(a) Explain the genetic mechanism behind inbreeding depression. Why does continuous inbreeding lead to a reduction in fertility…

(a) Genetic mechanism of inbreeding depression and its effect on fertility and life capacity (20 marks)

Inbreeding depression is the decline in the mean performance of inbred animals, in traits such as fertility, survival, growth and production, compared with the non-inbred population. Inbreeding (mating of relatives) raises the inbreeding coefficient F, so heterozygosity falls by the fraction F and homozygosity rises correspondingly.

Genetic mechanism, two explanations:

1. Dominance (partial dominance) hypothesis: populations carry many deleterious recessive alleles at low frequency, hidden in heterozygotes by the dominant normal allele. Inbreeding makes these loci homozygous, exposing the recessive alleles, so harmful effects appear, from mild loss of vigour to sub-lethal and lethal defects (as in genetic defects of cattle such as BLAD and complex vertebral malformation).
2. Overdominance hypothesis: heterozygotes at some loci are superior to both homozygotes, and inbreeding, by reducing heterozygosity, loses this advantage. It is a less general explanation. Epistasis, the break-up of co-adapted gene combinations, adds to the depression.

The decline in the mean for a trait is roughly proportional to F: ΔM = −F × (the sum of dominance effects over the loci, 2Σdpq). So it is larger where dominance is greater and the inbreeding higher, and it does not occur for traits with purely additive genes.

Why fertility and life capacity fall: fitness traits (fertility, conception, embryo and calf survival, birth weight, viability, disease resistance, longevity) show more directional dominance, since natural and artificial selection has made favourable alleles common and dominant, while the unfavourable ones persist as hidden recessives. So these traits show the largest inbreeding depression. In practice:

• lower conception rate, more embryonic and fetal death, smaller litters and lower semen quality;
• more stillbirths, lower birth weight and calf survival, slower growth and later maturity;
• lower immunity, and so more disease and shorter productive life.

Control: avoid mating close relatives, keep inbreeding rate low (ΔF = 1/2N_e) with enough sires, use rotational mating and crossbreeding, and cull carriers and defective individuals.

(b) Hardy-Weinberg law of equilibrium and factors altering it in livestock populations (15 marks)

The Hardy-Weinberg law states that, in a large population with random mating, and without mutation, migration, selection or genetic drift, the gene frequencies and genotype frequencies remain constant from generation to generation. For an autosomal locus with two alleles at frequencies p and q (p + q = 1), the genotype frequencies after one generation of random mating are p² (AA), 2pq (Aa) and q² (aa), so p² + 2pq + q² = 1. For example, if q = 0.2, then aa = 0.04, Aa = 0.32 and AA = 0.64. The equilibrium is reached in a single generation for an autosomal locus (several generations for a sex-linked one), and it can be tested by the chi-square test.

Factors that alter the equilibrium in livestock:

• Selection: culling and preferential use of bulls and cows in breeding change gene frequencies; this is the chief tool of the breeder.
• Mutation: a small, slow change, unless there is repeated mutation.
• Migration (gene flow): introduction of animals or semen (artificial insemination, importation, crossbreeding) alters the frequencies.
• Genetic drift: a small population, a closed herd, or the use of only a few sires produces random change in frequencies (bottleneck and founder effects).
• Non-random mating: inbreeding changes genotype frequencies (more homozygotes) and assortative mating does likewise, but neither alters the gene frequencies.
• Small population size and overlapping generations also disturb the equilibrium.

(c) Use of repeated measurements to distinguish temporary and permanent environmental effects (15 marks)

Many traits in livestock are measured repeatedly on the same animal (milk yield in successive lactations, litter size, fleece weight, calving interval). The record of an animal in one measurement is the sum of its genetic value (additive genes, A), a permanent environmental effect (P_e) and a temporary environmental effect (T_e): P_ij = μ + A_i + P_e,i + T_e,ij.

• Permanent environmental effects are non-genetic effects common to all the records of an animal, such as udder damage, early nutrition and body size, and the environment of its growth, together with non-additive gene effects.
• Temporary environmental effects act on one record only, such as the year, season, feeding, disease or calving in a particular lactation.

How records separate them: the variance between animals is σ²(A) + σ²(Pe) (and non-additive), while the variance within animals (between records of the same animal) is σ²(Te). Analysis of variance of repeated records gives the between-animal component and the within-animal component, and their ratio is the repeatability r = [σ²(A) + σ²(Pe)]/σ²(P), the intraclass correlation of records. Then:

• temporary environment variance fraction = 1 − r;
• permanent environment variance fraction = r − h², when the heritability h² is known from another source (sire or parent-offspring analysis), since r is an upper limit for h².

Uses: r shows how reliably the first record predicts future ones (milk yield about 0.4 to 0.6; litter size only about 0.1 to 0.2); the heritability of the average of n records is n h²/[1 + (n − 1)r], so more records improve selection where r is low; and the estimate is used in predicting most probable producing ability, culling decisions and BLUP repeatability models.