Maintaining purebred pedigrees and how to lessen chance of getting disease?

Many breeds of dogs are known for a high incidence of genetic disorders. German shepherd and Saint Bernard dogs are predisposed to developing a crippling condition called hip dysplasia.

Q: What advice would you give to dog breeders who want to maintain their dogs' purebred pedigrees, but also want their dogs to be as healthy as possible?

Many races of dogs are relatively new with most of them appearing (were bred) in the last few hundred years. These variations are caused by small mutations in certain genes and this is also the problem. To keep a race pure, it has to be interbred to maintain the special set of mutations. And this makes the dogs vulnerable to collect more damaging mutations, especially when the number of animals used for breeding are too small. This is the same problem, that animal conservation projects face in zoos.

A good example for that is the Dalmatian dog. Its characteristic spotted pattern is caused by genes, that can also cause sensineural deafness. To avoid this, deaf dogs are excluded from the breeding and a backcross project was started.

Outbreed your dog every couple of generations with a bloodline that is slightly different or at the very least a similar looking breed.

Multifactorial Disorders

Figure 1 The main symptoms of diabetes, a multifactorial disorder

Although complex disorders often cluster in families, they do not have a clear- cut pattern of inheritance. This makes it difficult to determine a person’s risk of inheriting or passing on these disorders. Complex disorders are also difficult to study and treat because the specific factors that cause most of these disorders have not yet been identified. Researchers continue to look for major contributing genes for many common complex disorders.

Plant Breeding: Steps and Methods of Plant Breeding for Disease Resistance!

Traditional farming can only yield limited food for humans and animals. Better management can increase yield but only to a limited extent.

But plant breeding as a technology increased yield to a very large extent. In India, “Green Revolution” was responsible for our country to not only meet our requirements in food production but also helped us to export it.

Monkambu Sambasivan Swaminathan (M.S. Swaminathan) initi­ated collaboration with Dr. Borlaug which reached the highest point into the “Green Revo­lution” through introduction of Mexican varieties of wheat in India. Green Revolution de­pended mainly on plant breeding techniques for high yielding and disease resistant varieties in wheat, rice, maize, etc.

1. What is Plant Breeding?

Plant breeding is the genetic improvement of the crop in order to create desired plant types that are better suited for cultivation, give better yields and are disease resistant. Conventional plant breeding is in practice from 9,000-11,000 years ago. Most of our major food crops are derived from the domesticated varieties.

But now due to advancements in genetics, molecular biology and tissue culture, plant breeding is being carried out by using molecular genetics tools. Classical plant breeding includes hybridization (crossing) of pure lines, artificial selection to produce plants with desirable characters of higher yield, nutrition and resistance to diseases.

When the breeders wish to incorporate desired characters (traits) into the crop plants, they should increase yield and improve the quality. Increased tolerance to salinity, extreme temperatures, drought, resistance to viruses, fungi, bacteria and increased tolerance to insect pests should also be the desired traits in these crop plants.

Various Steps Required For Developing New Varieties:

The various steps required for developing new varieties are as follows:

(i) Collection of Germplasm:

Germplasm is the sum total of all the alleles of the genes present in a crop and its related species. The germplasm of any crop species consists of the following types of materials:

(i) cultivated improved varieties,

(ii) improved varieties that are no more in cultivation,

(iii) old local or ‘desi’ varieties, (iv) pure lines produced by plant breeders, and (v) wild species related to the crop species.

The entire collection (of plants/seeds) having all the diverse alleles for all genes in a given crop is called germplasm collection. A good germplasm collection is essential for a success­ful breeding programme.

(ii) Evaluation and Selection of Parents:

The germplasm is evaluated to identify plants with desirable combination of characters. Selection of parents is picking up seeds of only those plants for multiplication which have the desired traits. For example, grain length in rice is variable— longer grains, intermediate grains and shorter grains. If we select the seeds of the longest grains and sow them to grow the next generation, the selected population of rice plants will have on average, longer grains than the original population.

(iii) Cross-Hybridization among Selected Parents:

Hybridisation is the most com­mon method of creating genetic variation. Hybridisation is crossing of two or more types of plants for bringing their traits together in the progeny. It brings about useful genetic/ heritable variations of two or more lines together. Line is a group of individuals related to descent and have similar genotype. The individuals or lines used in hybridisation are called parents. Hybridisation takes a lot of time.

As stated earlier a wheat variety HUW 468 took 12 years to develop. Hybridisation may involve a single cross (two plants) or multiple cross (more than two plants). Wheat variety C-306 was developed through multiple cross between C-591 (Reagent 1974 x Ch2-3) and hybrid of P-19 x C-281. Hybridisation may further be:

(ii) intervarietal (= intraspecific) or

(iv) intergeneric. Intervarietal hybridisation is the process of crossing individuals of different lines or varieties of the same species to produce hybrid, e.g., different varieties of wheat are mated. Interspecific hybridisation is the process of crossing individuals of two different species to produce a hybrid. Examples of interspecific hybridisation are the development of rice variety ADT-37 from a cross between Oryza japonica and O. indices and all the sugarcane varieties being cultivated today. In intergeneric hybridisation, the cross is between two different genera.

The procedure of hybridisation involves the following steps.

(a) Selection of Parents with Desired Characters:

All the desirable traits which are required in the new crop variety are first selected.

The selected plants as parents are allowed to undergo self breeding to bring about homozygosis of the desired traits.

The removal of anthers (male parts) from a bisexual flower, before the anthers mature is called emasculation. This prevents self-pollination in these flowers.

The emasculated flowers are immediately covered by paper, plastic or polythene bags. The process is called bagging. It prevents unwanted pollen to come in contact with emasculated flowers. This prevents contamination from foreign pollen grains.

The emasculated and bagged flowers must be tagged by writing every step with date and time. The bagging and pollination is incomplete without tagging.

(f) Artificial Pollination (= Crossing):

Pollen grains are collected from the covered flowers of the ‘male’ parents in clean sterile paper/polythene bags or test tubes. The collected pollen grains can be stored for later use. When the stigma of the emasculated flower of ‘female’ parent matures, the covering bag is removed for a short while. The stigma is dusted with pollen grains by means of a clean brush. Controlled pollination by bringing selected pollen grains in contact with a stigma through human efforts is called artificial pollination.

