I have been studying for some time now the effects of domestication upon animals in captivity and how genetics can be related to health and behaviors as well as appearance. I thought it might be interesting to talk about some of the ways genetics can effect animals health and lifespan. This is not meant to be an argument against any breed/color, simply talking about health issues that are connected to the genetics behind them. If I get anything wrong, feel free to correct me. I'm still learning a lot and want to learn more.
I hope this helps new breeders as they learn more about how genetics can affect health!
Genetics are the programming behind any living animal. They are the living plan that shapes and forms an animal its whole life. It decides size, shape, coloration, pattern, behaviors, immune system strength, production ability, litter/clutch size, and so much more. So, basically, its way to complicated to talk all about here. However, I can mention some of the ways that human selection can lead to issues in poultry and how to work around that so that no animals have to suffer any issues because of their genetics.
Inbreeding: Most important in any talk about genetics and health is a short discussion on inbreeding and inbreeding depression. In truth, inbreeding is not bad. Pure and simple, two related animals breeding together is not the cause of the health issues seen in inbred animals. Instead, it is the fact that when two individuals with similar genetics breed together there is no room for improvement and any health issues in them will just be added together, time and time again. Not only that, but good genes may be lost as the gene pool shrinks. In other words, inbreeding leads to many of the problems seen in domestic dogs, cats, horses, and ferrets, but chickens are usually selected for health as well as appearance. I personally am against prolonged inbreeding, since almost no matter what you will probably see issues springing up in the chickens such as lack of fertility or vigor, smaller size, shorter life-span, ect. However, the best way to avoid issues with inbreeding while selecting for consistency is in out-crossing for new genetics, selecting against any weakness or health problems, and culling birds with health issues before they are used for breeding.
Lavender: Tail shredder issues, or fraying of the feathers, can be seen in homozygote Lavs (two lavenders bred together). As far as I know it doesn't affect any thing healthwise in the bird, but it does affect their appearance and in bad cases can mean they can't control their body temperature as well. It has been stated selection against this issue will lead to healthier feathering with less fraying, however, the exact genetics behind this can be difficult to say. Before breeding lavender chickens, do your research int o their genetics to better understand how to produce only healthy birds.
Ear Tuft Gene (Et): When two Et chickens are bred together, the homozygote eggs generally die between 17-19 days of incubation, meaning just before hatching. A few may hatch, but usually die soon afterwards, though a very rare individual might live to maturity. Heterozygotes also have increased chick death a day or so before hatching, meaning they will be fully developed but fail to hatch. This affects about 41.6% of heterozygote tufted chicks. After hatching they may still be weak and more prone to dying as well, so take extra care for them. It is thought to be linked with defects in the ear structure as well. Avoid such things by only breeding healthy Ets with non-Ets.
Extra Spurs (a dominant gene): A rooster with too large or too many spurs may have trouble getting around and injure themselves by tripping or getting caught on wire. If this seems to be an issue, trimming the spurs may help. Extra spurs is genetically linked in certain breeds, such as the Cubalaya.
Double Frizzle/Frazzle: When two Frizzles are bred together it leads to a chicken that has delicate, breakable feathers that tend to fall out and lead to difficulties in the elements. Many people have to keep their frizzles indoors to keep them safe from the cold, and they are also more fragile to bullying chickens. It has also been said they don't live as long. the gene also leads to enlarged heart, spleen, gizzard and alimentary canal. The best way to avoid this is just not breeding two frizzle chickens together but only a Frizzle to a normal-feathered chicken.
Hen-feathering: Hen feathering is the result of high levels of estrogen in the feather follicle of certain roosters, which causes them to have the rounded feathers of a hen instead of the pointed hackle and saddle feathers of a rooster. These birds are still very much a rooster in behavior, with crowing and protective instincts, however it has been said it could be linked to low fertility. The best way to avoid this is to only select for a rooster with high fertility. I have not seen this issue in any of the sebrights I have worked with.
Mega-meat: The size of the chickens breast is determined by genetics. Chickens that are too large may have issues with heart-attacks, bruising, sores on their body, weak legs, lowered immunity, lameness, inability to breed naturally and shortened life-spans. The best way to avoid this is to select for vigor and hardiness as well as size. A chicken that cannot roost, forage, or breed on its own is not a sustainable breed (broilers are a hybrid, not a pure-bred chicken).
Creeper Gene: The short legs of certain breeds, such as the Japanese Bantam, are caused by one copy of the creeper gene. Two copies of this gene is lethal.
Recessive Polydactyly: This trait that causes extra toes to form also leads to leg deformities, a significant decrease in hatchability and a high number of deaths after hatching. There are various kinds of polydactyly. Most cause foot malformation and many cause death before hatching. Some may have extra wing tips as well or thicker wings.
Dominant Rumpless: No tail vertebrae. This can lead to reduced hatchability. It is different then "roachback" which is recessive.
Rose comb: Has been associated with poor fertility in certain breeds (in homozygous, or double dose). Again, the best way to avoid this is by selecting only strong, fertile roosters and hens for breeding.
Naked Neck: Has been associated with up to 10% increase in embryonic mortality. However, all and all a healthy gene according to studies, which show that naked-neck chickens naturally occur in feral populations in warm climates, as it helps them to stay cool. The bright red color of the neck and head is natural in these chickens.
Vaulted Skull: A genetic issue where a hole in the crest of a chicken leads directly to the brain. This opening means that any injury to the protruding brain can lead to instant death. The opening may grow smaller or even close as the chick matures, or it may not. When breeding two vaulted skull birds together around 30% of the eggs will die before hatching and around 25% of the chicks will die before their second week. This gene was introduced into silkies from the Polish breed ad is not necessary to form a large crest. It is best to select against any chicken that has a failure to thrive. It is easy to avoid issues with holes leading to the brain with breeding for the natural silkie crest.
I hope this helps some in explaining a few of the traits that can be linked with health issues. Again, this is meant as a reference to people interested in breeding chickens, so they can understand what to select for and what to avoid in the breed/color they work with. I hope it helps. (and its also just fun to talk about chicken genetics too).