This page will go over the scientific biological aspects of Chao. Please be warned that section goes into complicated details, and is intended for advanced Chao breeders only!
Chao, like other organisms, have a genetic makeup. This genetic makeup is what defines their physical appearance and personality, but Chao can also carry inactive genes which do not visibly affect them but can still be passed on to their children. For this reason, genetics plays a significant role in breeding.
The Chao Genome
The following diagram lists the currently known genes in the Chao genome.
The Chao genome is complicated, and we still do not know all of the information that is stored within it. It is very likely that there are more personality details than in the list above.
Chao are diploid organisms, meaning that they have two alleles for each one of their genes, as mentioned in the diagram above. An allele is a possible type or value for that gene. For example, a Chao might carry the red and blue alleles for its Base Colour gene, or the E grade and B grade alleles for its Swim Grade gene.
The alleles do not necessarily need to be different, and it can be very helpful for breeding if they are identical. A Chao which has different alleles for a gene is called inpure (or heterozyguous) for that trait. A Chao which has matching alleles for a gene is called pure (or homozyguous) for that trait. The Chao that you start off with are totally pure in every way: their Base Colour alleles are Normal and Normal, their Tone alleles are Two-Tone and Two-Tone, and so on.
Genotypes and Phenotypes
The genotype of a Chao is its full hereditary information, including any information which cannot be seen. The phenotype of a Chao is its actual observable properties, such as the colour it appears to be and the fruit that it likes the most.
It is important to make the distinction between the two of these. Two Chao may have the same genotype but look different, and another two Chao may look identical but have different genotypes. For example, your Chao may be a Two-Tone Red, but that doesn't mean it doesn't carry the Mono-Tone allele or other colour alleles.
There is no way to view the genetics of a Chao without hacking, so you just need to keep in mind whether a Chao is pure or inpure, and try to remember its family tree.
The last thing you need to know about Chao genetics is the way in which genes and alleles interact with each other; that is, the relationship between them and what visual result (phenotype) is attained.
All of the colour alleles for the Base Colour gene have equal dominance (with one exception). This means that if a Chao has the red and blue alleles for its Base Colour gene, then there is an equal (50/50) chance of it actually being red or blue when it hatches.
The exception to this rule is the Normal colour allele, which is recessive. This means that any other colour overrides the Normal colour, making the Normal colour the hardest one to breed for. A Chao will only have the Normal colour phenotype (visual result) if both of its colour alleles are the Normal colour. This is why the Breeds page recommended that you keep at least two of your pure Two-Tone Normal starter Chao.
Please note that colours can't be mixed in any way. For example, the red allele and white allele cannot be combined to produce a pink Chao. This is referred to as incomplete dominance, and it doesn't exist in Chao. There is a fixed set of colour alleles, and a Chao can only have one of those fixed colours.
The two alleles of the Tone gene — two-tone and mono-tone — have equal dominance. This means that if a Chao has both the two-tone and mono-tone alleles, then there is an equal (50/50) chance of it actually being two-tone or mono-tone when it hatches. Of course, if the Chao has matching alleles, such as mono-tone and mono-tone, then it is pure for that trait and there is a 100% chance of it being mono-tone.
The two alleles of the Shininess gene — shiny and non-shiny — have equal dominance. This means that if a Chao has both the shiny and non-shiny alleles, then there is an equal (50/50) chance of it actually being shiny or non-shiny when it hatches. Of course, if the Chao has matching alleles, such as shiny and shiny, then it is pure for that trait and there is a 100% chance of it being shiny.
All of the alleles for the Jewel Coat gene have equal dominance (with one exception). This means that if a Chao has the Ruby and Sapphire alleles for its Jewel Coat gene, then there is an equal (50/50) chance of it actually being Ruby or Sapphire when it hatches.
The exception to this rule is the Non-Jewel allele, which is recessive. This means that any other Jewel Coat allele overrides the Non-Jewel allele, making it more likely that a Jewel Chao's child will also be a Jewel Chao. A Chao will only have the Coloured Chao phenotype (visual result) if both of its Jewel Coat alleles are the Non-Jewel allele.