Segmental Duplications in the Chicken Genome Identified By Single Nucleotide Variant (SNV) Analysis in Two Inbred Lines

Segmental duplications (SD) are genomic regions with nearly identical sequence. Here we present the identification of  segmental duplications on chromosome 1 in two highly inbred pooled lines by SNV validation analysis. SDs in both lines were discovered during the validation process for novel SNV in these lines. This resulted in variants that appeared to segregate, as some genotyped individuals incorrectly appeared as heterozygous.

Duplication identification was carried out using the KBiosciences Kompetitive Allele Specific PCR genotyping system (KASP). This allowed for both a numerical and visual examination of the existence of variants. Follow up analysis of the possible duplications included comparison of the mean depth of coverage (DP) across the genome versus the DP for the variants showing duplication (DP ≥ ~2 x mean). The flanking sequences for the duplicated variants were also queried using NCBI Blast to search for multiple hits  to different genomic regions.  Independent commercial lines were also used to confirm the existence of the duplications.

Results from the KASP assay, Blast, and DP analysis confirmed that selected variants on chromosome 1 had flanking sequences that mapped to multiple genomic locations with SNV loci that showed ≥ ~2 the mean genomic DP. Results suggest SDs caused primers to amplify both the alternate and reference alleles making them appear as segregating. This was due to fixation of different alleles in the genome that are incorrectly mapped to the same genomic location within regions of a SD.

Support: USDA-NIFA-AFRI grant and Hatch project #5358.