Genetics and Sire Selection

1. Genetics and Sire Selection

4. CONCEPT OF GENETIC MERIT

5. Basic Genetics The phenotype is the actual measurement that is taken on an animal (birth weight, weaning weight, scrotal circumference, etc.) or how it appears (color, horned/polled, etc.). The phenotype is controlled by two factors - genetics and the environment. The environment includes everything non-genetic, such as feed availability, weather conditions, health, etc. Genetics will be covered in more detail.The phenotype is the actual measurement that is taken on an animal (birth weight, weaning weight, scrotal circumference, etc.) or how it appears (color, horned/polled, etc.). The phenotype is controlled by two factors - genetics and the environment. The environment includes everything non-genetic, such as feed availability, weather conditions, health, etc. Genetics will be covered in more detail.

6. DETERMINATION OF GENETIC MERIT

7. GENETIC LIKENESS Additive genetic relationship Inbreeding

8. CAPITALIZING ON GENETIC MERIT

9. Genetic Effects Additive Genetics Non-additive Genetics

10. Additive Genetics These are the genetic effects that get passed from one generation to the next. This is each gene’s influence independent of other genes and the environment.

11. Additive Genetics It is the independent effect of all of the genes that influence a trait added together. Heritability is the proportion of the total variability that a trait has that is attributed to additive genetics.

12. TYPICAL HERITABILITY ESTIMATES - LOW

13. TYPICAL HERITABILITY ESTIMATES - MEDIUM

14. TYPICAL HERITABILITY ESTIMATES - HIGH

15. Selection Additive genetic effects are the basis of selection. Whether natural or artificial the intent is to concentrate superior genes in the next generation.

16. Selection In highly heritable traits this is easily and rapidly accomplished. In lowly heritable traits it takes many generations to make any progress and other factors still play a large role.

17. Selection Selection can occur both within herd/flock and by importing genetics (AI, service sires, replacement females). Goal is to increase the proportion of desirable genes.

18. Non-additive Genetics There are a group of genetic effects that are not independent of other effects This group of genetic effects which influences a trait cannot be simply added together and thus the entire group is referred to as non-additive genetic effects.

19. Non-additive Genetics These include such effects as dominance, genetic and environmental interactions.

20. Non-additive Genetics These genetic effects are in response to how genes influence each other at certain loci (dominance), environmental influences or what genes are located at other loci. Heterosis is an example of non-additive genetic effects.

21. Crossbreeding Non additive genetics are the basis of crossbreeding because it allows us to take advantage of dominance. Crossbreeding creates greater heterozygosity in the offspring.

22. Crossbreeding The dominant trait is often the favored trait and therefore instead of the offspring being the average of the parents it often performs similar to the parent with the favored trait. The term for this effect is heterosis.

23. WHAT IS HETEROSIS The advantage a crossbred has over the average of the breeds represented in the cross Read definition. Benefits from heterosis are realized in reproduction, survival, growth and milking ability. The increase in production when heterosis is maximized is about 21% greater when compared to a straight-bred situation. Production being defined as weaning weight per cow exposed. This increase comes in more cows getting bred, more calves surviving to weaning, and those calves weighing more due to increased growth and greater milk availability.Read definition. Benefits from heterosis are realized in reproduction, survival, growth and milking ability. The increase in production when heterosis is maximized is about 21% greater when compared to a straight-bred situation. Production being defined as weaning weight per cow exposed. This increase comes in more cows getting bred, more calves surviving to weaning, and those calves weighing more due to increased growth and greater milk availability.

24. HETEROSIS Chart showing the effect of heterosis on the 3 major categories of the beef operation. Greatest effect is on reproduction through weaning (which includes survival), growth (which includes milking ability) is moderately affected and there is little influence on carcass traits. For most Kentucky beef producers reproduction has the greatest impact on their profitability and a good crossbreeding program can help maximize that aspect of production. Therefore, you have more calves, which are bigger, to sell.Chart showing the effect of heterosis on the 3 major categories of the beef operation. Greatest effect is on reproduction through weaning (which includes survival), growth (which includes milking ability) is moderately affected and there is little influence on carcass traits. For most Kentucky beef producers reproduction has the greatest impact on their profitability and a good crossbreeding program can help maximize that aspect of production. Therefore, you have more calves, which are bigger, to sell.

