen, and beef semen in dairy herds. J. Dairy Sci. 104:806-8075. Canvas
Van Vleck, L.D., Pollak, E.J., Branford Oltenacu, E.A. 1987. Genetics for the Animal Sciences. W.H. Freeman and Company, New York. Pp 357-368. Canvas
ETHICS, BEHAVIOR, LONGEVITY
Eriksson, S., Jonas, E., Rydhmer, L., Röcklinsberg, H. 2018. Invited review: Breeding and ethical perspectives on genetically modified cattle. J. Dairy Sci. 101, 1-17. Canvas
Neeteson-van Nieuwenhoven, A.M., Merks, J., Bagnato, A., Liinamo, A.-E. 2006. Sustainable transparent farm animal breeding and reproduction. Livestock Science 103, 282–291. Canvas
Röcklinsberg, H., Gamborg, C., Gjerris, M., Rydhmer, L., Tjärnström, E., Wallenbeck, A. 2016. Understanding Swedish dairy farmers’ view on breeding goals - ethical aspects of longevity. In Olsson et al. Food futures: ethics, science and culture. 13th Congress of the European Society for Agricultural and Food Ethics, Porto, 28 Sept 1 - Oct 2016. Canvas
GENETIC MODIFICATIONS
Jenko, J., Gorjanc, G., Cleveland, M.A., Varshney, R.K., Whitelaw, C.B.A., Woolliams, J.A., Hickey, J.M. 2015. Potential of promotion of alleles by genome editing to improve quantitative traits in livestock breeding programs. Genetics Selection Evolution 47-55. Canvas
GENOMIC SELECTION, MAS
Dekkers, J.C.M. 2004. Commercial application of marker- and gene-assisted selection in livestock: Strategies and lessons. J. Anim. Sci. 82:E313-328. Canvas
García-Ruiz, A., Cole, J.B., VanRaden, P.M., Wiggans, G.R., Ruiz-López, F.J., and Van Tassell, C.P. 2016. Changes in genetic selection differentials and generation intervals in US Holstein dairy cattle as a result of genomic selection PNAS July 12, 2016. 113 (28) E3995-E4004. Canvas
Jonas, E & deKoning, DJ, 2015. Genomic selection needs to be carefully assessed to meet specific requirements in livestock breeding programs. Frontiers in Genetics. Volume 6, Article 49, 1-8. Canvas
Meuwissen, T., Hayes, B. 2016. Genomic selection: A paradigm shift in animal breeding. Animal Frontiers, Vol. 6, No. 1. Canvas
Sonesson, A.K, Ødegård, J. 2016. Mating structures for genomic selection breeding programs in aquaculture. Genetics Selection Evolution 48:46. Canvas
GENOTYPE BY ENVIRONMENT INTERACTIONS
Hammami, H., Boulbaba, R and Gengler, N. 2009. Genotype by environment interaction in dairy cattle. Biotechnol. Agron. Soc. Environ. 13(1), 155-164. Canvas
SUSTAINABLE BREEDING, GENETIC RESOURCES
Djekic, I.V., 2021. Meat supply chain in the perspective of UN SDGs. Theory and practice of meat processing. 2021;6(3):242-247. https://doi.org/10.21323/2414-438X-2021-6-3-242-247 Canvas
EFFAB, 2012. European forum of farm animal breeders. Read about CODE-EFABAR at http://www.responsiblebreeding.eu/. Canvas (link)
FAO, 2010. Breeding strategies for sustainable management of animal genetic resources. FAO Animal production and health guidelines. No. 3. Rome. Pages 94-139; Section D Developing straight-breeding programmes and Section E Developing cross-breeding programmes. Available on http://www.fao.org/docrep/012/i1103e/i1103e.pdf Canvas (link)
See also https://sustainabledevelopment.un.org/?menu=1300.
GenTORE, 2021. Supporting farmers to get the right balance between resilience and efficiency. Resilience + efficiency = Sustainability https://www.youtube.com/watch?v=6a5QEtbLaig (GenTORE Video, NOTE: there are more videos from researchers within GenTORE to be found on youtube if you are interested).
