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1

 Understand the formula P=G+E

  1. P=phenotype G=Genotype E=environment environmental effects are non-genetic factors that affect performance (phenotype)

2

Understand GxE interactions

Genotype x Environment The "relative" performance of different genotypes "depends" upon the environment Different Breeds/ Strains within a species may be genetically adapted to specific environments Not all interactions are genetically-adapted, they can be environmentally adpated

3

Selection

The process that determines which individuals become parents, how many offspring they produce, and how long they remain in the breeding population.

4

Mating

The process that determines which selected males are bred to which selected females; playing cupid

5

What is performance testing

Systematic measurement of performance (phenotype) in a population

6

How is performance testing used?

Varies among species and breeders in a species, usually Seedstock producers participate

7

What are some commonly measure traits for performance testing?

Beef cattle: pregnancy, feed conversion, yearling weight Dairy cattle: days dry, milk yield, fat and protein in milk Horses: wither height, time to move, winnings Swine: days to 230lbs., litter size, feed conversion, loin eye area Poultry: hatchability, breast weight, #of eggs, shank length Sheep: birth weight, greece fleece weight, clean fleece weight

8

Pedigree data

Info on the genotype or performance of ancestors and/or collateral relatives of an individual. Used to select a sire, dam and genetic predictions

9

Progeny data

info on the genotype or performance of descendants of an individual. Used to predict breeding value

10

What is the difference between selection of simply-inherited and polygenic traits?

Polygenic traits are affected by many genes w/no known single gene having an overriding influence. Simply-inherited traits use one or just a few genes.

11

Law of Segregation

During gamete formation, the alleles for each gene segregate from each other so that each gamete carries only one allele for each gene

12

Law of independent Assortment

Genes for different traits can segregate independently during the formation of gametes

13

Law of Dominance

Some alleles are dominant while others are recessive; an organism w/at least one dominant allele will display the effect of the dominant allele

14

Punnett Square

A device for determining genotypes of possible zygotes obtainable from a mating

15

Complete Dominance

The expression of the heterozygote is identical to the expression of the homozygous dominant genotype

16

Partial Dominance

The expression of the heterozygote is intermediate to the expressions of the homozygous genotypes but more resemebles the expression of the homozygous dominant genotpe

17

Codominance (No Dominance)

The expression of the heterozygote is exactly midway between the expression of the homozygous genotypes

18

Over Dominance

The expression of the heterozygote is outside the range defined by the expressions of the homozygous genotypes but mostly closely resembles the expression of the homozyous dominant genotype

19

Epistasis

An interaction among genes at different loci such that the expression of genes at one locus depends on the alleles present at one or more loci. Masking is when one locus masks the other. Modifying is breeding for a specific trait

20

Compare and contrast sex chromosomes in mammals and birds

Mammals: male determines sex, uses XY and XX Birds: Female determines sec, uses ZW and ZZ

21

Sex-linked inheritance

the pattern of inheritance for genes located on sec chromosomes (X or Y) ex. calico cats and color blindness

22

Sex-limited inheritance

The phenotypic expression is limited to one sex (gender) however, other gender still has alleles for trait ex. antlers and facial hair

23

Sex-Influence inheritance

Modes of gene expression differ between males and females; allele may be dominant in one gender, but recessive in the other gender. ex. horns in sheep and scurs in cattle

24

What is gene or allelic frequency?

Frequency of a particular allele p= frequency of dominant allele q= frequency of recessive allele

25

What is genotypic frequency?

Frequency of a particular one-locus genotype P=Dominant Homo H=Hetero Q=Recessive Homo

26

What are F1 and F2 generations?

F1: first generation of crosses between two unrelated populations F2: Subsequent generation of crosses produced by mating F1 individuals among themselves

27

What are the effects of Outbreeding and Inbreeding on genotypic and gene frequencies?

Outbreeding: mating of same species but different breed Inbreeding: mating of relatives

28

What are the effects of outbreeding and inbreeding on heterozygosity and homozygosity?