25. TYPICAL HIGH HETEROSIS

27. TYPICAL MODERATE HETEROSIS

29. TYPICAL LOW HETEROSIS

31. Selecting breeds that have characteristics that are compatible with the management system. Selecting breeds that complement each other. Breed Complementarity Breed Complimentarity is using breeds to meet specific purposes. Utilize breeds that are more maternal when generating replacement females and emphasize more growth and leanness when selecting a terminal type bull. The following charts show how some breeds are categorized for certain traits. The following charts are based on research from the USDA Meat Animal Research Center in Clay Center, Nebraska. Breed Complimentarity is using breeds to meet specific purposes. Utilize breeds that are more maternal when generating replacement females and emphasize more growth and leanness when selecting a terminal type bull. The following charts show how some breeds are categorized for certain traits. The following charts are based on research from the USDA Meat Animal Research Center in Clay Center, Nebraska.

32. Crossbreeding Systems Maintain high heterosis Utilize breed complementarity Many complicated systems that we will not get into. For more information on systems look in Genetics chapter of KY Beef Book. In general, try to maintain high heterosis. A rule of thumb is to not keep replacement females that have more than 75% of any breed. Use breeds that fit into your environment and management practices. Don't expect high producing animals to perform well in a limited environment. Keep it simple. You are not likely to stick with a complicated system. Choosing two breeds and rotating between them every 4 years may be right for your situation.Many complicated systems that we will not get into. For more information on systems look in Genetics chapter of KY Beef Book. In general, try to maintain high heterosis. A rule of thumb is to not keep replacement females that have more than 75% of any breed. Use breeds that fit into your environment and management practices. Don't expect high producing animals to perform well in a limited environment. Keep it simple. You are not likely to stick with a complicated system. Choosing two breeds and rotating between them every 4 years may be right for your situation.

33. Crossbreeding Calculator Click on image to launch Crossbreeding Calculator in a new window.Click on image to launch Crossbreeding Calculator in a new window.

34. Economics of Heterosis- An Example in Beef 30 head herd 85% Weaned/Cow Exposed 525 lb Wean Wt. $85/cwt

35. Herd Economics of Heterosis

36. Herd Economics of Heterosis

37. Herd Economics of Heterosis

38. Herd Economics of Heterosis

39. Herd Economics of Heterosis

40. Selection and/or Crossbreeding

41. Selection of Breeding Stock Sires Replacement Females Culling

42. Sire Selection Reproductive Soundness Structural Soundness Performance Visual Appraisal There are four major criteria we should look at when selecting a bull: Breeding Soundness - discuss BSE and the necessity to conduct on purchased bulls are all bulls prior to breeding season. Analogy to an insurance policy. Structural soundness - discuss functional soundness, such as good feed and legs and overall structure. Bull must be able to forage, cover large distances and breed cows effectively. Also, structural defects are highly heritable and therefore will pass on to offspring. Performance - to be discussed in more detail.There are four major criteria we should look at when selecting a bull: Breeding Soundness - discuss BSE and the necessity to conduct on purchased bulls are all bulls prior to breeding season. Analogy to an insurance policy. Structural soundness - discuss functional soundness, such as good feed and legs and overall structure. Bull must be able to forage, cover large distances and breed cows effectively. Also, structural defects are highly heritable and therefore will pass on to offspring. Performance - to be discussed in more detail.

43. Visual Appraisal Disposition Structure Feet and Legs Shoulder and Hip Top-line Type

44. Body Capacity Muscling (Beef, Sheep, Swine and Broilers) Udder (Dairy, Swine and Beef?) Other Factors Horns Color Comb Etc.

46. Performance Actual Measurements (P) Contemporary Group Ratios or Deviations Breeding Values (BV) When purchasing a bull you will be given incredible amounts of information on the bulls. Which information is the most beneficial for making genetic improvements in the herd. We will discuss these in detail in next three slides. When purchasing a bull you will be given incredible amounts of information on the bulls. Which information is the most beneficial for making genetic improvements in the herd. We will discuss these in detail in next three slides.

47. Actual Measurements Not very useful when trying to determine how good an animal’s offspring will be because environment has a large influence on actual measurements. Advantageous management often masks poor genetics. Actual Measurements – Actually not a very useful piece on information when trying to determine how good a bulls calves will be. The reason is that the environment has a large influence on actual measurements. Advantageous management often masked poor genetics.Actual Measurements – Actually not a very useful piece on information when trying to determine how good a bulls calves will be. The reason is that the environment has a large influence on actual measurements. Advantageous management often masked poor genetics.