After pollination, the emasculated flower is covered again till the stigma remains receptive. Bags are discarded when fruits begin to develop. The seeds produced by these flowers of the female parent are the hybrid or Ft Seeds. These seeds are stored for testing. These seeds are sown in the next season. There will be segregation, independent assortment and recombination in the F2 and later generations are obtained from these F, seeds.

(iv) Selection and Testing of Superior Recombinants:

This step comprises selecting, among the progeny of the hybrids, those plants that have the desired character combination. The selection process yields plants that are superior to both of the parents. These plants are self-pollinated for several generations till they come to a state of uniformity (homozygosity) so that the characters will not separate in the progeny. Selection is of two types— self pollinated and cross pollinated.

(a) Selection in Self-pollinated Crops:

The degree of cross pollination is less than 5%. There is repeated self pollination of selected plants till superior homozygous genotypes are obtained. The best one is used as new variety. The self-pollinated progeny of homozy­gous plant constitutes a pure line. All the plants in pure line have identical genotype. The wheat variety HUW 468 is a good example of pure line. Variation appearing later in such a pure line is due to environment.

(b) Selection in Cross-pollinated Crops:

The cross-pollinated crops are heterozy­gous for most of their genes and their population contains plants of several different genotypes. Some of these genotypes are superior but many are inferior. Superior genotype plants are selected and are allowed to crossbreed (these plants are not allowed to self breed) so that heterozygosity is also maintained. Selection can be continued in a few successive genera­tions of cross-pollinated crops.

(v) Testing, Release and Commercialisation of New Cultivars:

The newly selected lines are evaluated for their yield and other agronomic traits of quality, disease resistance, etc. This evaluation is done by growing these in the research field and recording their perfor­mance under ideal fertiliser (application), irrigation, etc. After the evaluation in the research fields, the testing of the materials is done in the farmer’s fields, for at least three growing seasons at different locations in the country, representing all the agro climatic zones. The material is evaluated in comparison to the best available crop cultivar. Thus the seeds of new variety are multiplied and made available to the farmers.

Examples of some improved varieties:

(1) Wheat— Kalyan Sona, Sonalika.

(3) Sugarcane— Saccharum barberi, Sachharum officinarum

(4) Rapeseed mustard Brassica— Pusa swarnim

High Yielding Varieties (HYVs):

India is an agricultural country. Agriculture contributes about 33 per cent of India’s GDP and gives employment to about 62 per cent of the population. After India’s independence, one of the main challenges faced by the country was enough food production for the increasing population. The development of several high yielding varieties of wheat and rice in 1960 increased yields per unit area. This phase is often called the Green Revolution. Some high yielding varieties (HYVs) of Indian hybrid crops are given in the figure 9.15.

In 1960 to 2000 wheat production increased from 11 million tonnes to 75 million tonnes while rice production increased from 35 million tonnes to 89.5 million tonnes. It was due to the development of semi-dwarf varieties of wheat and rice. Nobel Prize winner Norman E. Borlaug of International Centre for Wheat and Maize Improvement in MEXICO developed semi-dwarf wheat.

In 1963, many lines like Sonalika and Kalyan Sona were selected from these that were high yielding and disease resistant. They were introduced all over the wheat growing areas of India. Some more improved varieties of wheat are (i) Lerma Roja 64-A, (ii) Sonora 64-Early, (iii) Safed Lerma, (iv) Chhoti Lerma, (v) Sharbati Sonora.

Semi-dwarf rice varieties were developed from IR-8 at International Rice Research Institute (IRRI), Philippines and Taichung Native-1 from Taiwan. The developed varieties were introduced in 1966. Later on better yielding semi dwarf varieties Jaya and Ratna were developed in India. As stated earlier M.S. Swaminathan contributed much for Green Revolution in India.

Saccharum barberi was originally grown in North India, but had poor sugar content and yield. However, Saccharum officinarum had higher sugar content and thicker stems but did not grow well in North India. These two species were crossed to have sugar cane varieties combining the desirable qualities of high sugar, high yield, thick stems and ability to grow in the sugarcane belt of North India.

Plants producing a large crop of small seeds are called millets. Hybrid bajara, jowar and maize have been developed in India. From hybrid varieties, the development of several high yielding varieties resistant to water stress has been possible.

2. Plant Breeding for Disease Resistance:

Fungal, bacterial, viral and nematode pathogens attack the cultivated crops. Crop losses can be upto 20-30 per cent. In such situation if the crops are made disease resistant, food production is increased and use of fungicides and bactericides would also be reduced. Before breeding, it is important to know the causative organism and the mode of transmission. Some fungal diseases are rusts, e.g., brown rust of wheat, red rot of sugarcane and late blight of potato by bacteria— black rot of crucifers and some viral diseases are tobacco mosaic, turnip mosaic, etc.

Disease is an abnormal unhealthy condition produced in an individual due to defective nutrition, defective heredity, unfavourable environment or infec­tion. Disease causing organism is called pathogen. The individual in which a disease is caused by a patho­gen is called host. The development of disease in a plant depends on three factors: (i) host genotype, (ii) patho­gen genotype and (iii) the environ­ment as shown in the figure 9.16.

Some host genotypes possess the ability to prevent a pathogen strain from producing disease. Such host lines are called resistant, and this ability is called resistance or disease resistance. The term strain has a similar meaning for the pathogen as line has for the host.

Those lines of a host that are not resistant to the pathogen are called susceptible. A successful breeding for disease resistance depends mainly on the following two factors: (i) a good source of resistance, and (ii) a dependable disease test. In disease test, all the plants are grown under conditions in which a susceptible plant is expected to develop disease. Therefore, disease resistant crop plants should be produced to avoid infec­tion.

Methods of Breeding for Disease Resistance:

Breeding is carried out either by conventional breeding techniques described earlier or by mutation breeding. The conventional method of breeding for disease resistance is hybrid­ization and selection. The various sequential steps are: screening germplasm for resistance sources, hybridization of selected parents, selection and evaluation of hybrids and testing and release of new varieties. Some of the released crop varieties bred by hybridization and selection for disease resistance to fungal, bacterial and viral diseases are given below:

Some released crop varieties bred by hybridization and selection, for disease resistance to fungi, bacteria and viral diseases.