Outbreeding: increases the frequency of heterozygosity and decreases the frequency of homozygosity Inbreeding: increases the frequency of homozgyosity and decreases the frequency of heterozygosity

29

What is the Hardy-Weinberg Equilibrium?

A state of constant gene and genotypic frequencies occurring in a population in the absence of forces that change those frequencies.

30

How does H-W E relate to genotyipc and allelic/gene frequencies?

p^2+2pg+q^2=1 P=p^2 H=2pg Q=q^2

31

What are primary and secondary differences between simply-inherited and polygenic traits?

Simply-inherited is a trait affected by one or only a few genes (loci), phenotyes tend to be qualitative or categorical, sometimes categories are rated w/a score, typically affected very little by the environment. Polygenic is a trait affected by many genes, phenotypes tend to be quantitative, typically affected by the environment.

32

How is selection of polygenic traits different than simply inherited traits?

Instead of identifying genotypes a breeder tries to identify breeding values of individuals for traits of importance and to select those w/the best breeding value

33

What is quantitative genetics?

The branch of genetics concerned with influences on measurement of, relationships among, genetic prediction for, and rate of change in traits that are or can be treated as quantitative.

34

Utilization of population mean µ in the Genetic Model for Quantitative Traits ( P=µ+G+E) 

In animal breeding, genotypic values and environmental factors are relative to the population being considered. 

35

G=BV+GCV (Breeding value+ Genetic Combination Value)

The part of an individual's genotypic value that is due to the effects of gene combinations and cannot therefore be transmitted from parent to offspring

36

E=Ep+ET (Permanent Environementa Effects + Temporary Environmental Effects) 

Permanent Effects (calfhod nutrition, Horse training, injuruy), Temporary Effects (forage quality, track conditions, season temps) 

37

Heritability 

What extent differences we observe in animal performace is due to inheritance; easure of the strength of the relationship between performance and the breeding values for a trait in a population

38

Repeatability

A measure of the strength of the relationship between single performance records and producing abilities for a trait in a population

39

What is the importance of contemporary groups?

Correctly formed: increase Heritability and Repeatability

Incorrectly formed: decrease Heritability and Repeatability; distort Performance records and genetic prediction for individual animals; usually occur when some animals get preferential treatment 

40

What are the factors taht affect genetic change?

Directly Proportional: accuracy of selection; selection intensity; genetic variation 

Inversely Proportional: Generation interval 

41

Accuracy of Selection 

The measure of the strength of the relationship between true breeding values and their predictions for a trait under selection

42

Selection of Intensity

Measure of how "choosy" breeders are in deciding which individuals are selected

43

Genetic Variation 

The variability of breeding values within a population for a trait under selection 

44

Generation interval 

The amount of time required to replace one generation w/the next

45

What are the two methods used for Genetic Prediction 

Selection index: used to compare animas using data from genetially SIMILAR groups

BLUP (Best Linear Unbiased Prediction): Used to compare anials using Data from genetically DIVERSE groups 

46

What are Sire Summaries? 

Most visible product of large scale genetic evaluation, Contain three types of data: animal indentification; misc. info including simply-inherited traits; and prediction and accuracy measures 

47

What are nucleus breeding schemes?

A cooperative breeding program in which elite animals are concentrated in a nucleus herd of flock and superior germ plasm is then distributed among cooperating herds or flocks 

48

What are the methods of multiple-trait selection?

