The objectives of this study were to provide the buffalo research community with an updated SNP map for the Axiom Buffalo Genotyping (ABG) array with genomic positions for SNP currently unmapped and to map all cattle QTL from the CattleQTLdb onto the buffalo reference assembly. To update the ABG array map, all SNP probe sequences from the ABG array were re-aligned against the UOA_WB_1 assembly. With the new map, the number of mapped markers increased by approximately 10% and went from 106 778 to 116 708, which reduced the average marker spacing by approximately 2 kb. A comparison of results between signatures of autozygosity study using the ABG and the new map showed that, when the additional markers were used there was an increase in the autozygosity peaks and additional peaks in BBU5 and BBU11 could be identified. After sequence alignment and quality control, 64 650 (UMD3.1) and 76 530 (ARS_UCD1.2) cattle QTL were mapped onto the buffalo genome. The mapping of the bovine QTL database onto the buffalo genome should be useful for genome-wide association studies in buffalo and, given the high homology between the two species, the positions of cattle QTL on the buffalo genome can serve as a stepping stone towards a water buffalo QTL database.

中文翻译：

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更新的 Axiom 水牛基因分型阵列图和牛数量性状基因座到新水牛参考基因组组装图

本研究的目的是为水牛研究界提供 Axiom Buffalo 基因分型 (ABG) 阵列的更新 SNP 图，其中 SNP 的基因组位置目前未映射，并绘制来自CattleQTLdb 的所有牛 QTL到水牛参考组件上。为了更新 ABG 阵列图，来自 ABG 阵列的所有 SNP 探针序列都针对 UOA_WB_1 组件重新对齐。使用新地图，映射标记的数量增加了大约 10%，从 106 778 个增加到 116 708 个，这将平均标记间距减少了大约 2 kb。使用 ABG 和新图谱的自体结合研究特征之间的比较结果表明，当使用额外的标记时，自体峰增加，并且可以识别出 BBU5 和 BBU11 中的额外峰。经过序列比对和质量控制，64 650（UMD3.1）和76 530（ARS_UCD1.2）牛QTL被定位到水牛基因组上。将牛 QTL 数据库映射到水牛基因组上应该有助于水牛的全基因组关联研究，