How breeding works today — genomics, data and technology in selection
Modern dog breeding is profoundly different from what it was twenty years ago. The integration of advanced genomics, digitalized health screening, assisted reproductive technologies and biometric data monitoring has transformed selection from an art based on eye and experience into a discipline that combines intuition and science. The goal remains the same as ever — improving health, morphology and temperament while minimizing hereditary diseases — but the tools to achieve it have changed radically.
Genomic selection and DNA testing
The most profound revolution in dog breeding of the last twenty years is the possibility of reading the DNA of breeding dogs before planning a mating. It is no longer necessary to wait to see the puppies to discover what is hidden in the genetic makeup of the parents — today it can be known in advance.
Predictive genetic tests
Modern genetic tests identify healthy carriers of autosomal recessive diseases — dogs that show no symptoms but can pass the disease on to their offspring if mated with another carrier. For the Shiba Inu, this means being able to rule out in advance the risk of hereditary conditions such as GM1 gangliosidosis or many other breed-specific diseases. Protocols such as MyDog DNA, certified by the Vetogene laboratories (a spin-off of the University of Milan), analyse over 240 genetic markers in a single screening — the kind of panel that ten years ago would have cost thousands of euros and weeks of waiting, and today is accessible to any serious breeder.
Genetic diversity profiles
DNA tests are not only useful for looking for diseases. They also make it possible to calculate the true inbreeding coefficient (genomic COI) — not the theoretical one based on the pedigree (which assumes that all ancestors are unrelated, something rarely true), but the actual one based on the mapping of the individual dog’s DNA. The difference can be significant: two dogs with a pedigree COI of 6% can have very different genomic COIs depending on how much DNA they have actually inherited from common ancestors.
This figure makes it possible to plan matings that maintain the genetic diversity needed for the health of the line — a crucial aspect for breeds such as the Shiba Inu, whose gene pool was drastically reduced by the near-extinction of the post-war period.
Trait mapping
Early selection based on genes is already a reality for some simple traits: coat colour, size, certain conformations. The study we contributed to — “ASIP Promoter Variants Predict the Sesame Coat Color in Shiba Inu Dogs” — is a concrete example: for the first time it is possible to predict genetically whether a mating can produce red sesame puppies, a colour that previously could only be selected by trial and error.
For complex traits such as general conformation or temperament, mapping is still under development — they are controlled by many genes with small effects, not by a single switch. But progress in canine genomics is accelerating: studies such as the 2025 one on Labrador Retriever guide dogs have shown that genomic prediction of behavioural traits is possible, even though the accuracy varies enormously between different traits.
Health screening and phenotyping
Genetic tests tell what is in the DNA. Health screening tells how that DNA is expressed in the real dog — and there are things that DNA alone cannot predict.
Official certifications
Before entering a serious breeding program, every dog undergoes imaging diagnostics for the orthopaedic and eye diseases most relevant to the breed:
Hip dysplasia: official X-ray evaluated by the ENCI reading centre. The result (from A, excellent, to E, severe) determines whether the dog is suitable for breeding. Only subjects with grades A and B should be bred.
Patellar luxation: clinical evaluation that classifies the stability of the kneecap on a scale from 0 (normal) to 4 (permanent luxation). In the Shiba it is one of the most closely monitored orthopaedic conditions.
Eye diseases: ophthalmological examination for cataracts, progressive retinal atrophy (PRA), glaucoma and other hereditary conditions. It must be repeated periodically because some diseases only manifest with age.
Global databases
The health results of breeding dogs no longer live in the breeder’s drawers. Public databases and official registries — from ENCI in Italy to the OFA database in the United States — make it possible to consult the clinical and genetic results of registered dogs, study bloodlines over time and identify patterns of health or disease across generations.
For the Shiba Inu, the shiba-pedigree.ru database has become an essential tool: it collects genealogical and health data of thousands of Shibas worldwide, allowing breeders to verify the history of a line before planning a mating with subjects they do not know personally.
Morphofunctional evaluation
Dog shows are not (only) beauty contests. They are the most structured form of phenotyping available in dog breeding: specialist breed judges evaluate the dog’s conformation in motion, the skeletal structure, proportions, expression and temperament, comparing them against the standard. The judgement of several independent experts on several occasions — the path required to obtain a championship title — provides a standardized and repeatable assessment of the morphological and temperamental quality of a subject.
