Little Feathered Buddies

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*Breeding & Genetics
     - Basic Genetics
     - Sex-Linked Mutations
     - Crossovers
     - Allelic Mutations
     - Coloration Mechanics Pt 1
     - Coloration Mechanics Pt 2
     - Genetic Calculators
     - Oddities: Tricolor Tiel
     - Oddities: The Spot Gene
     - Cockatiel Split Signs

     - Hormone Control
     - Nestboxes
     - Egg candling
     - Egg binding
     - Miscellaneous topics

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Breeding & Genetics

Basic Genetics

This article will focus on the genetic aspects of color breeding since color is the trait that gets the most attention from aviculturalists. But some bird species are selectively bred for other characteristics such as feather quality, singing ability, and body shape and size. 

Basic principles

Genes are the basic unit for transmitting inherited traits from parent to offspring. Genes are made of DNA, and each gene affects a specific characteristic. Some characteristics are controlled by a single gene, while others result from the interaction of as many as 100 different genes. With the exception of red blood cells, every cell in the body contains a complete set of genes.

Chromosomes are long pieces of DNA made of linked genes. The number of genes on each chromosome varies depending on the size of the chromosome - usually anywhere from  a few hundred to a few thousand. Chromosomes are arranged in matched pairs, with one chromosome in each pair coming from the individual's mother and the other from the father. It's generally estimated that birds have 40 to 80 pairs of chromosomes - the number varies depending on the species, and for many species the number is unknown.

Most chromosome pairs are autosomal, which means that both chromosomes in the pair are the same size and shape and carry the same number of genes. But the sex chromosomes are special, because one chromosome has a different (smaller) shape than the other and carries fewer genes. In some species the smaller sex chromosome might not carry any genes at all. So at least some of the genes on the larger sex chromosome do not have a gene to pair up with on the smaller sex chromosome, and this one unpaired gene controls the relevant characteristic by itself. These are called sex-linked traits.

As the name suggests, the sex chromosomes determine the gender of the individual. In humans, the sex chromosomes are called X and Y based on their shape, and an XY pair makes a male and an XX pair makes a female. In birds the sex chromosomes look more like a Z and a W (with the Z being the larger chromosome), but most discussions call them X and Y because these terms are more familiar. 

But the ZW sex-determination system is actually very different than the XY system of mammals, because gender determination in birds is the opposite of the way it works with humans. In the ZW system,  males are ZZ (XX) and females are ZW (XY), and the hen determines the sex of the baby. Each chick receives one sex chromosome from each parent; reverting to XY terminology, each chick will get an X chromosome from its father regardless of the baby's sex.  If the chick receives the Y chromosome from its mother it will be female, and if it receives her X chromosome it will be male.

All the pairs of chromosomes split up during the formation of ova and sperm (gametes), with each gamete  receiving one chromosome from each pair. There are changes in the chromosome pairs during the separation process as segments of genes within each chromosome pair trade places, moving from one chromosome to the other. This gene-shuffling process is why we call it recombinant DNA, and it allows for much greater genetic diversity in the offspring than there would be if the chromosome pairs simply split apart without shuffling the genes first. When conception occurs, each chromosome from one parent pairs up with the matching chromosome from the other parent, to create a new individual with the correct number of genes and chromosomes. 

A mutation is a spontaneous change in a gene's DNA during the formation of sperm and ova. The offspring receives an altered gene that the parent didn't have, and can pass this gene along to its own descendants. Mutations can occur with any gene, sometimes with disastrous results. But the mutations that cause color variations are basically benign, and we humans like them and work hard to perpetuate them. Color mutations can occur in the wild too but they get bred out or submerged in the general population, and the normal color prevails.

Mutations change color in one of two ways: by modifying or eliminating pigment in the feather, or by changing the structure of the feather so it reflects light differently. Mammals have one type of pigment (melanin) but birds have two or more. The pigments found in birds are melanin (for dark colors like brown, black, and grey), carotenoids or psittacins (different types of pigment controlling red, yellow, and orange) and porphyrins (the green in some species). In many parrot species the appearance of green or blue is not caused by actual pigments in the feathers; it's an optical illusion caused by the way light reflects off of special structures in melanin-bearing feathers.

A hybrid is the offspring of birds from different species. Hybridization is a controversial topic in aviculture because many of the birds produced this way are fertile, and it is feared that they will end up polluting the gene pool of the pure species.  A first-generation hybrid is easy to identify but it might not be possible to tell that a bird has a grandparent or great-grandparent from a different species. So please, don't breed hybrids.

Dominant and recessive

Genes carry the instructions for a particular trait. When both genes in a particular pair carry the same instructions, they are homozygous.  When they each call for something different they are heterozygous. The way these instructions are carried out is mainly determined by whether each gene is dominant or recessive.

