Below is a list of health concerns in the breed and testing available to help eliminate progression of each (I provided an easy to understand snippet modified from a full version available at the adjoining links):
Epilepsy: If this disease is to be controlled, breeders need to make it a high priority! Pedigrees of affected dogs should be shared openly (and there are databases available to breeders). Because this disease is so devastating, it is strongly advised that a dog that is a first-step relative of an epileptic dog should not be bred. More distant relatives will need to be bred with care because they have a potential for carrying epilepsy genes. The closer they are related to an affected dog, the greater the risk. Most affected dogs will begin to have seizures around two years of age. http://www.ashgi.org/home-page/genetics-info/epilepsy-other-neurological-issues/epilepsy/canine-epilepsy There is currently no genetic screening test for this disease.
Hip Dysplasia: An abnormal hip joint can lead to a type of severe 'arthritic' degeneration of the cartilage at the joint, causing a loss of its thickness and elasticity; important in absorbing shock during movement, and can result in pain. Bone growth can be produced around the joint, which decreases the range of motion. There are environmental factors such as weight, level of exercise, and weather that can affect the severity of expression. http://www.offa.org/hd_info.html To help reduce the odds of HD being passed down to the next generation, radio-graphs can be examined by veterinarians to help determine the soundness of the hip joints.
Elbow Dysplasia: Three forms of elbow abnormalities can occur and can be inherited independently of one another, range of motion in the elbow is decreased, which can lead to lameness. Environmental factors also play a role in expression. http://www.offa.org/ed_types.html To help reduce the odds of ED being passed down to the next generation, radio-graphs can be examined by veterinarians to help determine the soundness of the elbow joints.
Eye Certification (CERF): OFA Eye Certification examinations are ocular screening exams performed by board certified veterinary ophthalmologists. The diagnoses obtained can only determine current observable eye conditions. http://www.offa.org/eye_evaluation.html While eye certification is a great tool to determine at the moment if an appearance of any eye conditions exist, it is not a genetic test to determine if eye conditions will later develop. For this, we need to genetically test for the concerning eye conditions in the Australian Shepherd: PRA-prcd and HC.
Progressive Retinal Athrophy (PRA-prcd): The first symptom of this disease is rod degeneration which causes dogs to first become night-blind, usually having poor sense of direction. Later, cones start degenerating, leaving dogs with cataracts and total blindness. PRA-prcd is a genetic autosomal recessive disease. This means the disease affects dogs with a P/P genotype only. The dogs with a P/N genotype are carriers of the disease. http://www.prcdtest.com/en/pra-prcd-disease/
Hereditary Cataracts (HC): This disease results in a clouding of the lens of the eye caused by a breakdown of tissue which leads to an inability to see clearly and can cause total blindness. Usually the cataracts start small and grow progressively. A mutation of the HSF4 gene is linked to HC in Australian Shepherds. The disease is dominant but not completely penetrant (only one copy of the mutation is required for a dog to develop the disease). However, incomplete penetrance means that a dog that has the mutation will not always develop HC. http://www.animalgenetics.us/Canine/Genetic_Disease/HC.asp
Multidrug Sensitivity (MDR1): A dog which has MDR1 may react negatively to certain drugs. This mutation is only a problem because dogs are given drugs in some veterinary practices/procedures. If dogs were in the wild, they wouldn't receive drugs, so MDR1 would be of no concern. One should be aware of the possibility of MDR1 and avoid giving the problematic drugs (DRUGS TO AVOID). Dogs carrying the MDR1 mutation, even if they have two copies can still be bred. Half of the breed carries at least one copy of this mutation. Eliminating all of these dogs from breeding programs would cause a severe restriction in the gene pool possibly resulting in serious problems for the breed. http://www.ashgi.org/home-page/genetics-info/faq/mdr1-faqs
Degenerative Myelopathy (DM)
Degenerative myelopathy is an autoimmune disease that occurs late in life and attacks the myelin coating of nerves. Dogs with DM may display weakness and lack of coordination in the hind limbs worsening over time until complete paralysis occurs. Affected dogs will have two copies of the gene but not every dog with two copies will get the disease. Dogs with this mutation should be bred to dogs that are clear. http://www.ashgi.org/home-page/genetics-info/immune-mediated-diseases/degenerative-myelopathy