Crop Variety Resistance to diseases
Wheat Himgiri Leaf and stripe rust, hill bunt
Brassica Push swarnim White rust
Cauliflower Pusa shubhra, Pusa Snowball K-l Black rot and Curl blight black rot
Cowpea Pusa Komal Bacterial blight
Chilli Pusa Sadabahar Chilly mosaic virus. Tobacco mosaic virus and Leaf curl

Conventional breeding is often constrained by the availability of limited number of disease resistance genes that are present and identified in various crop varieties. Inducing mutations in plants sometimes leads to desirable genes being identified. Plants having these desirable characters can either be multiplied directly or can be used in breeding. Other breeding methods that are used are mutation, selection among somaclonal variants and genetic engi­neering.

Polyploidy in Crop Improvement (Polyploidy Breeding):

An organism which has more than two sets of chromosomes or genomes per cell is called polyploidy and this condition is known as polyploidy. Most important crops having polyploidy condition are wheat, bananas, cotton, potatoes, sugarcane and tobacco. Polyp­loidy occurs in nature due to the failure of chromosomes to separate at the time of anaphase either due to non-disjunction or due to non-formation of spindle. It can be artificially induced by application of colchicine.

Depending upon the number of genomes present in a polyploid, it is known as triploid (3n), tetraploid (4n), pentaploid (5n), hexaploid (6n), etc. Polyploids with odd number of genomes (i.e., triploids, pentaploids) are sexually sterile because the odd chromosomes do not form synapsis. They are, therefore, propagated vegetatively, e.g., Ba­nana, Pineapple. Polyploids also do not cross-breed freely with diploids.

Polyploidy is of two types— autopolyploidy and allopolyploidy.

It is a type of polyploidy in which there is a numerical increase of the same genome, e.g., autotriploid (AAA), autotetraploid (AAAA). Some of the crop and garden plants are autopolyploids, e.g., Maize, Rice, Gram. Autopolyploidy induces gigas effect.

It has developed through hybridisation between two species followed by doubling of chromosomes (e.g., AABB). Allotetraploid is the common type. Allopolyploids function as new species, e.g., Wheat, American Cotton, Nicotiana tabacum. Two recently produced allopolyploids are Raphanobrassica and Triticale. Thus Triticale is a hybrid of wheat (Triticum turgidum) and rye (Secale cereale). Among artificially produced allopolyploidy, Triticale is the first man made crop derived by crossing wheat and rye.

Autoallopolyploidy is a type of allopolyploidy in which one genome is in more than diploid state. Commonly autoallopolyploids are hexaploids (AAAABB), e.g., Helianthus tuberosus.

Mutation is a sudden and heritable change in a character of an organism. Mutation can be due to a change in any one of the following: (a) base sequence of the concerned gene, (b) chromosome structure and chromosome number.

Spontaneous Mutations:

Mutations occurring naturally are called spontaneous muta­tions. They are both germinal and somatic. Useful somatic mutations can be incorporated in crop improvement only in vegetatively propogated plants, e.g., seedless grape, naval orange, Bhaskara banana. Vegetative propagation is also useful in maintaining germinal varia­tion got through sexual reproduction, e.g., apple, mango, potato, sugarcane. Thus sponta­neous mutations are the source of all the genetic variations occurring in all living things today.

Mutagens and Induced Mutations:

Rate of spontaneous mutations is very low. There­fore, rate of mutation is increased by means of certain agents called mutagens. Mutagens are of two types (a) chemical and (b) physical mutagens. Chemical mutagens are some chemicals such as ethylmethane sulphonate (EMS) and sodium azide, that induce mutations.

Physical mutagens are different kinds of radiation like X-rays, gamma-rays, ultraviolet rays, etc., that cause mutations. These mutagens induce changes in DNA and chromosomes, which produce mutations. Mutations produced in response to mutagens are known as induced mutations. They were first produced by Muller (1927) with the help of X-rays on Drosophila and by Stadler in maize. Use of induced mutations in plant breeding to develop improved varieties is called mutation breeding.

In India, over 200 varieties have been developed through mutation breeding.

Selection amongst Somaclonal Variation:

Genetic variation present among plant cells during tissue culture is called somaclonal variation. The term somaclonal variation is also used for the genetic variation present in plants regenerated from a single culture. This variation has been used to develop several useful varieties.

Some of the somaclonal variations are stable and useful, e.g., resistance to diseases and pests, stress tolerance, male sterility, early maturation, better yield, better quality, etc. Thus somaclonal variations have produced wheat tolerant to rust and high temperature, Rice to leaf ripper and Tungro virus, Potato to Phytophthora infestans (late blight of Potato), etc. Other useful variations include high protein content of Potato, short duration Sugarcane and increase shelf life of Tomato.

Genetic Engineering (Recombinant DNA Technology):

This is a process in which the alteration of the genetic makeup of cells is done by deliberate and artificial means. This process involves transfer or replacement of genes to create recombinant DNA.

This is done by cutting DNA molecules at specific sites to get fragments containing desirable and useful genes from one type of cell. Thereafter, these genes can be inserted into a suitable carrier or vector. Now, these recombinant DNA can be put into completely differ­ent cell of a bacterium or plant or animal cell. By this method, they acquire useful characters, such as disease resistance or to make useful enzymes, hormones, vaccines, etc.

This process involves manipulation or engineering of the DNA (genes), therefore, the term ‘genetic engineering’ has been used. The recombinant DNA molecules can be cloned and amplified to an unlimited extent.

3. Plant Breeding for Developing Resistance to Insect Pests:

Insects and pest infestation are two major causes for large destruction of crop plant and crop. Insect resistance in host crop plants is due to morphological, biochemical or physi­ological characters. Hairy leaves of many plants are associated with resistance to insect pests.

For example, resistance to jassids in cotton and cereal leaf beetles in wheat. Solid stems in wheat lead to non-preference by the stem saw fly and smooth leaved and nectar-less cotton varieties does not attract bollworms. Low nitrogen, sugar and high aspartic acid in maize develops resistance to maize stem borers.