A dominant gene is the one whose instructions will be followed (expressed) in a heterozygous pair, and the instructions from the recessive gene in this pair will be ignored completely. Both genes in the pair have to be recessive in order for the recessive trait to be expressed - in other words the individual has to homozygous for the recessive trait. A bird who is heterozygous (one dominant gene, one recessive) is said to be split for the recessive characteristic. This means that the bird is carrying the gene and can pass it to its descendants but does not display the trait itself.

With dominant genes, for appearance purposes it usually doesn't matter whether the individual is homozygous or heterozygous - the individual  will look the same in either case. But there are a few gene pairs where having two dominant genes produces a different effect than having just one. These are double factor traits, also called semi-dominant or partial dominant. There are also co-dominant genes, where each gene in a heterozygous pair has an influence on the visual outcome.

Common recessive genes include some types of pied and blue (whiteface). The relationship between pastelface and whiteface is an example of co-dominant genes.

Phenotype and genotype

Phenotype is a fancy word meaning a description of the bird's physical appearance.  The genotype is a description of the bird's genetic makeup; it often begins with the phenotype and adds information on splits and any other hidden factors. For example, a bird whose phenotype is "pied" might have a genotype of "pied split lutino".  Sometimes it is possible for different genotypes to produce a similar phenotype.  For example, in cockatiels the emerald mutation and the dominant silver mutation are produced by different genes, but they look very similar to each other.

Sex-linked characteristics

Several color mutations in birds are sex-linked, which means that the mutation is carried on the X chromosome. There are some dominant sex-linked mutations, but the way they work is fairly straightforward so they are not discussed here. Most sex-linked mutations are recessive and their action is complicated. The rest of this section describes the way recessive sex-linked mutations are transmitted and the effect that the chick's gender has on the expression of the mutation.

A female chick who receives a sex-linked mutation on the X she gets from her father will be visual for the color, because there is no gene on the Y for it to pair up with and this one gene is in sole control of the trait. So it's easy to tell whether a female has a sex-linked gene because it's visible - she can't be split to a sex-linked mutation. She will pass this mutation to all of her sons (since they'll all be getting this same X from her) and to none of her daughters (since they'll all be getting the Y from her which can't carry the gene for this trait).

Females can only inherit the trait from their father but males can get it from either parent, since they receive an X chromosome from father and another X from mother.  But since the mutation is recessive, a male has to receive the gene from both parents to be visual for the color. If he only gets it from one parent he will be split to it.

It is possible for birds to have the genes for more than one sex-linked mutation. In females, multiple sex-linked genes obviously have to be on the same X since she only has the one. With males, the genes can be on the same X or on different X's.

Understanding the operation of recessive sex-linked genes is sometimes useful for sexing chicks. Females can not be split to these mutations, and males must receive the gene from both parents to be visual for the mutation.  So if you have a chick with a sex-linked color and the mother is NOT that same color, the chick has to be a female who inherited the gene from her father.

The most common sex-linked recessive genes are lutino, cinnamon, opaline/pearl, and slate.

There is an illustrated discussion of sex-linked inheritance in the Sex-Linked Mutations section.


It gets even more complicated!  The Basic Principles section told how segments of DNA can cross from one chromosome in a pair to the other during the formation of ova and sperm.  This is called a crossover, and crossovers can affect the breeding outcome when the father bird has the genes for more than one sex-linked mutation. The only crossovers that are significant for color-breeding purposes is when two different sex-linked mutations change position with respect to each other. This means that if they were on different X's before the crossover they end up on the same X after the crossover, and vice versa. The chick who receives one of these X's will inherit more (or fewer) sex-linked mutations than you would normally expect.

The rate of crossovers is not known with any precision, and it's likely that they vary from species to species.  The further apart the genes are on the X, the more likely it is that a crossover will occur.  The crossover rates used by the Ara Project Genetic Calculator vary from 3% for crossovers between lutino and cinnamon, to 30% for crossovers between opaline/pearl and those colors.

Crossovers seem to be the most difficult genetic concept to grasp. If this brief discussion made your eyeballs cross over, maybe the more detailed discussion in the Crossovers section will help clarify matters.


There are some color genes that have mutated more than once, resulting in related mutations that are different variations of the same gene.  Different versions of the same gene are called alleles, and with allelic mutations you can have the genes for two different color mutations in the same gene pair.  This complex topic is discussed in detail in the Allelic Mutations section.  

Multiple-gene interactions

Sometimes multiple genes work together to produce complex results. Alas, this topic is beyond the scope of this article. Not enough is known about multiple-gene interactions in birds to talk about how they might apply to color genetics.

Copyright 2014 Carolyn Tielfan all rights reserved