1. In-Service: Animal Breeding and Genetics Dr. Alan Fahey March 24 th 2011 NCE-MSTL, University of Limerick

2. Contact Information alan.fahey@ucd.ie 01-7166248 Room 238 Vet Sciences Centre, School of Agriculture, Food Science, and Veterinary Medicine, UCD, Belfield, Dublin 4.

3. Topics Covered Variation Dominance Inbreeding and Crossbreeding Progeny and Performance Testing Problem based learning sessions How to use an AI Catalogue

4. Variation

5. Variation LCH 2006 7(a) iii Differences among individuals within a population Tells us about the uniformity of the population Variation exists for performance, genetic, and environmental components

6. Continuous Variation DiscreteVariation Quantitative traits have continuous variation Quantitative traits are controlled by many genes Each gene has a small effect Qualitative traits have discrete variation Qualitative traits are controlled by a single gene Single gene has a large effect

7. Why is Variation Important? Variation is the source of genetic change If there is little genetic variation then it is difficult to find an individuals with better genetic potential

8. Why is Variation Important? Variation is the source of genetic change If there is little genetic variation then it is difficult to find an individuals with better genetic potential

9. Dominance

10. Dominance: Glossary Allele - Alternate forms of genes. Genes occur in pairs in body cells, one gene of a pair may have one effect and another gene of that same pair (allele) may have a different effect on the same trait. Heterozygote – one dominant and one recessive allele Homozygote – both alleles are either dominant or recessive Genotype – combination of genes for a trait

11. Complete Dominance (2000 Q7d) Kk, kk (wrinkled) KK (smooth) The expression of the heterozygote is identical to the expression of the homozygous dominant genotype Ss, ss (non-starchy)SS (starchy) Cross: KKSS x KkSs Alleles:K K S S x K k S s F1 Genotype:KKSS;KKSs;KkSS ;KkSs F1 Phenotype:All smooth and starchy

12. Partial Dominance YY yy The expression of the heterozygote is intermediate to the expression of the homozygous dominant genotype and more closely resembles the homozygous dominant genotype Yellow Green Yy

13. No Dominance rr RR The expression of the heterozygote is exactly midway to the expression of the homozygous genotypes White Roan Rr Red Shorthorn Cattle Cross:Rr x Rr (Roan x Roan) Alleles:R r x R r F1 Genotype:RR; Rr ;Rr ; rr F1 Phenotype:red; roan;roan; white

14. Over Dominance Yy yy The expression of the heterozygote is outside the range defined by the homozygous genotypes and most closely resembles the expression of the homozygous dominant genotypes Yellow Green YY

15. Inbreeding and Crossbreeding

16. Inbreeding v Crossbreeding 2007 HL 7(a) i Recessive – an allele whose phenotype is masked when the dominant allele is present Inbreeding depression - loss in performance due to inbreeding Locus – the location of a gene on a chromosome

17. Related animals have more genes in common Animals of outstanding genetic merit are likely to have relatives that have above average genetic merit Inbreeding

18. www.eurogeneaiservices.com C C

19. Related animals also have more unfavourable genes in common Some recessive genes cause genetic diseases, or adversely affect reproduction, survival or fitness of animals Only cause problems in animals that carry two copies of the gene - homozygous recessive animals Inbreeding

20. Matings between related animals are more likely to produce offspring that are homozygous for these genes than matings between unrelated animals Whenever selection is practiced in a closed population (eg breed, closed herd) over a long period of time, there is an gradual increase in inbreeding This increase is cumulative and inevitable Inbreeding

21. Inbreeding depression – Reverse of hybrid vigour – A decrease in performance of inbreds (fertility, survivability) Line-breeding – Dramatic form of inbreeding – Mating of individuals within a particular line – Designed to maintain a substantial degree of relationship to a highly regarded ancestor without causing high levels of inbreeding – Many breeds were formed by line-breeding e.g. father- daughter or mother-son matings Inbreeding

22. Why inbreed? 1)Increase in uniformity 2)Create opportunity for hybrid vigour (in crosses of inbreds 3)To identify deleterious recessive alleles in population 4)Necessary for breeders of registered purebreds as matings to non-purebred ineligible for registration Inbreeding