Breeding methods for insect pests resistance include the same steps as for any other agronomic character like yield or quality as described above. Sources of resistance genes may be cultivated varieties, germplasm collections of the crop or wild relatives of the crop.

4. Plant Breeding for Improved Food Quality:

It is estimated that more than 840 million people in the world do not have adequate food to meet their daily requirements. Three billion people suffer from protein, vitamins and micronutrient deficiencies or ‘hidden hunger’ because these people cannot afford to buy adequate vegetables, fruits, legumes, fish and meat. Their food does not contain essential micronutrients specially iron, iodine, zinc and vitamin A.

This increases the risk for disease, reduces mental abilities and life span. Breeding of crops with higher levels of vitamins and minerals or higher protein and healthier fats is called biofortification. This is the most practical aspect to improve the health of the people.

Plant breeding is undertaken for improved nutritional quality of the plants. Following are the objectives of improving:

(1) Protein content and quality

(2) Oil content and quality

(4) Micronutrient and mineral content.

Maize hybrids that had twice the amount of the amino acids lysine and tryptophan, compared to existing maize hybrids were developed in 2000. Wheat variety with high protein content Atlas 66 has been used as a donor for improving cultivated wheat. It was possible to develop an iron rich variety containing more than five times as much iron as in usually consumed varieties.

There are eight essential amino acids. When these amino acids are present in the protein of our diet in sufficient amount, they constitute protein quality. Proteins of cereals and millets are deficient in two amino acids, i.e., lysine and tryptophan. Whereas pulses are deficient in methionine and cysteine both are sulphur containing amino acids.

Indian Agricultural Research Institute (IARI), New Delhi, has also developed many vegetable crops that are rich in minerals and vitamins. For example, vitamin A enriched carrots, pumpkin, spinach, vitamin С enriched bitter gourd, Bathua, tomato, mustard, cal­cium and iron enriched spinach and bathua and protein enriched beans (broad lablab, French and garden peas).

Single Cell Protein (SCP):

As we know demand of food is increasing due to increase in human and animal popu­lation, the shift from grain to meat diets does not solve the problem as it takes 3-10 kg of grain to produce 1 kg of meat by animal farming. More than 25 per cent of human population is suffering from hunger and malnutrition. One of the alternate sources of proteins for animal and human nutrition is single cell protein (SCP).

Microorganisms are used for the preparation of fermented foods (e.g., cheese, butter, idlis, etc.). Some microorganisms (e.g., blue green algae- Spirulina and mushrooms- fungi) are being used as human food. Now efforts are being made to produce microbial biomass using low cost substrates. Microbes like Spirulina can be grown on waste water from potato processing plants (containing starch), straw, molases, animal manure and even sewage, to produce food rich in proteins, minerals, fat, carbohydrates and vitamins. This biomass is used as food by humans.

The cells from microorganisms such as bacteria, yeasts, filamentous algae, treated in various ways and used as food, are called single cell protein (SCP). The term SCP does not indicate its actual meaning because the biomass is not only obtained from unicellular microorganisms but also from multicellular microorganisms.

Thus SCP is produced using bacteria, algae, fungi (yeasts, etc). The substrates used for SCP production range from C02 (used by algae) through industry effluents like whey (water of curd), etc. to low-cost organic materials like saw dust and paddy straw. Commercial production of SCP is mostly based on yeasts and some other fungi, e.g., Fusarium graminearum. In most cases, SCP has to be processed to remove the excess of nucleic acids. SCP is rich in high quality protein and is poor in fats. Both high quality of protein and low quantity of fats constitute good human food.

It has been estimated that a 250 kg cow produces 200 g of protein per day. In the same period 250 g of a microorganism like Methylophilus methylotrophus because of its high content of biomass production and growth, can produce about 25 tonnes of protein.

Some Common Microbes as SCP producers:

(i) Cyanobacteria – Spirulina

(ii) Bacteria – Methylophilus methylotrophus

(iii) Yeasts – Candida utilis

(iv) Filamentous fungi – Fusarium gramiearum

(i) It is rich in high quality protein and poor in fat content,

(ii) It reduces the pressure on agricultural production systems for the supply of the required proteins,

(iii) SCP production is based on industrial effluents so it helps to minimise environ­mental pollution,

(iv) SCP can be produced in laboratories throughout the year.

Role of Plant Breeding:

Plant breeding has played an important role in enhancing food production:

(i) Triticale is a man-made alloploid developed from Triticum turgidum and Secale cereale.

(ii) Lysine-rich maize varieties like Shakti, Rattan and Protina have been developed.

(iii) Through mutation breeding, more than 200 varieties of crops have been developed.

(iv) Disease resistance in plants has been introduced through breeding.

(v) All the sugarcane varieties that are cultivated today are interspecific hybrids.

(vi) Plant breeding has also given us improved varieties of crops like Sonora-64 of wheat and Taichung Native -1 of rice.

Let's conclude Most successful crosses have at least 1 high-quality, adapted parent that is preferred by farmers in the TPE. It is often difficult to use unadapted donor parents directly to develop varieties. Pre-breeding may be needed. BC1- or BC2-derived populations may be more efficient in terms of generating high-quality, high-yield lines than two-way, three-way, or double crosses because they leave adapted gene blocks in the elite recurrent parents intact. At least 2000 plants should be screened in the F2 (more, if 3-way or double crosses are used. A standard pedigree description system should be used, to facilitate exchange of information with other breeding programs. Bulk inbreeding in the F2 and F3 generations is used by some breeders to inexpensively produce relatively uniform lines in which to begin pedigree selection. Pedigree selection should focus only on highly heritable, easily-scored traits. The goal is to produce a large sample of adapted lines of appropriate quality to submit to replicated yield testing. Pedigree selection through the F6 or F7 generation may be needed to produce visually uniform lines, but there is little genetic variability among F6 sister lines derived from the same F5 plant. Regularly occurring checks should be included in pedigree nurseries, but their frequency should not exceed 10% of the total number of plots. Selection among families of closely-related lines can be used in advanced pedigree generations. Individual lines in a family can be treated as replicates, and planted in different blocks to overcome the effect of field variability. This design combines the features of an advanced pedigree nursery and an observational yield trial. Extent of inbreeding in pedigree dogs revealed in new study

German shepherd dogs are prone to an abnormal development of the hip joints.