48. Contemporary Group Ratios Calculated by dividing the average of all animals of the same sex raised together, under similar conditions, into each animal’s measurement. Average animal = ratio of 100. A ratio of 114 means the animal was heavier/larger than the average by 14%. Still not a very good predictor of how a animal’s offspring will perform. Half the offspring in the worst herd in the country will ratio over 100. Contemporary Group Ratios – Calculated by dividing the average of all the bulls that are raised together, under similar conditions, into each individual bulls measurement. The average bull would receive a ratio of 100. A ratio of 114 means the bull was heavier/larger than the average by 14%. Still not a very good predictor of how a bull’s calves will perform. Remember half the bulls in the worst herd in the country will ratio over 100. Contemporary Group Ratios – Calculated by dividing the average of all the bulls that are raised together, under similar conditions, into each individual bulls measurement. The average bull would receive a ratio of 100. A ratio of 114 means the bull was heavier/larger than the average by 14%. Still not a very good predictor of how a bull’s calves will perform. Remember half the bulls in the worst herd in the country will ratio over 100.

49. Breeding Values A prediction of the genetics a parent will pass on to their offspring, when compared to other animals. Take into account the actual measurement on the animal, all relatives’ measurements and environment. EPDs – A prediction of the genetics a bull will pass on to his calves, when compared to other bulls within the breed. EPDs take into account the actual measurement on the bull, all ancestral measurements and the environment that the bull was raised in. By doing so, many of the errors associated with selection are eliminated. EPDs – A prediction of the genetics a bull will pass on to his calves, when compared to other bulls within the breed. EPDs take into account the actual measurement on the bull, all ancestral measurements and the environment that the bull was raised in. By doing so, many of the errors associated with selection are eliminated.

50. Breeding Values Not a perfect science, so use as risk management tool. EPDs – A prediction of the genetics a bull will pass on to his calves, when compared to other bulls within the breed. EPDs take into account the actual measurement on the bull, all ancestral measurements and the environment that the bull was raised in. By doing so, many of the errors associated with selection are eliminated. EPDs – A prediction of the genetics a bull will pass on to his calves, when compared to other bulls within the breed. EPDs take into account the actual measurement on the bull, all ancestral measurements and the environment that the bull was raised in. By doing so, many of the errors associated with selection are eliminated.

51. TERMS FOR ESTIMATION OF GENETIC MERIT BV = breeding value EPD = expected progeny difference PTA = predicted transmitting ability (dairy)

53. EPD In this example we have a group of first calf heifers and want to select a bull that will give lighter calves at birth. In comparing the two bulls they are very similar in terms of their physical appearance and their genetics for growth and traits of importance. Which bull will give us lighter calves at birth? If we were to breed these bulls to a comparable set of females, in terms of their genetics and environment, we would expect calves by the bull on the right to weigh 2.9 lbs less at birth than calves by the bull on the left. The two key words are EXPECT and AVERAGE. We would expect the difference to be 2.9 lbs, however, the calculation of EPDs is not an exact science. If we were to do a study at UK with these bulls and bred them to 1000 cows each, the average difference in birth weight may not be 2.9 lbs, it may be 2 lbs or it may be 4 lbs. However, EPDs do a very good job in sorting bulls, so you can be fairly confident that the bull on the right will give you the lighter calves. Look at EPDs as risk management, you will make mistakes when using EPDs to select bulls, but you will make far fewer mistakes than if you were using actual measurements or ratios. Also, remember that we are dealing with averages. The bull on the right will have some calves that weigh more at birth than some of the calves by the bull on the left, however, on average the bull on the right will have lighter calves. Also, when using EPDs it is important to use EPDs alone for that trait, do use them in combination with actual measurements. This is a very hard concept for producers to accept, but is a must. Since the EPD calculations have already included the actual measurement including it again will only increase the risk of making an error in your selection. In this example we have a group of first calf heifers and want to select a bull that will give lighter calves at birth. In comparing the two bulls they are very similar in terms of their physical appearance and their genetics for growth and traits of importance. Which bull will give us lighter calves at birth? If we were to breed these bulls to a comparable set of females, in terms of their genetics and environment, we would expect calves by the bull on the right to weigh 2.9 lbs less at birth than calves by the bull on the left. The two key words are EXPECT and AVERAGE. We would expect the difference to be 2.9 lbs, however, the calculation of EPDs is not an exact science. If we were to do a study at UK with these bulls and bred them to 1000 cows each, the average difference in birth weight may not be 2.9 lbs, it may be 2 lbs or it may be 4 lbs. However, EPDs do a very good job in sorting bulls, so you can be fairly confident that the bull on the right will give you the lighter calves. Look at EPDs as risk management, you will make mistakes when using EPDs to select bulls, but you will make far fewer mistakes than if you were using actual measurements or ratios. Also, remember that we are dealing with averages. The bull on the right will have some calves that weigh more at birth than some of the calves by the bull on the left, however, on average the bull on the right will have lighter calves. Also, when using EPDs it is important to use EPDs alone for that trait, do use them in combination with actual measurements. This is a very hard concept for producers to accept, but is a must. Since the EPD calculations have already included the actual measurement including it again will only increase the risk of making an error in your selection.