23. Inbreeding % in Irish Cattle Charolais (-∆-), Limousin (--), Hereford (--), Angus (--), Simmental (- ▲ -), and Holstein-Friesian (-₀-) breeds across year of birth. Mc Parland et al., 2007

24. Inbreeding Depression Inbreeding Class (%) Milk Yield (kg)Fat Yield (kg)Protein Yield (kg) Somatic Cell Score 0 <F ≤ 6.256.81.90.27.6 6.25 <F ≤ 12.5-47.5-0.9-1.910.8 12.5 <F ≤ 25-160.9-6.0-4.82.4 > 25-172.5-4.8-5.914.6 Mc Parland et al., 2007

25. Crossbreeding Mating of two non-related individuals from different breeds Breed A are homozygous recessive at the B locus (bb) Breed B are homozygous recessive at the B locus (BB) Crossing breed A and B lead to heterozygosity at locus B (Bb) Creates hybrid vigour (heterosis)

26. Hybrid Vigour= extra performance above mid-parent mean

27. Hybrid Vigour Greatest in traits associated with reproduction, survival and overall fitness Opposite of inbreeding depression Crossbreeding creates animals which are heterozygous at more loci Lower proportion of offspring are homozygous for recessive genes that adversely affect reproduction etc. Greater between genetically diverse breeds

28. Progeny Test

29. Performance v Progeny Testing 2007 HL 7(a) ii Performance testing is carried on the individual animal e.g feed intake, growth This is carried out at a central location (one environment) This information is used to determine the genetic merit of the animal and its ancestors

30. Progeny Test A team of sires are mated to females in several herds Detailed phenotype information is recorded on all progeny This provides information on sires progeny across several environments This is used to calculate the genetic merit of the sire, dam, and progeny

31. Sire Progeny Farm 1 Progeny Farm 2 Progeny Farm 3 Progeny Farm n Phenotypes and Pedigree Stored in Database e.g ICBF and Sheep Ireland

32. A.I. Catalogues

36. Teaching resources General Information www.icbf.com http://www.icbf.com/publications/glossaryatol.php (glossary) http://www.icbf.com/publications/glossaryatol.php http://www.icbf.com/publications/2008cattlestat.php (cattle statistics) http://www.icbf.com/publications/2008cattlestat.php http://www.icbf.com/publications/index.php (publications) http://www.icbf.com/publications/index.php www.sheep.ie http://www.sheep.ie/publications/glossary.php (glossary) http://www.sheep.ie/publications/glossary.php http://www.sheep.ie/publications/referencedocs.php (publications) http://www.sheep.ie/publications/referencedocs.php Sheep Breed Societies www.belclaresheep.com www.charollaissheep.com www.pedigreesheep.com www.irishtexel.com www.vendeensheep.ie www.mayosheepproducers.com www.suffolksheep.org

37. Teaching resources Dairy Cattle – www.irishshorthorns.com www.irishshorthorns.com – www.ihfa.com www.ihfa.com – www.ukjerseys.com www.ukjerseys.com – www.brownswissusa.com www.brownswissusa.com Beef Cattle – www.aberdeen-angus.co.uk www.aberdeen-angus.co.uk – www.irishangus.ie www.irishangus.ie – www.ibbcs.com www.ibbcs.com – www.aubrac.ie www.aubrac.ie – www.irishblondedaquitaine.ie www.irishblondedaquitaine.ie – www.charolais.ie www.charolais.ie – www.irishhereford.com www.irishhereford.com – www.irishlimousin.com www.irishlimousin.com – www.irishpiemontesesociety.ie www.irishpiemontesesociety.ie – http://www.irishsimmental.com/ http://www.irishsimmental.com/ Rare Irish Breeds – www.kerrycattle.ie www.kerrycattle.ie – www.irishspecklepark.com www.irishspecklepark.com – www.dextercattle.co.uk www.dextercattle.co.uk Rare Irish Breeds www.kerrycattle.ie www.irishspecklepark.com www.dextercattle.co.uk

38. Breeding Game http://pbskids.org/dragonflytv/games/dog_br eeding_v37.swf http://pbskids.org/dragonflytv/games/dog_br eeding_v37.swf