Tandem Selection

Independent Culling Levels

Economic Selection Index

49

Tandem Selection

Slection first for one trait, then another

Serial selection: breeder selects for a trait until selection target is met

Selection target: a level of breeding value considered optimal in an absolute or practical sense

Doesnt work well when traits are unfavorably correlated

50

Independent Culling Levels 

Min. standards for traits undergoing multiple-trait selection

Animals failing to meet any one standard are rejected regardless of merit in other traits

Animal breeders tend to use an intuitive/experiential approach rather than mathematical precise approach

51

Economic Selection Index

An index or combination of weighting factors and genetic info

phenotypic data or genetic prediction

Economic Selection indexes are used in multiple-trait selection to predict aggregate breeding value 

52

Understand backcrossing/introgression

A mating system used to incorporate an allele or alleles existing on one population into another population. The mating of a hybrid to a purebred of a parent breed or line

53

Understand Topcrossing/ Grading Up 

Mating system designed to create a purebred population by mating successive generations of non-purebred females to purebred sires. A mating syste designed to convert a population from one breed into another by mating successive generations of females descended from the first breed to sires to the second breed. 

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55

What are the mating systems based on performance?

Random mating; positive assortative mating; negative assortative mating

**look at chart for comparisons**

56

Corrective Matings

A mating system designed to correct progeny faults from one or both parents

57

Comlpementarity

An improvement in the overall performances of offspring resulting from the mating of individuals 

58

When would a producer used Positive Assortative 

To breed top end cows to top bulls 

59

When would a producer use negative assortative 

Use corrective matings to correct problems in certain cows

60

When would a producer used random matings

Use young bulls randomly to breed heifers and middle cows 

61

Understand When and why (why not) linebreeding/linecrossing and crossbreeding is used in performance mating?

Increase Heterozygosity; decrease homozygosity; masking of the expression of deleterious recessiv alleles w/major effects; increases Hybrid Vigor (heterosis); Hybrid Vigor: ertility and survivability traits, Conception rate, litter size, weaning rate; Breed complementarity; get an intermediate phenotype, maternal x paternal (terminal) crosses

62

Whst are maternal breeds and exs? 

Traits from the dam, maternal instinct, angus, herefored 

63

What are paternal breeds and exs?

Traits from the sire, market traits Charolais, Limousin

64

What are terminal crosses?

Combinwes a maternal rotation for producing females w/terminal sires for producing market offspring

65

What is inbreeding?

The mating of relatives, the mating of relatives more closely related than avg. 

66

What are the effects of inbreeding in mating systems?

Increase homozygosity

Greater prepotency

Expression of deleterious recessive aleles

Decreases in performance-inbreeding depression

67

What is inbreeding depression and how is it related to Hybrid Vigor?

A decrease in the performance of inbred offspring, mostly noticeable in traits like fertility and survivability

68

What are the reasons to inbreed?

To increase uiformity and to create an opportunity for hybrid vigor

69

What is purebreeding/straightbreeding?

The mating of purebreds of the samebreed, crossing these breeds result in substantial levels of hyrid vigor

70

What is outbreeding?

The opposite of inbreeding, the mating of unrelated individuals 

71

What are the two types of outbreeding?

Crossbreeding and linecrossing 

72

What are the effects of outbreeding in mating systems?

Increase heterozygosity

Decrease homozygosity

Masking expression deleterious recessive alleles w/major effects

Increases hyrid vigor

73

When and how are inbreeding and outbreeding used in the industry structure?

Crossbreeding is commonly used by commercial producers

Seedstock producers commonly use linecrossing to enhance purebreeding 

74

When is Hyrid Vigor at a max.?

H.V. is maximized in the F1 generation or the first cross of unrelated populations

75

How is H.V. retained and/or diminished?

Hybrid vigor remaining in later generations of hybrids i.e. generations subsequent to the first cross

RHV=F2HV/F1HV

76

What is crossbreeding? 

The mating of sire of one breed to dams of another breed. Crossbreeding systems are mating systems are mating system that uses crossbreeding to maintain a desirable level of hybrid vigor and/or breed complementarity. 

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How are crossbreeding systems evaluated?