54. EXAMPLES OF EPD’S/PTA’S

58. Dairy – Lifetime Net Merit Net Merit (NM$) = Yield $ + Udder $ + Other $ Yield = (MFP $ - FEED $) * No. Lactations * Actual Yield

61. NON-GENETIC INDEXES (PHENOTYPIC INDEXES) Average Earnings Index (other thoroughbred indexes) Production – Type Index (PTI) - Jersey Type – Production Index (TPI) - Holstein

62. Jersey PTI PTI= (8 x PTAP) + (2 x + PTAF) + (2 x FTI) + (2 x PTAPL) – (1 x PTASCS) P=Protein, F=Fat, FTI=Functional Type Index, PL=Productive Life, SCS= Somatic Cell Score

63. HOLSTEIN TPI PTAT : PTA for type TPI= 36 x [w1x PTAP ] + 18 x [w2 x PTAF ] + 15 x [w3 x PTAT] + 10 x [w4 x UDC] + 5 x [w5 x FLC] + 11 x [w6 x PL] -5 x [w7 x SCS/.13] + 1241 UDC=udder composite, FLC=feet & leg composite

64. OTHER GENETIC ISSUES Single gene traits Dominance Recessive traits Inbreeding Molecular avenues

65. Hyperkalemic Periodic Paralysis (HYPP) Muscular disease in horses and humans Causes uncontrolled muscle twitching and weakness; in severe cases can cause sudden collapse and even death Inherited as an autosomal dominant trait

67. Recessive Traits Identifiable only as homozygotes (i.e. both genes in a pair of genes are recessive) Even if lethal, reducing the frequency takes a long time If frequency is .5 in the population to begin with and recessive gene is lethal, it will take about 8 generations to reduce the gene frequency to .1

68. OTHER TRAITS

69. INBREEDING/LINEBREEDING Inbreeding – the mating of related individuals which increases the likelihood that genes at a given site on the chromosomes (locus) are identical by descent; indiscriminant with regard to whether genes are good or bad Linebreeding – repeated matings back to a common ancestor over generations – a mild form of inbreeding

70. Molecular Technology Parentage Marker Assisted Selection Single Gene Traits Horned/Polled Red/Black Genetic Defects

71. Molecular Technology Marker Assisted Selection Multiple Gene Traits Marbling Tenderness Milk Production Reproduction Other Production Traits

72. Uses for Molecular Technology Direct Selection Single Gene Traits

73. Uses for Molecular Technology Direct Selection Single Gene Traits Multiple Gene Traits

75. NBCEC vs. Genetic SolutionsMarbling Score Results Marbling score used was 100 points lower than that used in NBCEC data, e.g., for direct comparison these would be 458, 469 & 470. Differences are directly comparable. Even after adjusting for 100 pt scaling difference we see that the Genetic Solutions cattle had a 40-50 pt lower marbling score. For comparison the range within the select grade (or low choice) is 100. BUT the difference between 0 star & 2 star genotypes is remarkably similar.Marbling score used was 100 points lower than that used in NBCEC data, e.g., for direct comparison these would be 458, 469 & 470. Differences are directly comparable. Even after adjusting for 100 pt scaling difference we see that the Genetic Solutions cattle had a 40-50 pt lower marbling score. For comparison the range within the select grade (or low choice) is 100. BUT the difference between 0 star & 2 star genotypes is remarkably similar.

76. NBCEC vs Genetic Solutions% Choice Results Again remarkably similar 2 vs. 0 star difference even though, on average, some 12% fewer of the Genetic Solutions cattle graded.Again remarkably similar 2 vs. 0 star difference even though, on average, some 12% fewer of the Genetic Solutions cattle graded.

77. Should producers be buying bulls with Genestar Marbling? Not so fast Depends Maybe

78. Example Bull A is a 2 star for marbling and has a Marbling EPD of +1.0 Bull B is a 0 star for marbling and has a Marbling EPD of +2.0 Which bull should you use to increase marbling?

79. Marbling EPDs

80. Interpreting Test Results The most logical and useful way to report test results is to include tests in EPD calculation Direct gene and/or marker tests can be included in National Genetic Evaluation programs