Hansen Axelssson, H. 2013. Breeding for Sustainable Milk Production - From Nucleus Herds to Genomic Data Doctoral Thesis 2013:43, SLU. (Summarizing chapter) Epsilon/Canvas
Jordbruksverket, 2009. A short version the action plan for the long-term sustainable management of Swedish animal genetic resources 2010-2020. Canvas
Meuwissen, T. 2009. Genetic management of small populations: A review. Acta Agriculturae Scand Section A. 59:71-79. Canvas
Olesen, I., Groen, A.F. and Gjerde, B. 2000. Definition of animal breeding goals for sustainable production systems. J. Anim. Sci. 78: 570-582. Canvas
Philipsson J., Rege, J.E.O., Zonabend E. and Okeyo A.M. 2011. Sustainable breeding programmes for tropical farming systems In: Animal Genetics Training Resource, version 3, 2011. Ojango, J.M.,
Malmfors, B. and Okeyo, A.M. (Eds). International Livestock Research Institute, Nairobi, Kenya, and Swedish University of Agricultural Sciences, Uppsala, Sweden. Canvas
Rydhmer, L, Zira, S, Hoffman, R, Röös, E. 2022. Defining better breeding goals with sustainability assessments. Practice abstract. GenTORE. https://mcusercontent.com/115e344f8d49820b7452d8f90/files/a7e554cd-dbef-91d6-c597-dd548c0f49b3/WP6_PA4_v2.pdf. Canvas
Woolliams, J, Berg, P, Mäki-Tanila, A, Meuwissen, T, Fimland, E. 2005. Sustainable management of animal genetic resources. Nordic gene bank farm animals. Norway. ISBN 82-997123-1-9. A number of books will be available to borrow from the course leader.
USE OF REPRODUCTION TECHNOLOGIES
Gordon, IR. 2017. Reproductive Technologies in Farm Animals. 2nd edition. CABI Publishing. EBOOK ISBN 9781786392626. Available on internet. Chapter 1.3-1.3.5, 1.3.9. (Current RTs); 2.1-2.1.5 (AI); 2.3 (intro), 2.3.3-2.3.4 (Semen sexing); 3-3.1.3 (Embryo transfer); 3.3-3.3.1 (Application ET); 4.1 (Intro, not 4.1.1-) (In vitro embryo prod.); 2.4 (DNA Technology, read to get an overview, not all details). Read online: ProQuest Ebook Central - Detail page, you need to be logged in as SLU student (if from home via VPN).
Kashinatan, P., Wei, H., Xiang, T., Molina, J. A., Metzger, J., Broek, D., Kasinathan, D., Faber, D.C., Allan, M.F. 2015. Acceleration of genetic gain in cattle by reduction of generation interval. Scientific Reports 5: 8674. Canvas
AQUACULTURE
(Useful for your project work!)
Carlberg, H., J. Nilsson, E. Brännäs, and A. Alanärä, 2018. An evaluation of 30 years of selective breeding in the Arctic charr (Salvelinus alpinus L.) and its implications for feeding management. Aquaculture 495: 428–434. Canvas
Gjedrem, T., and M. Rye, 2018. Selection response in fish and shellfish: a review. Reviews in Aquaculture 10: 168–179. Canvas
Houston, R. D., Y. H. Jin, T. L. Jenkins, S. L. C. Selly, S. A. M. Martin et al., 2020. Harnessing genomics to fast-track genetic improvement in aquaculture. Nature Reviews Genetics 21:389-409. Canvas
Kause, A., A. Nousiainen, and H. Koskinen, 2022. Improvement in feed efficiency and reduction in nutrient loading from rainbow trout farms: the role of selective breeding. Journal of Animal Science 100: skac214. Canvas
Vandeputte, M., G. Corraze, J. Doerflinger, F. Enez, F. Clota et al., 2022. Realised genetic gains on growth, survival, feed conversion ratio and quality traits after ten generations of multi-trait selection in rainbow trout Oncorhynchus mykiss, fed a standard diet or a “future” fish-free and soy-free diet. Aquaculture Reports 27: 101363. Canvas