Find the system whose upside is expecially beneficial for the situation and whose downside is relatively less harmful 

 

79

Merit of component Breeds 

Breeds in system must be well chosen and must bring favorable attributes to the traits, sometimes can be improved w/crossbreeding 

80

Hybrid Vigor/Heterosis

Probably the most important reason for crossbreeding maximal hybrid vigor is only found in F1 generation 

81

Breed Complementarity

Production of more desirable offspring by crossing breeds that are genetically different from each other but have complementary attributes

Sire x Dam- the classic form

Hybrid Seedstock- crossing genetically diverse breeds

82

Consistency of Performance 

An ideal crossbreeding system should produce a consistent product

Crossbreeding systes vary in their ability to provide consistency

83

Replacement Considerations

Crossbreeding systems can be designed allowing commercial breeders to produce replacement animals from their own hybrid population 

84

Simplicity

Crossbreeding systems should be relativey simple

85

Accuracy of Genetic Prediction 

The higher the accuracy of genetic prediction, the lower the selection risk, and the more predictable the offspring

86

 Rotational Systems 

Spatial Rotations: Purebred Sires-all sires used simultaneously and Crossbred Sires- only difference, breed composition

Rotations in Time: sire breeds are not used simutaneously, but are introduced in sequence

87

Terminal Sire Systems

Maternal-breed females are mated to paternal-breed males to efficiently produce progeny that are especially desirable from a market standpoing 

88

Static Terminal System

replacement females are either purchased or produced from separate purebred populations within the system

89

Rotational/ Terminal System: 

90

Pure Composite System

a mating system limited to matings within a single composite breed

91

Composite/ Terminal System

a crossbreeding system combining maternal composite breed for producing replacement females w/terminal sires for producing market offspring 

92

Artifical Insemination 

Advantages: genetic improvement, control of STDs, accurate breeding records, exonomic, safety

Disadvantages: need trained technician, need to corral and restrain females, costs

93

Embryo Transfer

Advantages: can increase offspring from genetically superior females, obtain offspring from aniamls that cant carry pregnancies to term

Disadvantages: costly, need trained technicians, need to corral and restrain females

94

In Vitro Fertilization

Advantages: utilization of prepubertal and slaughterhouse animals, increase number of pregnancies possible, decrease generatio interval 

Disadvantages: expensive, trained technicians needed

95

Sex Control: 

increase speed of genetic changes, improve accuracy of selection and selection intensity, decrease generation interval 

96

Cloning

Advantages: immediate improvement in avg. genetic merit of a herd or flock, causes uniformity, large increase in accuracy of selection and intensity of selection

Disadvantages: no genetic variation for future improvemennt, environmental effects could be detrimental, excessive inbreeding possible, costly 

97

Same-sex mating 

rate of genetic change would be increased by increasing accuracy of seleciton and selection intensity 

98

How are hormones used in some of the Reproductive Biotechnologies?

Used to sync females so that they can be artificailly inseminated at the same time 

used in embryonic transfer to cause females to over-ovulate

99

What is conversation genetics? 

The branch of genetics dedicated to preservation of germ plasm, maintains genetic diversity

100

Molecular Technologies 

DNA fingerprinting, Marker Assisted Selection, Gene Transfer/ Transgenics/ GMOs

101

DNA fingerprinting 

A laboratory method for graphically characterizing an individual's DNA, creating a unique genetic "fingerprint"

Identificaiton of parentage, measurement of "purebred" status in grading up/topcrossing through backcrossing, prediction of H.V. 

102

Marker Assisted Selection

Selection of specific alleles using genetic markers

103

Gene Transfer/Transgenics/ GMOs

Transplantatio of specific genes from one individual to another using laboratory techniques

Improved production traits, improve animal health

104

Recommendations for commonsense animal breeding 

Be knowledgable: understand the basic concepts of genetics, selection, mating, and biotechnology

Use good info: good decisions are based on good info

take time to think: whats best for the animal?

Be consistent; set goals and stick to them

Keep it simple: complex breeding progrmas are difficult to maintain

Be patient: change doesnt happen overnight; randomness will sometimes lead to setbacks