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. 2020 Jun 30;11:22. doi: 10.1186/s13100-020-00216-w

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© The Author(s) 2020

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 2 — High-throughput genotyping of ALVE integrations by KASP assay. Genotype calls are based on relative intensity of the fluorescent tags conjugated to the wildtype and ALVE integration specific primers, with each dot representing a single chicken DNA sample. Red points (top left) represent individuals homozygous for the ALVE integration, blue points (bottom right) for individuals homozygous for the wildtype allele, and green points (top right) are heterozygotes. Black points are sample negative controls and pink points are ambiguous samples either due to their location outside genotype clusters, or their relative fluorescence positions at earlier cycle stages. Three plots are shown as examples, with all twenty in Fig. S4. ALVE3 shows high numbers of individuals in all three genotypes. ALVE-TYR is fixed in both WPR lines and absent in all WLs and the RIR (hence no heterozygotes). Homozygous individuals for ALVE_ros003 were rare, so genotype confidence was derived by pooling data from multiple generations (not shown)