The extent of inbreeding in purebred dogs and how this reduces their genetic variation is revealed in a new study by Imperial College London researchers. Inbreeding puts dogs at risk of birth defects and genetically inherited health problems.

These issues and the researchers' findings are highlighted in an upcoming TV programme entitled "Pedigree dogs exposed," which will air on BBC One on Tuesday 19 August 2008 at 21.00 BST.

Particular dog breeds are believed to be prone to particular health problems and birth defects. For example, Dalmation dogs are predisposed to deafness, many Boxer dogs have problems with heart disease, and disproportionate numbers of German Shepherd dogs have an abnormal developmentof the hip joints known as hip dysplasia.

Inbreeding in pedigree dogs arises because certain dogs, prized for exhibiting the characteristics desirable for that breed, are used to father many litters of puppies. When dogs from these litters come to be mated, some will be paired with dogs having the same father from other litters. Over generations, more and more dogs across a particular pedigree are related to one another and the chances of relatives mating increase.

Recessive genetic variants only have adverse health effects such as deafness when an individual carries two defective copies of the gene. If a popular sire carries just one defective copy, he will not show the problem himself and nor will his puppies. However, the defect may become common in later generations if his grandpuppies and great grandpuppies are mated with each other, rather than introducing new genetic traits by breeding outside their relatives.

Although the problems associated with inbreeding have been known for many years, prior to the new study it had not been systematically measured. For this study, researchers from Imperial used mathematical modelling to analyse how dogs were related to one another within ten different dog breeds including the Boxer and Rough Collie.

They looked at the parentage of eight generations of dogs, using records collected from 1970 to the present day by the UK Kennel Club.

The researchers' analysis showed that, for example, Boxer dogs were so closely related to one another and had such little genetic variation between them that genetically, 20,000 dogs looked like a population of about 70. In the Rough Collie breed, 12,000 dogs looked in genetic terms like a population of about 50.

Such small effective population sizes mean that the chances of a dog breeding with a close relative, resulting in birth defects and genetically inherited health problems, are high. The researchers argue that those involved in breeding dogs should encourage breeding from a larger pool of potential mates in order to create greater genetic variation and lessen dogs' chances of inheriting genetic disorders. They suggest measures such as limiting how many times a popular dog can father litters encouraging mating across national and continental boundaries and relaxing breed rules to permit breeding outside the pedigree.

Professor David Balding, the corresponding author of the research from the Division of Epidemiology, Public Health and Primary Care at Imperial College London, said: "The idea that inbreeding causes health problems in particular dog breeds is not a new one, but we believe ours is the first scientific study to explore this issue and analyse the extent of inbreeding in a systematic way, across many breeds. We hope that following our work, dog breeders will make it a high priority to increase the genetic diversity within different breeds. Otherwise, we will see growing numbers of dogs born with serious genetically inherited health problems."

The researchers carried out their analysis as part of an effort to explore how understanding disease in dogs can help inform research into human disease. The research was funded by the Biotechnology and Biological Sciences Research Council.

Further information about the research is provided in the study, which is published in the journal Genetics: "Population structure and inbreeding from pedigree analysis of purebred dogs," Genetics, 179(1): 593–601, 2008. doi:10.1534/genetics.107.084954 Calboli FC , Sampson J, Fretwell N, Balding DJ

Dog DNA tests alone not enough for healthy pedigree, experts say

Breeding dogs on the basis of a single genetic test carries risks and may not improve the health of pedigree lines, experts warn.

Only a combined approach that makes use of DNA analysis, health screening schemes and pedigree information will significantly reduce the frequency of inherited diseases.

This approach will also improve genetic diversity, which helps to counteract the risk of disorders, researchers say.

Scientists at the University of Edinburgh's Roslin Institute made the recommendations having reviewed the various approaches that are being taken to minimise potential defects in pedigree animals.

Pedigree dog breeds are created for desirable physical and behavioural characteristics, which often stem from breeding between closed familial lines over years and - in some cases - centuries.

This approach means that inherited diseases can become more common in pedigree populations. Around half of all King Charles Cavalier Spaniels, for instance, are affected by an inherited heart murmur that can be life-threatening.

Health screening dogs before selecting animals to breed from has already helped to reduce the prevalence of some diseases, such as floating knee-cap in the Dutch Kooiker breed.

DNA tests are now available to help identify dogs carrying gene mutations that are known to cause some severe illnesses. It is hoped that this technology will help to eliminate disease-causing genes from pedigree lines.

But ruling out breeding dogs solely on the basis of a single failed DNA test result will reduce the gene pool of pedigree lines and make inbreeding more common, researchers say. It could also inadvertently increase the prevalence of other genetic diseases which have not been tested for.

The researchers recommend limiting the use of individual stud dogs to promote more diversity in pedigree lines.

They also recommend cross-breeding to introduce even greater genetic diversity. Breeding the offspring that result from cross-breeding with the original pedigree for ten generations can produce animals that share 99.9 per cent of their genetic material with purebred animals, but that lack the gene faults that cause disease.

This approach has been successful in generating Dalmatians lacking a genetic defect that causes kidney stones, which is common in the breed.

Dr Lindsay Farrell, of The Roslin Institute, said: "Although carrying a specific genetic variant may raise the likelihood that an animal will suffer from the associated disease, it is not guaranteed. When making breeding decisions, genetic testing needs to be considered alongside health screening and family history. That will help to keep as much genetic diversity as possible in our pedigree dogs and, at the same time, reduce the prevalence of inherited diseases."

Professor Kim Summers, of The Roslin Institute, said: "Breeders are keen to embrace DNA testing to improve the health of their breed. We need to make sure that these powerful technologies are used to best advantage."

The article is published in the journal Canine Genetics and Epidemiology.


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Downs LM, Hitti R, Pregnolato S, Mellersh CS. Genetic screening for PRA‐associated mutations in multiple dog breeds shows that PRA is heterogeneous within and between breeds. Vet Ophthalmol. 201417(2):126–30.

