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Development of an SNP ‐based parentage verification panel for lovebirds
Author(s) -
Zwan H.,
Visser C.,
Schoonen M.,
van der Sluis R.
Publication year - 2019
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12859
Subject(s) - snp , biology , genetics , genome , tag snp , single nucleotide polymorphism , snp array , population , allele frequency , selection (genetic algorithm) , computational biology , allele , genotype , gene , computer science , medicine , environmental health , artificial intelligence
Summary The genus Agapornis , or lovebirds, are popular pet parrots worldwide. Currently, breeders are dependent on pedigree records as a selection tool as no molecular parentage verification test is available for any of the nine species. The A. roseicollis reference genome was recently assembled. This was followed by the sequencing of the whole genomes of the parents of the reference genome individual at 30× coverage. The parents’ reads were mapped against the reference genome to identify SNP s. Over 1.6 million SNP s, shared between the parents, were discovered using the Genome Analysis Toolkit pipeline. SNP s were filtered to a panel of 480 SNP s based on Genome Analysis Toolkit parameters. The panel of 480 SNP s was genotyped in a population of 960 lovebirds across seven species. A panel of 262 SNP s was compiled that included SNP s successfully amplified across all species. The 262‐ SNP panel was reduced based on the observed heterozygosity ( H O ) and minor allele frequency ( MAF ) values per SNP to include the lowest number of SNP s with the highest exclusion power for parentage verification. Two smaller panels consisting of 195 SNP s with MAF and H O values >0.1 and 40 SNP s with MAF and H O values >0.3, were constructed. The panels were verified using 43 families from different species with known relationships to evaluate the exclusion power of each panel. The 195 SNP panel with an average exclusion probability of 99.9% and MAF and H O values >0.1 was proposed as the routine Agapornis parentage verification panel.