部分鸡种Brd2基因SNP和INDEL分析

Brd2(bromodomain containing protein 2)基因位于MHC(major histocompatibility complex)基因家族中,探究不同鸡种Brd2基因的SNP和Indel位点具有重要意义。试验选取我国26个优良的地方鸡种,对Brd2基因进行目标捕获测序,以NCBI中原鸡(Gallus gallus)的Brd2基因序列为参照,筛选出Brd2基因外显子和内含子中的SNP和Indel以及氨基酸的改变位点,最后制作进化树。在26个鸡种中,Brd2基因的外显子筛选出25个SNP位点,没有检测到Indel位点;内含子筛选出30个Indel位点,没有筛选出SNP位点;外显子中氨基酸仅有4个发生错义突变,其余均发生同义突变。从进化树看出,26个鸡种分为3大类:安卡鸡、雪山草鸡、文昌鸡、北京油鸡和萧山鸡类聚在一起;泰和乌骨鸡、SPF-来航鸡、河南斗鸡和广西黄鸡类聚在一起;剩余的鸡种类聚在一起,但同源性相对较低。在我国优质鸡种中Brd2基因具有一定的保守性,不同鸡种同源性较低。

SNP and INDEL analysis of Brd2 gene in indigenous chicken breeds

Inquiring the SNP and Indel loci of the Brd2 gene belonging to MHC family is of great significance. Capturing high throughput sequencing in Brd2 of 26 Chinese indigenous chicken breeds using Gallus gallus (National Center for Biotechnology Information) as a reference sequence, we screened SNP, Indel and amino acid sites and constructed an evolutionary tree. The results showed that 25 SNP loci and no Indel sites were found in the Brd2 expressed region, while 30 Indel sites and no SNP loci were screened out in the intron region of the 26 chicken breeds. Amino acids had only four missense mutations and the rest were of synonymous mutation. Phylogenetic tree showed that those chicken breeds could be divided into three categories. Anka chicken, Xueshancao chicken, Wenchang chicken, Beijing oil chicken and Xiaoshan chicken were clustered in one class, Taihe chicken, SPF- Leghorn chickens, Game fowl and Guangxi yellow chicken were categorized into another cluster, and the remaining chicken breeds were clustered into the third class that have a relatively low homology. Brd2 polymorphism is conservative but homology is low in indigenous chicken.