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Safra N, Schaible RH, Bannasch DL. Linkage analysis with an interbreed backcross maps Dalmatian hyperuricosuria to CFA03. Mamm Genome. 200617(4):340–5.

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Genetic Effects of Inbreeding

When two closely related organisms mate, their offspring have a higher level of homozygosity: in other words, an increased chance that the offspring will receive identical alleles from their mother and father. In contrast, heterozygosity occurs when the offspring receives different alleles. Dominant traits are expressed when only one copy of an allele is present, while recessive traits require two copies of an allele to be expressed.

Homozygosity increases with subsequent generations, so recessive traits that might otherwise be masked may start appearing as a result of repeated inbreeding. One negative consequence of inbreeding is that it makes the expression of undesired recessive traits more likely. However, the risk of manifesting a genetic disease, for example, isn't very high unless inbreeding continues for multiple generations.

The other negative effect of inbreeding is the reduction genetic diversity. Diversity helps organisms survive changes in the environment and adapt over time. Inbred organisms may suffer from what is called reduced biological fitness.

Scientists have also identified potential positive consequences of inbreeding. Selective breeding of animals has led to new breeds of domestic animals, genetically suited to specific tasks. It can be used to preserve certain traits that might be lost from out-crossing. The positive consequences of inbreeding are less well studied in humans, but in a study of Icelandic couples, scientists found that marriages between third cousins resulted in a greater number of children, on average than those between completely unrelated couples.

Playing COI

Breeding dogs is a numbers game. Even though math problems are the last thing on your mind, what you are doing when you breed is calculating the best odds for getting a desired result. But a little applied mathematics, in the form of a coefficient of inbreeding (COI) can be helpful and even enlightening. Now that technology allows even the mathematically challenged to put them to use, COIs are a tool that should be applied by every breeder.

Research in the fields of genetics, immunology, and veterinary medicine, is turning up more and more information indicating that high levels of inbreeding can have deleterious effects on health. Inbreeding depression, a complex of behavioral and physical reproductive problems, has long been recognized. Inbreeding can increase the frequency of a disease in a population, sometimes quite rapidly. Inbreeding leads to increased incidence of immune-mediated disease and cancer.

All pure breeds of domestic animals are inbred. (Keep in mind that to a scientist “inbreeding” means the breeding of related animals, which would include what we call “linebreeding.”) But how much is too much? Without it, the breeds could never have been developed and would not breed true to type. However, almost all breeds of purebred dog already have well-established type. There is no mistaking a Chihuahua for a St. Bernard. Or even a Greyhound from a Whippet. Given this, breeders would be well advised to retain as much genetic diversity as possible within the existing breed population in order to avoid or reduce such unwanted health problems as those mentioned above. Along with screening and maintaining detailed health records, another tool available to you is the COI. Track COIs on your breeding stock. Calculate them on proposed matings, with an eye to keeping the numbers low if they already are or lowering them where possible.

So, how is this done? Via a formula called Wright’s Coefficient of Inbreeding. It appears directly beneath the title of this article. Before you drop this publication in a math-phobic panic attack, be advised that the only practical way to use it is with a computer. For those who enjoy math or want more detailed background, there is an excellent discussion of applying the formula hands-on in Malcolm Willis’ Genetics of the Dog, pages 320-326. For the rest of you, there are other options.

The easiest way to incorporate COIs into your strategy is to purchase a pedigree database program that will calculate them. Select pedigree software than offers COI calculation as a feature. You will also need a comprehensive pedigree database, including as many of the ancestors of present-day dogs as possible. Some vendors can provide starter databases for various breeds.

Now that we’ve soothed the math anxiety, what exactly is a COI? It is the probability that a homozygous gene pair will be identical by descent from both sides of a pedigree. In the formula, FX is your dog’s COI, FA is that of the ancestor common to both sides of the pedigree. n 1 and n 2 are the numbers of generations on each side between your dog and that ancestor. In other words, if your dog Flux is a double-grandson of FAbulous the calculation tells you how likely it is you can get exactly the same gene passed down to Flux through each of his parents. (In case you are wondering, the probability is 12.5%.) If FAbulous happened to be a Collie Eye Anomaly carrier, Flux would have a 12.5%, or a one in eight chance, of having CEA thanks to FAbulous. Total actual risk would be dependent on whether there were any other carrier or affected individuals in the remainder of the pedigree, but whatever that might be, it is evident that FAbulous provided a significant part of it.

Multiply this times a dog’s 20 thousand genes and it is apparent how quickly you can concentrate some genes—both good and bad—while others drift out of your kennel’s gene puddle. Multiply that by all the people breeding a particular kind of dog and it can have remarkable effects on the breed’s gene pool, especially if large numbers of them are making similar mating selections via the use of popular sires or heavy linebreeding on the product of successful kennels.

COIs can be calculated on any number of generations, the simple two-generation example of Flux and FAbulous was useful to make a point (and keep the math simple) but few purebred dogs have only one common ancestor on both sides of the pedigree and the more generations that can be included in the calculation the more common ancestors will be found and the more accurate the COI will be. The typical three to five generation pedigrees in common use are almost always insufficient. In my breed, the Australian Shepherd, five generations may appear to be loosely linebred or even outcrossed, but pedigrees extended to 10 generations will prove this is often not the case.

But how far should you go? How many generations to use will vary from breed to breed, depending on how many founders a breed had, how populous the breed is, whether there have been genetic bottlenecks, whether “new blood” has been introduced, and how long the breed has been in existence.

Some breeds descend from a very few individuals who are its genetic founders. Samoyeds, for example, go back to about 20 dogs. Tracing everyone back to the founders in such a situation will result in COIs that may vary only by tiny fractions of a percent. Therefore selecting some intermediate number of generations for the calculation is the best option, unless the breed is very recent in origin and only a handful of generations away from those few founders.

For breeds with large populations, sufficient generations should be calculated that the results will have leveled out, so only tiny numerical differences will be achieved by pushing the calculation back a generation further. For example, if a one-generation COI is calculated on good old Flux, the COI would be 0%. You are considering only his sire and dam who obviously aren’t going to be the same dog. Extending it far enough to include FAbulous (two generations) produced the 12.5% we saw earlier. What if the sire’s dam was one of FAbulous’s daughters? Going into the third generation would tell us the COI was 18.75%. If the dam’s dam was out of FAbulous’s full brother (linebreeding on the cross that produced FAbulous.), we go back to the 4 th generation to include FAbulous’s parents behind his brother the COI becomes 23.4%.

