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). Table and figure legends: Table S1. Statistical report of paired Illumina short read sequences of the additional 21 Holstein samples for genotyping with the Genome Analysis Toolkit. 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. Table S2.List of SVs identified in the criticial region of BTA18 in ONT sequences Table S3 List of DMR between HCE vs LCE HF samples that were identified using methylKit R package. Table S4 List of DMR between HCE vs LCE HF samples that were identified using chi-squared test as implemented in SeqMonk tool. Supplemental Figure S1. 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. Supplemental Figure S2. 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. 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). Supplemental Figure S3. 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). Supplemental Figure S4 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). Supplemental Figure S5 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. Supplemental Figure S6 The screenshot of the Jbrowser view of the deletion identified on BTA18 between 58,083 ,874–58 ,084 ,465 in HF animals.

本数据集包含论文《荷斯坦奶牛18号常染色体上产犊性状的数量性状基因座（Quantitative trait loci, QTL）嵌入复杂基因组区域》（doi: https://doi.org/10.3168/jds.2021-21625）的补充材料。以下为表格与图例说明：
1. 表S1：额外21份荷斯坦样本用于基因组分析工具包（Genome Analysis Toolkit, GATK）进行基因分型的配对Illumina短读长序列统计报告。该序列数据已提交至美国国家生物技术信息中心（National Center for Biotechnology Information, NCBI）生物项目（BioProject）数据库，可通过对应生物项目编号获取相关序列。后续将Illumina序列比对至ARS-UCD1.2参考基因组。
2. 表S2：在牛津纳米孔（Oxford Nanopore Technologies, ONT）测序得到的BTA18关键区域中鉴定到的结构变异（Structural Variants, SV）列表。
3. 表S3：使用methylKit R包鉴定得到的高产犊效率（High Calving Ease, HCE）与低产犊效率（Low Calving Ease, LCE）荷斯坦奶牛样本间的差异甲基化区域（Differentially Methylated Regions, DMR）列表。
4. 表S4：使用SeqMonk工具内置的卡方检验鉴定得到的HCE与LCE荷斯坦奶牛样本间的差异甲基化区域列表。
补充图S1：荷斯坦奶牛ONT测序样本中16 Kb缺失区域的整合基因组查看器（Integrative Genomics Viewer, IGV）截图。该图展示了BTA18上58,687,825–59,088,183 bp区间的染色体区段，涉及样本包括：杂合子荷斯坦奶牛DHFnano01（a）、DHFnano02（b），携带与父本产犊易发性相关纯合单倍型的公牛DHFnano03（c），其纯合单倍型与致病单倍型无关联的公牛DHFnano04（d），以及DHFnano01与DHFnano02的混合序列（e）。所有图示均展示了16,000 bp的无读段检测区域，该16 Kb缺失区间分别为：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，e) 58,846,131–58,861,709 bp。该16 Kb缺失区域位于QTL 95%置信区间（58,343,346–59,432,662 bp）内，并包含似然比检验（Likelihood Ratio Test, LRT）峰值位点58,860,538 bp。
补充图S2：卡林顿金发牛（Kärntner Blondvieh）（a）与弗莱维赫公牛（b）的ONT测序序列在BTA18上58,687,825–59,088,183 bp区间的IGV截图。两个样本均显示存在16,000 bp的无读段比对染色体区段，此前在荷斯坦样本中已检测到类似缺失（补充图S1）。该16 Kb缺失区间在(a)中为58,846,128–58,861,709 bp，在(b)中为58,846,252–58,861,709 bp。
补充图S3：荷斯坦公牛ERR2694948（a）、海福特母牛SRR8324584（b）与婆罗门瘤牛公牛SRR2016745（c）的Illumina测序序列在BTA18上58,687,825–59,088,183 bp区间的IGV截图。与ONT测序序列（补充图S1、S2）一致，Illumina序列中同样检测到16 Kb的无读段比对区段，该缺失区间分别为：a) 58,841,246–58,867,378 bp，b) 58,839,907–58,867,289 bp，c) 58,839,330–58,868,903 bp。
补充图S4：使用UOA_Angus_1组装版本进行序列比对的IGV截图。四张截图均展示了杂合子奶牛DHFnano01（a、b）与DHFnano02（c、d）比对至安格斯参考基因组的结果。上方两张图（a、c）展示了6.49–6.720 Mbp区间，包含原ARS-UCD1.2组装中16 Kb缺失区域的转换位置：6,496,595–6,714,292 bp（蓝色方框标注）。下方两张图（b、d）展示了6.714–6.720 Mbp区间，其中存在一段由无读段比对标记的类似缺失区段，区间为6,716,809–6,717,310 bp。该特殊区域与ARS-UCD1.2组装中16 Kb缺失区域对应的区段仅相距2,517 bp，但长度仅为501 bp，显著更短。
补充图S5：ARS-UCD1.2组装版本中18号染色体上的片段重复（Segmental Duplications, SD）分布情况。a) 全BTA18染色体上片段重复的环形可视化图：环内曲线代表检测到的片段重复，曲线的起止点对应重复序列的位置。在染色体末端及58–60 Mbp区间内，片段重复的数量显著高于染色体其余区域。红色曲线代表位于QTL 95%置信区间（58,343,346–59,432,662 bp）内的片段重复。b) BTA18上55 Mbp至60 Mbp区间的放大图：红色曲线代表QTL 95%置信区间内的片段重复，蓝色条带代表该区域内的基因转录本。
补充图S6：荷斯坦奶牛中BTA18上58,083,874–58,084,465 bp区间内缺失变异的Jbrowser视图截图。