Figure 3

aCGH and SQF-PCR results for CNVRs nos. 25 (A), 61-62 (B), and 90 (C). For each CNVR, results were reported for three goats indicated at the top in the correspondence of the related charts and images (C1 = Camosciata delle Alpi, animal no. 1; G1 = Girgentana, animal no. 1; G2 = Girgentana, animal no. 2; MG1 = Murciano-Granadina, animal no. 1; S1 = Saanen, animal no. 1; S3 = Saanen, animal no. 3). For the aCGH experiment, images have been reported for i) log₂ ratio plot of original data, ii) log₂ ratio plot of summary data (pointwise averaging of all computed profiles), iii) heatmap of log₂ ratios for original, smoothed/segmented, and summary data, and iv) maps of gains/losses for smoothed/segmented and summary data (gain is indicated in orange, loss is indicated in green). Red arrows indicate regions of copy gain. Smoothed/segmented data were obtained with several algorithms (Lowess, Wavelet, Quantreg, ruavg, CBS, CGHseg, BioHMM, cghFLasso, GLAD, and FASeg) averaged in the summary data [77].. Semiquantitative fluorescent multiplex PCR (SQF-PCR) electropherograms for fragments of three CNVRs are superimposed on that of the reference Camosciata delle Alpi goat after normalization against the control MC1R amplicon. Results obtained using DGAT1 for normalization are overlapping with those obtained with MC1R and for this reason are not reported.