With each additional generation the COI will tend to climb but at some point the increase from one generation to the next will be negligible. COIs should be calculated over sufficient generations so that most current dogs will be at this point.

If breed population is small, preserving its remaining genetic diversity is vital. Calculate COI’s back far enough to reach founders and then, working together, breeders can use them to equalizing representation of those founders in the over-all breed population. For example, if a breed had ten founders but most present individuals descended only from three of them, much of the genetic potential of the breed’s gene pool is at risk of being lost as genes from the less-represented founders fail to get passed down by their fewer descendents. You can preserve under-represented genes by equalizing founder representation by giving breeding preference to individuals that do not descend from the most-represented founders and in avoiding crossing their descendents to each other. Since low-population breeds are at greater risk from genetic disease, due to “no place to go,” maximizing genetic potential in this manner may be the line between extinction and survival. In fact, it is the very technique used by zoos and others who are trying to preserve endangered species in captivity.

Some breeds have suffered genetic bottlenecks. By the end of World War II, many European breeds, including the English Mastiff and French Poodle, were reduced to a handful of survivors. Today these breeds trace their pedigrees back to those dogs, who are therefore effective founders. Even though known pedigree exists behind them, there is little point in extending a COI calculation beyond them. The only reason would be to determine how inbred those effective founders were themselves and what their inter-relationships might have been.

Sometimes a breed’s gene pool may receive infusions of new genetic material. Some European registries allow registration of descendants of unpapered dogs brought in from the country of breed origin, such as a desert-bred Saluki from Arabia. Occasionally, even such conservative registries as the AKC will, at a parent club’s request, open a registry to new undocumented individuals. This has happened on several occasions since the 1980s when a few Basenjis were imported from Africa. Obviously, such “new blood” could have significant effects on the average COIs in a kennel or even throughout the breed, depending on how many dogs are added and how often. How much and with whom they are used in breeding will determine their contribution of new genes..

In calculating Australian Shepherd COIs, I use 10 generations because Aussie pedigrees are rarely complete to ten generations due to the breed’s recent origin. By running 10 generations, I get pretty much all there is to get for my breed.

Once you have a PC, software that does COIs, a good breed database, and sufficient knowledge of your breed’s history to decide how many generations to use in your calculations, it’s time to put it all to work.

First, run COIs on all your own dogs. Since few dogs will have such diverse pedigrees that only one common ancestor will be found, the COI will be a reflection of all the ancestors common to both sides of the pedigree. In order to have a handle on what the numbers you will get mean, in terms of level of inbreeding, it is helpful to keep in mind what various percentages would be equivalent to, if there were only one common ancestor or pair of ancestors in the pedigree:

Think back to our pal Flux and his 23.4% COI. He is very nearly the equivalent of a parent/offspring mating. If you bred him to his sister, given their already high level of inbreeding, the pups’ COI would be 44.4%. Anybody glancing at Flux’s pedigree would probably consider him inbred, and certainly heavily linebred. But it is possible to achieve high COIs without this kind of close breeding. Linebreeding on dongs several generations back can result in elevated numbers if the dogs appear frequently enough on both sides of the pedigree. While this inbred cross of FAbulous’s grandpups might serve the breeder’s short-term goals, it significantly increases the risk of turning up something unpleasant. And so would a linebreeding with a similar COI.

What’s a breeder to do? We are breeding dogs not numbers and many factors other than COIs need to be considered when planning a mating. Even so, whenever possible you should try to achieve litter COIs that are at or below the average COI of the two parents. Thus, if the sire had a COI of 20% and the dam was 10%, you would want the pups’ COI to be 15% or lower. If a kennel or line’s average COIs have crept dangerously high, serious consideration should be given to avoiding further crosses to dogs descending from the most frequently seen names in the pedigrees and, as much as possible, to finding mates which are significant outcrosses.

The nice thing about COIs is that they can’t be a secret. If you have a dog’s pedigree, you can calculate the COI. In the privacy of your own computer station, you can figure out the COIs of all the prominent dogs in your breed. You can play with hypothetical matings between any two dogs you choose and see what the pups’ COI would be.

For a real-life example, my dog Tank was the result of a father/daughter mating (their idea, not mine!) and had a COI of 40.9%. No doubt about it, he’s inbred. Using my pedigree software I can set up all kinds of hypothetical social activity for the old boy and see where the COI goes. He is heavily linebred on a particular stud dog of a number of years back. However, that dog is not common in most show-line Australian Shepherd pedigrees, so I can easily find mates—even those with fairly high COIs themselves—who will give him puppies with much lower COIs. If I’m really determined I can hypothetically mate him to working-line Aussie bitches and in many cases I will drop the COI to less than 5%. All of this without having to risk finding out what any of the owners of those bitches (especially the working breeders!) think of the idea of poor old show line Tank having a fling with their girls.

Getting reliable hereditary disease history on your dog’s ancestors and on his potential mates can be difficult to impossible. If you know your dog has family background for a disease and there is no available testing to let you know whether he might be carrying the genes for it, breeding for low COIs while at the same time avoiding doubling-up on any ancestors you know are problematic may reduce your risk of producing the problem. With a lower COI you are lowering the probability of pairing on those unwanted genes you know are back there somewhere.

Every breeder should play COI: Coefficients of inbreeding are an important tool to apply to your breeding program. Whatever the needs of your kennel or your breed, COIs provide you with a vital bit of information that should be part of your decision-making process.

Although Purebred Dogs Can Be Best in Show, Are They Worst in Health?

With its sweet and loving disposition, combined with silky fur and elegantly droopy ears, the Cavalier King Charles spaniel is a popular breed&mdashwith families paying hundreds, sometimes thousands, of dollars per puppy. Unfortunately, though, it is almost certain that their pet will also come with genetic disorders.

