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. 2019 Nov 14;10:1032. doi: 10.3389/fgene.2019.01032

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Copyright © 2019 Freem, Summers, Gheyas, Psifidi, Boulton, MacCallum, Harne, O’Dell, Bush and Hume

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Analysis of genomic sequences of founder layer and broiler birds. Genomic DNA sequences obtained from the 27 commercial broiler and transgenic layer birds used as founders in the inbreeding experiments were analyzed as shown in Panel (A). Panel (B) shows a PCA based upon a 13.4M filtered SNV panel derived from the variant call files for the set of birds sequenced. Note the first principle component (PC) separates the layers (left) and the broilers (right). The second PC identifies substantial variation within the two populations with the greatest variation in the layers. Panel (C) shows a PCA based solely upon SNVs identified within the members of the IRF gene family (See Table S6 ). Note that PC1 again separates broilers and layers, whereas PC2 identifies substantial variation within breed type.