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Chicken genetics are controlled by 76 paired (2n=76) chromosomes. As in all studies of genetics, genes located on DNA are studied to determine patterns of heredity for physical and behavioral traits (or phenotypes). Having an understanding of this is vital for breeders to understand to achieve the best results in both agriculture and exhibition. Because of the domestic chicken's importance to humans, the chicken genome was first avian and the first non-mammalian amniote genome to be sequenced. The chicken genome was first published in draft form in 2004 and updated in 2006.

Like most animals chickens are diploid, and they receive one chromosome in each pair from their mother and father via haploid (n=39) ovum and sperm respectively. Chickens have 76 autosomes, and the sex of a chicken is controlled by a single pair of sex chromosomes at the time of fertilization. As in mammals, sex is determined by an individual having a pair of the larger sex chromosome, or having a a mix of one large and one small one. Unlike in mammals, the larger chromosome is called Chromosome Z, and the smaller one Chromosome W, also differing is that in chickens a matched pair of the larger Z chromosome produces a male (Z/Z), and a combination of the two (Z/W) indicates a female.

Genetic makeup
The chicken genome was sequenced in 2004 by the International Chicken Genome Sequencing Consortium, and updated in 2006. The wild red junglefowl (Gallus gallus) is considered the same species and the genetic ancestor of domestic chickens, the traits that characterize the wild red junglefowl are considered to be the "wild type". Since domestication, various breeds have been developed which take advantage of uncommon mutations found in the red junglefowl, as well as newer mutations which have occurred since domestication. Recent research indicates that while the domestic chicken is primarily descended from the red junglefowl (including most of the genome and all of the mitochondrial DNA), hybridization with the grey junglefowl also likely occurred during domestication.

The chicken genome is composed of approximately 20,000 genes located on 8 autosomal macrochromosomes, 30 autosomal microchromosomes, and two sex chromosomes. At 1050 million base pairs, the chicken genome is only about 30% the size of the human genome. However, it is similar in "genetic length" (i.e. the number of genes). This discrepancy is largely because humans have more repetitive sequences and there is a higher rate of crossing-over in chickens. Despite the ancient evolutionary divergence, and the many physical differences, chickens and humans have many gene sequences which are nearly identical, many of these have functions which currently poorly understood by science.

Chickens, like all birds, have their autosomes separated into macrochromosomes, which are similar in size to those found in humans, and a larger number of very small microchromosomes. Microchromosomes probably evolved 100-250 million years ago. And though these tiny chromosomes represent only 25% of the total genome, they encode approximately 50% of the genes.

Genetic physical traits
Long before the sequencing of the chicken genome, breeders have had an understanding of genes and patterns of inheritance of many of the distinct physical traits which make each breed and variety distinct and true breeding.

Feather color traits
Chickens can have widely varied feathering pigmentation, and many genes work both together and independently to control and modify the color and patterning of the body feathers. In the wild bright pigmentation in feathers indicates to potential mates the overall fitness and foraging ability of an individual, or provides camouflage. Interestingly though there is one gene located on the microchromosome E22C19W28 which masks all other coloration genes. This gene is the dominant white gene (I). In both the heterozygous (I/i), and homozygous dominant (I/I) individuals feathering appears white. Leghorns and many white varieties of other breeds carry this allele. Having this allele has been shown to significantly reduce the incidence of detrimental feather pecking upon those individuals which show it.

Egg traits
Chrom 1 - Blue/olive eggs O closely linked to pea comb

Feather structure & placement traits
E22C19W28 - crest/frizzle

The naked neck gene causes an absence of feathering from the head and neck, and reduced feathering across the rest of the body. It is controlled by an incompletely dominant allele (Na) located near the middle of Chromosome 3. Since this allele is dominant, individuals which are either homozygous dominant (Na/Na) or heterozygous (Na/na+) will exhibit the naked neck characteristic though the heterozygous individual will exhibit less reduction in feathering - true breeding members of the breed must then be homozygous dominant, and all individuals in the recognized breed must be also. Individuals which are homozygous recessive (or wild type feathered) (na+/na+) would not exhibit any feather reduction characteristics of the Naked Necks and, baring mutation, would be unable to pass that trait down.

The silkie gene causes feathers to form without hooks, which causes the birds to have a "hairy" or "shaggy" look. The recessive silkie gene (h) is located much farther down Chromosome 3 (approximately 43 map units) than the naked neck gene.

Skin traits
Microchromosome 24 - Yellow skin - w - from grey junglefowl Z chrom - white skin y

Comb traits
Chrom 1 - rose comb R Chrom 1 (group III) - Pea comb P Chrom 2 - duplex comb - both D

Size
Z Chrom - Dwarfism dw