By age five, for example, half of all Cavaliers will develop mitral valve disease, a serious heart condition that leaves the dogs susceptible to premature death. By the same age, up to 70 percent will suffer from canine syringomyelia, a debilitating neurological disorder in which the brain is too large for the skull, causing severe pain in the neck and shoulders, along with damage to parts of the dog&rsquos spinal cord. And although Cavaliers may be a particularly obvious case of purebreds with problems, they aren&rsquot alone. Most purebred dogs today are at a high risk for numerous inherited diseases. Why did this happen&mdashand what can be done about it?

Consequences of breeding
For almost 4,000 years people have been breeding dogs for certain traits&mdashwhether it be a physique ideal for hunting pests like badgers or a temperament suitable for companionship. But the vast number of modern breeds&mdashand the roots of their genetically caused problems&mdashcame about over the past two centuries, as dog shows became popular and people began selectively inbreeding the animals to have specific physical features. Over time the American Kennel Club (AKC) and other such organizations have set standards defining what each variety should look like. To foster the desired appearance, breeders often turn to line breeding&mdasha type of inbreeding that mates direct relatives, such as grandmother and grandson. When a male dog wins numerous championships, for instance, he is often bred widely&mdasha practice known as popular sire syndrome (pdf)&mdashand his genes, healthy or not, then are spread like wildfire throughout the breed. As a result, purebred dogs not only have increased incidences of inherited diseases but also heightened health issues due to their bodily frames and shapes, such as hip dysplasia in large breeds like the German shepherd and the Saint Bernard, and patellar luxation, or persistent dislocation of the kneecap, in toy and miniature breeds.

How did we get to this situation? &ldquoHistorically, a breeder&rsquos primary concern was to produce dogs that look like the breed standard,&rdquo explains James Serpell, professor of ethics and animal welfare and director of the Center for the Interaction of Animals and Society at the University of Pennsylvania School of Veterinary Medicine. &ldquoEven if they did recognize health problems, breeders were too driven to produce what was perceived to be the most perfect breed.&rdquo

In the 1850s, for example, the bulldog looked more like today&rsquos pit bull terrier&mdashsturdy, energetic and athletic with a more elongated muzzle. But by the early 20th century, when dog shows became popular, the bulldog had acquired squat, bandy legs and a large head with a flattened muzzle. This altered figure makes it nearly impossible for them to reproduce without assistance, and the facial changes cause severe breathing problems in a third of all bulldogs. Breeders frequently turn to artificial insemination because the female bulldog&rsquos bone structure cannot support the male&rsquos weight during mating. Most cannot give birth naturally either, because the puppies&rsquo heads are too big for the birth canal.

Large head size and short legs are part of the written standard, so Serpell believes these standards would have forced the bulldog into extinction if breeders did not rely on artificial insemination. &ldquoBy essentially requiring judges to select animals that are the written standard, the club, in a way, signed the bulldog&rsquos death warrant,&rdquo Serpell says.

Despite the negative effects of controlled breeding, animal science experts point to the value of selecting for consistency. &ldquoA breed standard is the template providing information about the appearance and temperament and reflects the original function and purpose of the breed,&rdquo says Milan Hess, a Colorado-based veterinarian who works with the AKC. When choosing a dog as a pet, consumers look to the breed standard for certainty. &ldquoThey know what it will look like and how it will act,&rdquo says Thomas Famula, an animal-breeding specialist at the University of California, Davis.

Healthy choices
With the search for consistency yielding unforeseen flaws, however, who is to blame? Although the AKC sets the breed standards, it is principally a registry organization and has little control over the actual breeding process. Famula believes dog breeders hold the highest responsibility because they make the decisions about which dogs to mate. &ldquoIn the end, breeders are the ones creating the next generation of dogs,&rdquo Famula explains. But researchers like Famula and Jerold Bell, a geneticist at the Tufts University Cummings School of Veterinary Medicine, note that breeding practices are greatly influenced by the puppy buyers who Bell believes are largely ignorant about genetic issues. &ldquoThe public is completely unaware. They see a cute dog and are sold,&rdquo Bell says. When purchasing a puppy, buyers can ask for medical tests and family history of diseases but this rarely happens. &ldquoAlthough it&rsquos ultimately the breeders&rsquo responsibility, if there&rsquos no pressure from the buyer, the system won&rsquot change,&rdquo he adds, emphasizing that most of the top 10 diseases plaguing all dogs are controlled by single genes which, when identified, are easy to eliminate in the next generation.

Meanwhile many organizations breeding dogs for police work or to aid the disabled routinely do use data registries to maintain health information and make smart pairing decisions that reduce the prevalence of inherited ailments. The Seeing Eye, a guide dog school in Morristown, N.J., for example, uses genetic testing and keeps a database that tracks all dogs&rsquo potential problems. &ldquoWe have a geneticist on staff who evaluates each dog as a potential breeder, and we occasionally bring in dogs from other guide schools to ensure our gene pool doesn&rsquot get too restricted,&rdquo says Michelle Barlak, senior public relations associate at The Seeing Eye.

Moving forward
It is possible to improve a breed and maintain its characteristics, of course. Consider the dalmatian. The challenge: the genes responsible for the breed&rsquos sought-after characteristic spotting pattern also result in high levels of uric acid in the breed&rsquos urine, predisposing them to the formation of urate crystals that frequently cause urinary blockages. Selecting against uric acid, however, would result in a spotless dalmatian. Now there&rsquos new hope from work that began in 1973, when Robert Schaible, a geneticist at the Indiana University School of Medicine, started the Dalmatian&ndashEnglish Pointer Backcross Project. He paired an AKC champion dalmatian with an English pointer, a breed with normal uric acid levels and a disposition similar to that of the dalmatian, and then crossed a dog from that litter to another dalmatian and so on. In 2011, after 15 generations, the AKC allowed dalmatians from this healthier pedigree, spots intact, to register.

Looking ahead at the future of purebreds, Serpell emphasizes that the goal is not to get rid of them but rather to put the health of the animals first. &ldquoI don&rsquot think anyone wants the breeds to disappear,&rdquo Serpell says. &ldquoI don&rsquot want the bulldog to disappear, I just want the bulldog to be transformed back into an animal that can function properly and is reasonably healthy.&rdquo

This article is provided by Scienceline, a project of New York University's Science, Health and Environmental Reporting Program.