Genetic Selection and Breeding Programmes

Performance Equation: Performance is the result of Genotype + Environment ( $P = G + E$ ).
Benefits of Genetic Improvement: It is permanent, cumulative, sustainable in the long-term, and applicable to any production system.

Genetic Variation: Differences in genomic sequences within a species or population.
- Natural Sources: Genomic mutations, sexual reproduction, crossing over, independent segregation/assortment, random mating, and random fertilization.
- Artificial Sources: Transgenesis or gene editing.
Heritability ( $h^2$ ): The proportion of phenotypic variance explained by additive genetic variance, ranging from 0 to 1 (0-100%).
- Low ( $<0.1$ ): Fitness and fertility traits.
- Moderate ( $0.1-0.3$ ): Production traits (e.g., milk yield, growth rate).
- High ( $>0.5$ ): Conformation traits (e.g., stature).
Hybrid Vigour (Heterosis): Performance improvement in crossbred animals compared to purebreds.
Breeding Value: The genetic worth of an individual animal.
Genetic Correlation: Relationships between traits where selecting for one affects another (e.g., increasing milk yield may decrease fertility).

Best Linear Unbiased Prediction (BLUP): A statistical method that separates genetic factors from environmental influences by combining pedigree linkages with performance data.
Estimated Breeding Values (EBV): Predictions of genetic merit for specific traits derived from animal performance, pedigree, and progeny data.
Selection Indexes: Efficiently improvement of multiple traits simultaneously by weighting them according to economic value (e.g., $£PLI$ in dairy cattle, Maternal Index, or Terminal Sire Index).
Assisted Reproductive Technologies (ARTs): Includes Artificial Insemination (AI), sexed semen, and embryo transfer.

Mass Selection: Selection based on the individual's phenotype (e.g., coat colour).
Family Selection: Selection based on family or group averages (common in poultry).
Progeny Testing: Evaluation of parents (e.g., dairy bulls or rams) based on the performance of their offspring.
Genomic Selection: Selection based on thousands of DNA markers (SNPs), allowing for accurate predictions early in life and reducing generation intervals.

Definition: Define the production system (Intensive, Semi-intensive, Extensive) and breeding goals.
Information Collection: Gather phenotypes, genotypes, and pedigree/family relationships.
Determination: Establish selection criteria using genetic models and breeding value estimation.
Selection & Mating: Make mating decisions and structure the programme (e.g., crossbreeding).
Dissemination: Spread genetic gain throughout the population.
Evaluation: Monitor genetic response and diversity.

Inbreeding Depression: A reduction in performance known as "genetic load" caused by increased inbreeding.
Performance Reductions (per 1% increase in inbreeding):
- Fertility: $0.2\%$
- Fecundity: $0.3\%$
- Number of offspring weaned: $0.7\%$
- Adult survival: $0.5\%$
- Body weight: $0.3\%$
- Milk yield: $0.4\%$
- Litter weight: $0.9\%$
Management Strategies: Rotate genetics, use unrelated sires, and monitor inbreeding coefficients to balance genetic gain with diversity.