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

Print Syllabus

Syllabus

HV0195 Designing breeding programmes, 15.0 Credits

Utformning av avelsprogram

Subjects

Animal Science Agricultural Science

Education cycle

Master’s level

Modules

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

Language

English

Prior knowledge

180 credits at first cycle level

7 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.

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.

• If the student fails a test, the examiner may give the student a supplementary assignment, provided this is possible and there is reason to do so.
• If the student has been granted special educational support because of a disability, the examiner has the right to offer the student an adapted test, or provide an alternative assessment.
• If changes are made to this course syllabus, or if the course is closed, SLU shall decide on transitional rules for examination of students admitted under this syllabus but who have not yet passed the course.
• For the examination of a degree project (independent project), the examiner may also allow the student to add supplemental information after the deadline. For more information on this, please refer to the regulations for education at Bachelor's and Master's level.

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:

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