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      Development of an SNP-based parentage verification panel for lovebirds.

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          Abstract

          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 SNPs. Over 1.6 million SNPs, shared between the parents, were discovered using the Genome Analysis Toolkit pipeline. SNPs were filtered to a panel of 480 SNPs based on Genome Analysis Toolkit parameters. The panel of 480 SNPs was genotyped in a population of 960 lovebirds across seven species. A panel of 262 SNPs was compiled that included SNPs successfully amplified across all species. The 262-SNP panel was reduced based on the observed heterozygosity (HO ) and minor allele frequency (MAF) values per SNP to include the lowest number of SNPs with the highest exclusion power for parentage verification. Two smaller panels consisting of 195 SNPs with MAF and HO values >0.1 and 40 SNPs with MAF and HO 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 HO values >0.1 was proposed as the routine Agapornis parentage verification panel.

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          Author and article information

          Journal
          Anim Genet
          Animal genetics
          Wiley
          1365-2052
          0268-9146
          Dec 2019
          : 50
          : 6
          Affiliations
          [1 ] Focus Area for Human Metabolomics, North-West University, Hoffman Street, 2531, Potchefstroom, South Africa.
          [2 ] Department of Animal and Wildlife Sciences, University of Pretoria, Private Bag X20, Hatfield 0028, Pretoria, South Africa.
          Article
          10.1111/age.12859
          31579954
          0e3aa438-a0e9-4c14-84c7-a93d17499dd8
          © 2019 Stichting International Foundation for Animal Genetics.
          History

          Agapornis ,parrot breeding,pedigree confirmation,whole-genome resequencing

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