This is why at Shinjukawa every breeding dog must have obtained at least one championship title before being admitted to breeding: the championship is not a trophy, it is a certification of suitability.
Assisted reproductive technologies
Reproductive technologies have removed some of the physical barriers that once limited the breeder’s choices.
Artificial insemination
Artificial insemination (AI) makes it possible to use fresh, chilled or frozen semen, overcoming the geographical barriers that once forced breeders to use only local sires. An excellent stud dog in Japan can today contribute to the breeding program of a kennel in Italy — an opportunity unthinkable until a few decades ago, and particularly relevant for breeds such as the Shiba Inu where the most valuable bloodlines are in Japan.
Semen banks
The long-term preservation of genetic heritage is one of the most underestimated tools of modern breeding. The semen of an excellent stud dog can be frozen and stored for years — even after his death — allowing matings to be planned with a dog that no longer exists. It is a genetic insurance policy: if a line loses its best breeding dog, its heritage is not lost.
Progesterone monitoring
Quantitative progesterone testing has revolutionized the management of matings. Identifying the exact ovulatory peak of the dam — not approximately, but with precision to within hours — drastically increases the chances of conception, especially with frozen semen where timing is critical. In the Shiba, a notoriously low-prolific breed, this precision can make the difference between a successful litter and a failed attempt.
Computer science and data management
The ability to collect, store and analyse data has transformed breeding from an activity based on the breeder’s memory into a data-driven discipline.
Pedigree software and COI calculation
Modern pedigree software mathematically calculates the inbreeding coefficient over many generations, simulates hypothetical matings before they happen, and makes it possible to visualize the concentration of specific ancestors in the pedigree. The breeder can assess in advance how much a mating will concentrate or diversify the genetic heritage — and decide accordingly.
The COI is a monitoring tool, not an oracle: a low value does not guarantee healthy puppies, and a moderate value does not condemn them. But it is an essential thermometer for managing inbreeding over time and avoiding discovering the problems when it is too late.
BLUP evaluation — the estimated breeding value
BLUP (Best Linear Unbiased Prediction) is a statistical model originally developed for livestock science that is making its way into modern dog breeding. The principle is powerful: estimating the genetic value of a dog not only on the basis of its phenotype (how it looks and behaves), but on the basis of the data of all its relatives — offspring, siblings, parents, grandparents.
A dog can look excellent but produce mediocre offspring (its phenotype does not reflect its genotype). Another can look average but consistently produce superior offspring. BLUP tries to distinguish these two situations by estimating how much of the observed value is genetic (and therefore heritable) and how much is environmental (and therefore not heritable).
In cattle and pig breeding, BLUP has been standard for decades. In dogs it is still in its infancy, but recent studies — such as the 2025 one on Labrador Retriever guide dogs that applied GBLUP (genomic BLUP) to health and behavioural traits — are demonstrating that it is also applicable to dog breeding, with promising results especially for traits of moderate heritability such as hip dysplasia and certain behavioural characteristics.
Digital medical records
Tracking the longevity, fertility and health of bloodlines over time — through digital medical records and structured databases — makes it possible to identify patterns that casual observation would not catch. A line that produces dogs with an average lifespan of 14 years is different from one that stops at 10 — but to know that, systematic data collected over several generations is needed, not anecdotal memories.
Temperament evaluation and bio-sensorics
Modern breeding is not limited to producing beautiful, healthy dogs — it aims to produce dogs with the right temperament for the life they will lead.
Standardized behavioural tests
The scientific evaluation of temperament — through standardized tests that measure qualities such as stability, reaction threshold, ability to recover from stress, sociability and independence — makes it possible to select not just on the basis of “this dog seems calm to me” but on repeatable and comparable data. In Italy, for the Shiba Inu, the CIRN (Club Italiano Razze Nordiche) imposes the TVC — Temperament Evaluation Test (Test di Valutazione Caratteriale) — as a requirement for breeding dogs: a structured evaluation of temperament that verifies the subject’s temperamental suitability to the breed standard. For the Shiba, a breed with a strong and independent temperament, this evaluation is particularly important because the line between “independence of character” (desirable in the standard) and “difficulty in handling” (problematic for the owner) is thin.
