An updated Axiom buffalo genotyping array map and mapping of cattle quantitative trait loci to the new water buffalo reference genome assembly - Supplementary material

Supplementary material from the paper "An updated Axiom buffalo genotyping array map and mapping of cattle quantitative trait loci to the new water buffalo reference genome assembly" accepted by Animal Genetics. SUMMARY - 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.

本内容为发表于《Animal Genetics》的论文《更新后的Axiom水牛基因分型阵列图谱及将牛数量性状位点定位至新型水牛参考基因组组装序列》的补充材料。

研究概要：本研究旨在为水牛研究学界提供更新后的Axiom水牛基因分型（Axiom Buffalo Genotyping, ABG）阵列单核苷酸多态性（Single Nucleotide Polymorphism, SNP）图谱，为当前尚未完成基因组定位的SNP赋予准确位置，并将牛数量性状位点（Quantitative Trait Locus, QTL）数据库（CattleQTLdb）中的全部牛QTL定位至水牛参考基因组组装序列中。为更新ABG阵列图谱，本研究将ABG阵列的所有SNP探针序列重新比对至UOA_WB_1组装序列。新图谱使已定位标记的数量提升约10%，从106778个增至116708个，平均标记间距缩短约2kb。使用ABG阵列及新图谱开展的自体合性特征分析结果对比显示，引入新增标记后，自体合性峰的数量有所增加，且可在BBU5与BBU11染色体上识别出额外的峰。经序列比对与质量控制后，共计64650个（UMD3.1版本）与76530个（ARS_UCD1.2版本）牛QTL被定位至水牛基因组。将牛QTL数据库定位至水牛基因组的研究结果，可为水牛全基因组关联分析提供助力；鉴于两个物种间存在高度同源性，牛QTL在水牛基因组上的定位结果可作为构建水牛QTL数据库的基础。