Artificial selection and selective breeding

Artificial selection compared with natural selection

Domesticated plants and animals are the products of selection applied by people over many generations. Maize was derived from a grass whose ears carry a dozen hard seeds. Cabbage, cauliflower, broccoli and Brussels sprouts were all derived from one species of wild cabbage, each by breeders selecting on a different part of the plant. Darwin opened On the Origin of Species with pigeon breeding as a case of selection his readers already accepted.

The procedure has three steps, repeated. Identify the individuals with the desired heritable characteristic. Breed only from those. Select again from their offspring, over as many generations as required. Artificial and natural selection share a dependence on heritable variation and on differential reproduction; they differ in what determines which individuals reproduce. The variation is already present in the population, and breeding changes the frequency of each allele in the next generation.

The figure also shows the limit on the rate of change. The chosen parents are well ahead of the herd mean, but the following generation gains only part of that difference, because a parent's yield reflects its feeding, housing and other environmental conditions as well as its genotype, and those are not inherited. The proportion of the difference that does carry across is the heritability of the characteristic, and it determines how fast the mean moves.

Artificial selection

The breeding of organisms chosen by people for characteristics they want, so that the alleles for those characteristics become more common in the next generation. Also called selective breeding.

Progeny testing

Judging a breeding animal by measuring the performance of its offspring, used where the characteristic cannot be measured in the animal itself.

Three programmes the specifications name

Disease resistance in wheat and rice. Cereal crops are grown as large stands of genetically similar plants, which allows a fungal pathogen to spread rapidly, and a new race of rust or blast can cause severe losses across a growing region. Resistance alleles are often absent from the cultivated variety, so breeders screen wild relatives and old local varieties, whose populations have been exposed to these pathogens over long periods. Resistance in such material is not guaranteed, and where it is found it is often specific to particular pathogen races. A resistant wild plant is crossed with a high-yielding cultivated one, the offspring are screened by being deliberately infected, and the resistant ones are then backcrossed to the cultivated parent again and again. After several rounds the variety is the commercial one in nearly all respects and carries the resistance gene as well. Pathogen populations are themselves under selection for the ability to overcome the resistance, so new resistant varieties are required at intervals.

Maize, inbred and then hybridised. Maize breeding uses inbreeding as a deliberate step. Breeders self-pollinate a maize plant, then self-pollinate its offspring, and continue. Every generation of selfing halves the proportion of heterozygotes, so after six or seven generations the line is almost completely homozygous and every plant in it is near enough identical. Those inbred lines are feeble, small and low yielding, because the recessive alleles that were hidden in heterozygotes are now exposed in the homozygous state. Then two different inbred lines are crossed. The offspring are heterozygous at all the loci where the two parents differed, and they are uniform and higher yielding than either parent line. This is hybrid vigour. The effect is largest in maize and varies between crops and between pairs of lines. Growers obtain fresh hybrid seed each year rather than saving their own, because the following generation segregates and the uniformity is lost.

Milk yield in dairy cattle. The characteristic to be improved cannot be measured in half of the animals doing the breeding, because bulls do not lactate. So a bull is judged by progeny testing: he is mated to many cows, and the milk yields of his daughters are recorded and compared with the yields of the herds they are in. That estimate of his breeding value is far more useful than anything about the bull himself. A bull that tests well is then used on an enormous scale through artificial insemination, since one bull can father tens of thousands of calves, and semen can be frozen, stored and shipped between countries. Embryo transfer does the matching job on the female side, letting a cow of high breeding value produce many more calves than she could carry.

Milk yield per cow in the United Kingdom has roughly doubled since the middle of the twentieth century, with improved feeding and husbandry contributing alongside selection. A consequence is that a small number of bulls are ancestors of a large fraction of the world's Holstein cattle, which reduces the genetic diversity of the breed.

Reduced genetic diversity and its consequences

Artificial selection acts as a bottleneck. The breeder keeps a small number of parents, so alleles absent from those parents are lost, and drift removes further alleles in the small population that follows. Two consequences follow.

Inbreeding depression is the loss of vigour, fertility and disease resistance that follows repeated mating between close relatives. The mechanism is straightforward genetics. Relatives share alleles, so their offspring are more likely to be homozygous at any locus, and harmful recessive alleles that were hidden in heterozygotes are exposed. Small captive populations show it, pedigree breeds show it, and the inbred maize lines above are a deliberate demonstration of it.

Loss of variation for the future is the slower problem. A crop variety selected to the limit for yield under today's conditions holds a narrow set of alleles, and when the pathogen changes or the climate does, the alleles that would confer tolerance may not be present. Selection cannot act on variation that is absent, and that applies to a breeding programme as it applies to a wild population.

That is the argument for maintaining wild types. The wild relatives of crops, old local varieties, and rare breeds of farm animals hold alleles that current breeding programmes do not use but that may be needed later. Seed banks such as the Millennium Seed Bank and the Svalbard vault store such material, and the wild rice that supplied resistance to grassy stunt virus is a documented case of the reserve being used. Storage costs are low relative to breeding programmes, and alleles lost from all populations cannot be recovered.

Inbreeding depression

The reduction in vigour, fertility and disease resistance that follows repeated breeding between close relatives, caused by harmful recessive alleles becoming homozygous.

Hybrid vigour

The greater size, yield or vigour of the offspring of a cross between two inbred lines, compared with either parent line.

Animal-welfare and ethical considerations

Selective breeding raises questions that biology alone does not settle. A discussion of them should set out the evidence on each side before reaching a judgement.

Dog breeding is one case, because much of the selection is on appearance rather than on health or function. Breeding for a short flat face has left several breeds with airways too small for the head they sit in, so the dogs struggle to breathe and to cool themselves. Breeding for a long back and short legs has left another breed with a high rate of spinal disc disease. Breeding for a sloping back has been associated with hip problems. Closed breed registers, which forbid crossing to any dog outside the breed, restrict the breeding population, and the reported incidence of several inherited conditions is higher in some pedigree breeds than in mixed-breed dogs. The comparison depends on which breeds and which conditions are examined.

Farm animals raise similar questions. Dairy cows selected intensively for yield have higher recorded rates of lameness and mastitis, and broiler chickens selected for growth rate reach slaughter mass in half the time they took fifty years ago, with leg and heart problems that follow from carrying that mass on a skeleton the selection did not improve.

The arguments on the other side belong in the same answer. Selective breeding has contributed substantially to the yield increases behind the last century's food supply. Breeding for disease resistance reduces the use of pesticides and antibiotics. Some breeding is aimed squarely at welfare, such as selecting polled cattle that grow no horns, which removes the need to disbud calves. And breed standards can be rewritten: several kennel clubs have changed the wording of standards that rewarded the most extreme faces, which is evidence that the practice can be steered rather than only abandoned.