Department of Animal Science, College of Agriculture & Natural Resources, Razi University, 67346-67149, Kermanshah, Iran.
Animal Science Research Institute of IRAN (ASRI), Agricultural Research, Education & Extension Organization (AREEO), Karaj 3146618361, Iran.
An Acad Bras Cienc. 2021 May 10;93(3):e20191453. doi: 10.1590/0001-3765202120191453. eCollection 2021.
In the current study, allele specific expression analysis was performed in two subspecies cows (Bos taurus and Bos indicus) at SNP and gene levels. RNA-Seq data of 21,078,477 and 20940063 paired end reads from pooling of whole blood samples (Leukocyte) from 40 US Holstein (Bos Taurus) and 45 Cholistani cows (Bos indicus) obtained from SRA database in NCBI. Quality control and trimming of row RNA-Seq data were processed by FASTQC and Trimmomatic softwares. The transcriptome was assembled by TopHat2 software in two cow's population by aligning and mapping the RNA-Seq reads on bovine reference genome. The SNPs were discovered by Samtools software and ASE analysis was performed by Chi-square test. Results showed that 50183 and 137954 SNPs were discovered on the assembled transcriptome of Holstein and Cholistani cow samples, respectively, and 15308 SNPs were common in both breeds. 10158 SNPs from 50183 (20%) in Holstein and 31523 SNPs from 137954 (23%) in Cholistani cows were identified as ASE-SNPs. Reference allele and alternative allele count in Holstein and Cholistani cows were 3041 and 7155, respectively. Among 131 discovered SNPs in 41 genes with different expression in Holstein and Cholistani cows, 31 ASE-SNPs (5 in Holstein; 26 in Cholistani cows) were discovered.
在当前的研究中，在牛的两个亚种（Bos taurus 和 Bos indicus）中在 SNP 和基因水平上进行了等位基因特异性表达分析。从 SRA 数据库中获得的来自 40 头美国荷斯坦牛（Bos Taurus）和 45 头 Cholistani 牛（Bos indicus）的全血样本（白细胞）的 RNA-Seq 数据，每个样本的 21078477 和 20940063 对端读取数据进行了质量控制和修剪。使用 FASTQC 和 Trimmomatic 软件处理 RNA-Seq 数据的行质量控制和修剪。通过将 RNA-Seq 读取比对和映射到牛参考基因组，使用 TopHat2 软件在两个牛种群中组装转录组。使用 Samtools 软件发现 SNPs，并通过卡方检验进行 ASE 分析。结果表明，在荷斯坦牛和 Cholistani 牛样本的组装转录组中分别发现了 50183 和 137954 个 SNPs，在两个品种中共有 15308 个 SNPs。在荷斯坦牛中，从 50183 个 SNP 中（20%）鉴定出 10158 个 ASE-SNPs，在 Cholistani 牛中，从 137954 个 SNP 中（23%）鉴定出 31523 个 ASE-SNPs。荷斯坦牛和 Cholistani 牛的参考等位基因和替代等位基因计数分别为 3041 和 7155。在荷斯坦牛和 Cholistani 牛中差异表达的 41 个基因中有 131 个发现了 SNPs，其中 31 个 ASE-SNPs（荷斯坦牛 5 个；Cholistani 牛 26 个）被发现。
