Phase 2: Identifying SNP markers and compiling a parentage test panel

The second phase of the project is to identify SNPs in the genome. For more information on what SNPs are, refer to the page on More about genetics or watch the video below from 23AndMe.

The Agapornis genome consists of a little more than 1 000 000 000 or 1 billion or 1Gbp base pairs. We estimate that there is around 1 SNP every 300 bases (based on studies in other genomes) so we expect around 3.5 million SNPs in the Agapornis genome.

We need only about 200 SNPs to be included in the parentage verification panel. Therefore we need to filter the SNPs to select only those ones that can aid in verifying which birds are related. We will be using the reference genome that we have assembled in Phase 1 as well as the male bird’s parents, to identify these SNPs.

After the panel is compiled we need to test the panel in a broader population of birds to confirm that the markers are robust enough to verify parentage in all populations and levels of inbreeding.

For more information on how SNPs are used in parentage verification, click here.