Biometric sensors
Remote monitoring technologies make it possible to track vital parameters and stress indicators in puppies and dams — heart rate, temperature, activity levels, sleep patterns. They do not replace the breeder’s eye but complement it: a sensor detects a drop in activity in a puppy a few days before it becomes visible to the eye, and those few hours of advance notice can make the difference.
Early stimulation programs
Neonatal activities to optimize the development of the nervous system — from tactile stimulation in the first days of life to structured socialization in the first weeks — are one of the areas in which science has confirmed what the best breeders had been doing for a long time by instinct. Already during gestation, prenatal stimulation techniques on the mother can positively influence the neurological and sensory development of the puppies. It is an investment of time and constant presence that an intensive kennel cannot afford — and one of the reasons we only produce 3-4 litters a year.
European legislation — a historic change
The EU Regulation on the welfare and traceability of dogs and cats, approved by the European Parliament on 23 April 2026 and confirmed by the Council on 22 May 2026, introduces for the first time binding rules on breeding strategies:
This legislation, the first of its kind at European level, obliges all breeders to standards that the best were already applying by choice.
How we work at Shinjukawa
Of the technologies and methodologies described in this article, here are the ones we concretely apply in our breeding program:
Genetic testing and health screening: all our breeding dogs have their DNA deposited and undergo screening for hip dysplasia, patella and eye diseases, in addition to the TVC (Temperament Evaluation Test, Test di Valutazione Caratteriale) imposed by the CIRN — the Club Italiano Razze Nordiche, the body that protects the Shiba Inu in Italy among other Nordic breeds. Recently we have integrated the complete MyDog DNA protocol (Vetogene, University of Milan), which includes over 240 genetic tests — a natural evolution of our approach, made possible by the offer of a package that also includes the DNA deposit, previously managed separately.
Pedigree software and COI calculation: we use specialized software to calculate the inbreeding coefficient of our matings and simulate combinations before carrying them out. Our maximum COI is 12.5% — well below the critical thresholds and fully compliant with the new European legislation.
BLUP evaluation: we apply the estimation of breeding values through statistical tables based on the data of our breeding dogs and their offspring. It is an approach that requires data accumulated over several generations — and it is one of the concrete advantages of working continuously on the same lines since 2010.
Development of a dedicated BLUP software: we are developing in-house a BLUP application specifically designed for the Shiba Inu, which will take into account the specificities of the breed — from temperament to conformation according to the Nippo standard. It is a project born from the awareness that generic BLUP models, developed for livestock or Western working breeds, do not adequately capture the traits that define the Shiba. At present there are no equivalent tools dedicated to this breed.
Shows as phenotyping: every one of our breeding dogs has earned at least one championship title — not as a trophy, but as a standardized certification of morphological and temperamental suitability.
Prenatal stimulation and neonatal programs: we follow every litter from gestation to weaning with early stimulation techniques and monitoring of physical and cognitive development.
Not all available technologies are necessary for every kennel, and not all are applicable in the same way to every breed. Our choice has been to integrate the tools that give a real and measurable advantage in the selection of the Shiba Inu — without chasing technology for its own sake, but adopting it where it really makes a difference.
References
- EU Regulation on the welfare and traceability of dogs and cats, approved by the European Parliament on 23/04/2026 (558 votes in favour) and confirmed by the Council on 22/05/2026. Article 6 on breeding strategies.
- Wilson B.J. et al. (2013). “Estimated Breeding Values for Canine Hip Dysplasia Radiographic Traits in a Cohort of Australian German Shepherd Dogs.” PLOS ONE, 8(10), e77470.
- Frontiers in Veterinary Science (2025). “Breeding values and index creation for health and behavior traits in Labrador Retriever guide dogs.” — Application of GBLUP to health and behavioural traits.
- Belyakin S.N. et al. (2022). “ASIP Promoter Variants Predict the Sesame Coat Color in Shiba Inu Dogs.” Veterinary Sciences, 9(5), 222. MDPI.
- Wright S. (1922). “Coefficients of Inbreeding and Relationship.” The American Naturalist, 56, 330–338.
