Selective breeding and whole organism cloning
Selective breeding
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Selective breeding, also called artificial selection, is choosing which individuals reproduce, so that alleles for desired characteristics increase in frequency.
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It is the oldest of these manipulations — every domesticated plant and animal is a product of it.
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The mechanism is identical to natural selection except in one respect: who does the selecting.
- In natural selection, the environment determines which individuals survive and reproduce.
- In selective breeding, humans determine it.
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Because human preference is consistent and strong compared with most natural pressures, change is usually much faster and more directional.
The process
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The steps are the same whatever the organism:
- Identify the desired characteristic, and confirm it is heritable — selection cannot act on a difference caused only by environment.
- Select parents showing the characteristic most strongly.
- Breed them together.
- Select the offspring showing the characteristic most strongly.
- Repeat over many generations.
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Two refinements matter in practice:
- Progeny testing — judging an individual's breeding value by the performance of its offspring rather than its own appearance. This matters for traits an individual cannot display, such as milk yield in a bull.
- Genomic selection — using DNA markers across the genome to predict breeding value before an animal is mature or has offspring. New Zealand dairy breeding uses this, and its effect is to shorten the generation interval, so the same genetic gain is achieved in less time.
The genetic consequence
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Selecting the same characteristic generation after generation reduces genetic diversity, and this follows necessarily rather than being a side effect:
- Only individuals with the favoured alleles are bred, so alternative alleles are not passed on and are progressively lost.
- Breeding closely related individuals to fix a trait — inbreeding — increases homozygosity.
- Higher homozygosity means harmful recessive alleles are more often paired and therefore expressed, producing inbreeding depression: reduced fertility, slower growth, weaker disease resistance.
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The trade-off is unavoidable. The very process that fixes a desired trait removes the variation that would allow the population to respond to a new challenge — a novel disease, or changed conditions. Recognising this tension is the key analytical point of the page.
Whole organism cloning
- Cloning produces individuals that are genetically identical to an existing organism.
- Unlike selective breeding, cloning does not change allele frequencies through reproduction — it copies an existing genotype exactly, with no recombination and no new combinations.
Cloning plants: tissue culture
- Many plant cells are totipotent — able to develop into any cell type and regenerate a whole plant. This makes plant cloning comparatively straightforward.
- Micropropagation works as follows:
- A small piece of tissue, the explant, is taken from the parent plant.
- It is sterilised to prevent microbial contamination.
- It is placed on a nutrient medium containing sugars, minerals and plant hormones — auxins and cytokinins in the proportions that trigger root and shoot development.
- The cells divide to form a callus, an undifferentiated mass, which is then divided and induced to develop into plantlets.
- Plantlets are transferred to soil.
- Advantages: very large numbers from one parent, all with the desired genotype; production independent of season; disease-free stock can be generated.
Cloning animals: somatic cell nuclear transfer
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Animal cells are not totipotent, so the method is more involved.
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Somatic cell nuclear transfer (SCNT):
- A somatic (body) cell is taken from the animal to be cloned, containing its diploid nucleus.
- An egg cell from a donor is enucleated — its own nucleus removed.
- The somatic nucleus is transferred into the enucleated egg.
- An electrical pulse stimulates the cell to fuse and begin dividing.
- The resulting embryo is implanted into a surrogate mother.
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The offspring is genetically identical to the nucleus donor, not to the egg donor or the surrogate — except for mitochondrial DNA, which comes from the egg. So an animal clone is not quite a complete genetic copy, and saying so is worth a mark.
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Success rates are low, and abnormalities are common, largely because a somatic nucleus must be reprogrammed to behave like an embryonic one.
Biological implications
- Genetic biodiversity falls. Both techniques narrow the genetic base of a population — selective breeding by discarding alternative alleles, cloning by producing no variation at all.
- Survival of populations becomes more precarious. A population of low genetic diversity, and especially a clonal one, responds to a pathogen almost uniformly. If one individual is susceptible, all are, so a single disease can affect the entire population.
- Health of individuals may be affected. Inbreeding depression reduces fertility and disease resistance. Selecting hard for a single production trait can also produce individuals whose physiology is poorly balanced.
- Evolution of populations is redirected. Allele frequencies now track human preference rather than environmental fitness, so traits are fixed that would be disadvantageous in the wild — as with the non-shattering seed heads of cereals, which prevent the plant dispersing its own seed.
Worked Example
Worked Example
A horticultural crop is propagated entirely by tissue culture from a single high-yielding parent plant. It has been grown this way across a large region for fifteen years.
A new fungal pathogen arrives. Within two seasons it has infected essentially the entire regional crop.
Nearby, an older variety maintained by seed from many parent plants shows infection in some individuals but not others.
Explain why the cloned crop was so severely affected, and explain what this shows about the biological implications of cloning.
Answer:
Why the cloned crop was uniformly affected.
Every plant in the regional crop was produced by micropropagation from a single parent. Tissue culture involves mitosis only — there is no meiosis, no recombination and no fertilisation — so every plant is genetically identical to that parent and to every other plant.
This means there is no genetic variation in the population with respect to any trait, including resistance to this pathogen.
Resistance to a pathogen depends on alleles — for example, alleles coding for recognition proteins that detect the fungus and trigger a defensive response. Since the founding parent evidently lacked an effective resistance allele, no plant in the entire crop possesses one, because none could have arisen through recombination and there has been no opportunity for new combinations.
So when the pathogen arrived, every plant was equally susceptible, and infection spread through the entire crop rather than being checked at resistant individuals.
Why the seed-grown variety fared differently.
That variety is propagated sexually from many parent plants, so it retains genetic variation. Meiosis produces new combinations of alleles through independent assortment and crossing over, and fertilisation combines alleles from two parents.
Individuals therefore differ in their alleles, including any affecting resistance. Some carried alleles conferring resistance and survived; others did not and were infected. The result is partial infection rather than total loss.
Note this is not because the variety is inherently better — it is because it is variable. Variation means a pathogen encounters a range of genotypes, so some individuals are likely to resist whatever the pathogen happens to be.
What this shows about the biological implications.
- Genetic biodiversity. Cloning produces a population with essentially zero genetic diversity. This is the most extreme form of the narrowing that selective breeding produces gradually.
- Survival of populations. Uniformity means a population responds to any environmental challenge uniformly. If one individual is susceptible, all are. Genetic diversity acts as insurance against unknown future threats, and cloning removes it entirely.
- Evolution of populations. A clonal population cannot evolve in response to the pathogen. Natural selection requires heritable variation to act on, and there is none. Since the plants do not reproduce sexually, no new combinations can arise, and only mutation could introduce variation — far too slowly to matter across two seasons.
- Ecosystems. A regional crop failure removes a habitat and food source abruptly, and any organism dependent on that crop is affected too.
The underlying trade-off. Cloning is used precisely because it produces uniformity — reliable yield, predictable quality, guaranteed retention of a desirable genotype. Those benefits and this vulnerability are the same property viewed differently. It is not that cloning has an unfortunate side effect; the uniformity that makes it commercially useful is exactly what makes the population fragile.
This means the risk cannot be engineered away while retaining the benefit. It can only be managed — by maintaining diverse varieties alongside clonal ones, keeping genetic material in seed banks, and monitoring for new pathogens.