Nuts and Bolts of Genetic Improvement Genetic Model

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Nuts and Bolts of Genetic Improvement Genetic Model Predicting Genetic Levels Increase Commercial Profitability

Nuts and Bolts of Genetic Improvement Genetic Model Predicting Genetic Levels Increase Commercial Profitability Lauren Hyde Jackie Atkins Wade Shafer Fall Focus, Gettysburg, PA Sept. 14 th, 2015

Punnett Square

Punnett Square

Qualitative Traits • Controlled by one or few pairs of genes • Measured on

Qualitative Traits • Controlled by one or few pairs of genes • Measured on a categorical (either-or) scale • Examples – Black or red – Polled or horned – Genetic defects • Genotype determined through DNA testing

Genetic defects?

Genetic defects?

Quantitative Traits • Controlled by many genes • Measured on a continuous scale •

Quantitative Traits • Controlled by many genes • Measured on a continuous scale • Examples – Weaning weight (lb) – Ribeye area (sq in) • Transmittable part of genotype determined through statistical techniques (and DNA testing) – EPD = ½ * EBV

Genetic Model • Phenotype = Genotype + Environment • Phenotype is the observed level

Genetic Model • Phenotype = Genotype + Environment • Phenotype is the observed level of performance • Genotype is the genetic makeup of the animal • Environment is the effect that non-genetic factors have on performance

Genetic Predictions (EPDs) • Separate genetics from environment – Nature vs nurture • Estimated

Genetic Predictions (EPDs) • Separate genetics from environment – Nature vs nurture • Estimated using highly advanced statistical methods – BLUP – System of linear equations – Solve for x and y if 2 x + 3 y = 6 and 4 x + 9 y = 15

Mixed Model Equations

Mixed Model Equations

Heritability • Heritability - the proportion of phenotypic variation for a specific trait in

Heritability • Heritability - the proportion of phenotypic variation for a specific trait in a specific population that is due to transmissible genetic merit • Ranges from 0 to 1 – h 2 CE = 0. 19 – h 2 BW = 0. 38 – h 2 REA = 0. 46

Heritability • The higher the heritability of a trait, the more accurately an individual’s

Heritability • The higher the heritability of a trait, the more accurately an individual’s own performance predicts genetic merit • Even with high heritability we are limited in what we can learn about an animal’s true breeding value from its phenotype

Data • Large amounts of performance data are the solution – Animal’s own performance

Data • Large amounts of performance data are the solution – Animal’s own performance – Progeny performance – Performance of ancestors and other relatives • Progeny performance records are the most influential

Data Collection • Accurate pedigree records • Performance records for as many traits as

Data Collection • Accurate pedigree records • Performance records for as many traits as possible on complete contemporary groups – Performance Advocate

Contemporary Group • Same sex • Close in age (within 90 days) • Raised

Contemporary Group • Same sex • Close in age (within 90 days) • Raised in same management group from birth – Same pasture – Same feed

Contemporary Group • Should include as many cattle as can be compared accurately •

Contemporary Group • Should include as many cattle as can be compared accurately • But only takes two

Contemporary Group Example Animal ID Weaning Weight (lb) 2142 801 2134 783 2135 756

Contemporary Group Example Animal ID Weaning Weight (lb) 2142 801 2134 783 2135 756 2147 729 2139 671

Contemporary Group Example Animal ID Weaning Weight (lb) 2142 801 2134 783 2135 756

Contemporary Group Example Animal ID Weaning Weight (lb) 2142 801 2134 783 2135 756 2147 729 2139 671 • Average WW = 748 lb • 2142’s WW ratio = 107. 1

Contemporary Group Example Animal ID Weaning Weight (lb) 2142 801 2134 783 2135 756

Contemporary Group Example Animal ID Weaning Weight (lb) 2142 801 2134 783 2135 756 2147 729 2139 671

Contemporary Group Example Animal ID Weaning Weight (lb) 2142 801 2134 783 2135 756

Contemporary Group Example Animal ID Weaning Weight (lb) 2142 801 2134 783 2135 756 2147 729 2139 671 • Average WW = 780 lb • 2142’s WW ratio = 102. 7

Contemporary Group Example Animal ID Weaning Weight (lb) 2142 801 2134 783 2135 756

Contemporary Group Example Animal ID Weaning Weight (lb) 2142 801 2134 783 2135 756 2147 729 2139 671

Contemporary Group Example Animal ID Weaning Weight (lb) 2142 801 2134 783 2135 756

Contemporary Group Example Animal ID Weaning Weight (lb) 2142 801 2134 783 2135 756 2147 729 2139 671 • Average WW = 736 lb • 2142’s WW ratio = 111. 8

Contemporary Group Example • What happens when 2142 starts getting used in other herds?

Contemporary Group Example • What happens when 2142 starts getting used in other herds?

Contemporary Group Example • Progeny data will get his EPDs going in the right

Contemporary Group Example • Progeny data will get his EPDs going in the right direction • Faulty data will get washed away • BLUP is very robust

Sire Summary

Sire Summary

Interpretation • 35 R – BW EPD = -3. 0 (. 64) • 3

Interpretation • 35 R – BW EPD = -3. 0 (. 64) • 3 C Full Figures C 288 BLK – BW EPD = -0. 7 (. 96) • Difference – -3. 0 – (-0. 7) = -2. 3 – We would expect 35 R’s progeny to weigh -2. 3 pounds less at birth on average than 3 C Full Figures C 288 BLK’s

Accuracy • Measure of the strength of the relationship between the true breeding value

Accuracy • Measure of the strength of the relationship between the true breeding value and its prediction • Range from 0 to 1 • Affected by the number of progeny records • Higher values associated with less risk and lower values with more