Quantitative trait locus for calving traits on Bos taurus autosome 18 in Holstein cattle is embedded in a complex genomic region

The dataset contains the supplementary materials of the paper "Quantitative trait loci for calving traits on Bos taurus autosome 18 in Holstein cattle are embedded in a complex genomic region" (doi: https://doi.org/10.3168/jds.2021-21625). <br> <strong>Table and figure legends</strong>: <strong>Table S1.</strong> Statistical report of paired Illumina short read sequences of the additional 21 Holstein samples for genotyping with the <em>Genome Analysis Toolkit. </em>The sequence data have been deposited with links to the following bio-project numbers in the NCBI BioProject database. The Illumina sequences were then mapped to the ARS-UCD1.2 reference genome. <strong>Table S2</strong>.List of SVs identified in the criticial region of BTA18 in ONT sequences <strong>Table S3 </strong> List of DMR between HCE vs LCE HF samples that were identified using methylKit R package. <strong>Table S4</strong> List of DMR between HCE vs LCE HF samples that were identified using chi-squared test as implemented in SeqMonk tool. <strong>Supplemental Figure S1. </strong>Integrative Genomics Viewer (IGV) screenshots of the 16-Kb gap in the ONT sequenced Holstein samples. The figure shows the chromosomal section from 58,687,825 – 59,088,183 bp on BTA18 from the samples of the heterozygous HF cows DHFnano01 (a) and DHFnano02 (b), the bull DHFnano03, which has the homozygous haplotype associated with paternal calving ease (c), the bull DHFnano04, whose homozygous haplotype has nothing in common with the causal haplotype (d) and the combined sequence of DHFnano01/02 (e). All figures illustrate a region of 16,000 bp, where no read could be detected. This 16-Kb gap ranged from a) 58,846,131 - 58,861,709 bp, b) 58,846,130 – 58,861,709 bp, c) 58,845,714 – 58,861,715 bp, d) 58,846,129 – 58,861,715 bp and e) 58,846,131 – 58,861,709 bp. The 16-Kb gap was detected within the confidence interval of the QTL from 58,343,346 – 59,432,662 bp and included the LRT-peak position at 58,860,538 bp. <strong>Supplemental Figure S2. </strong>Integrative Genomics Viewer screenshots of the ONT sequences of the Kärntner Blondvieh (a) and the Fleckvieh bull (b) from 58,687,825 – 59,088,183 bp on BTA18<em>. </em>Both samples show a chromosomal segment of 16,000 bp, where no read could be aligned. A comparable gap was previously detected in the Holstein samples (Supplemental Figure S1). The 16-Kb gap ranged from 58,846,128 – 58,861,709 bp in (a) and from 58,846,252 – 58,861,709 bp in (b). <strong>Supplemental Figure S3. </strong>Integrative Genomics Viewer screenshots of the Illumina sequences of the Holstein bull ERR2694948 (a), the Hereford dam SRR8324584 (b) and the Brahman Zebu bull SRR2016745 (c) from 58,687,825 – 59,088,183 bp on BTA18. As in the ONT sequences (Supplemental Figure S1 and S2), a chromosomal segment of 16 Kb was detected in the Illumina sequences where no read was mapped. This 16-Kb gap ranged from 58,841,246 – 58,867,378 bp (a), 58,839,907 – 58,867,289 bp (b) and 58,839,330 – 58,868,903 bp (c). <strong>Supplemental Figure S4</strong> IGV screenshots of the alignment using the UOA_Angus_1 assembly. All four screenshots illustrate the alignment of the two heterozygous cows DHFnano01 (a and b) and DHFnano02 (c and d) to the Angus reference. The two upper figures (a and c) displayed the region from 6.49 – 6.720 Mbp and contained the converted position of the 16- Kb gap from 6,496,595 – 6,714,292 bp (highlighted in blue boxes), previously located in the ARS-UCD1.2 (Figure 2). The two bottom figures (b and d) signify the region from 6.714 – 6.720 Mbp including a comparable gap marked by missing reads from 6,716,809 – 6,717,310 bp. This special region was only 2,517 bp away from the region corresponding to 16-Kb gap in ARS-UCD1.2 assembly, but essentially smaller (501 bp). <strong>Supplemental Figure S5</strong> Distribution of the segmental duplications (SD) on chromosome 18 in the ARS-UCD1.2 assembly. a) Circular representation of the SDs across the entire BTA 18. The curves within the circle marks the detected SD, where at each curve the start- and endpoint constitute the positions of the corresponding duplication. At the distal end of the chromosome and in the region between 58-60 Mbp an increased number of SD compared to the residual chromosome. The red curves represent SD within the CI95% of the QTL (58,343,346 – 59,432,662 bp). b) zoom-in plot of the region between 55 Mbp and 60 Mbp on BTA18; the red curves represent SDs within he CI95% of the QTL, while blue bar represents the transcripts of the genes located in the region. <strong>Supplemental Figure S6</strong> The screenshot of the Jbrowser view of the deletion identified on BTA18 between 58,083 ,874–58 ,084 ,465 in HF animals. <br>