烟台黑猪SLA-DQA基因编码区多态性及生物信息学分析

Polymorphism and Bioinformatics Analysis of SLA-DQA Gene CDs in Yantai Black Pig

采用PCR-SSCP、克隆测序和生物信息学等方法对烟台黑猪SLA-DQA基因多态性进行研究,预测其蛋白质结构并分析其功能特征。结果显示:SLA-DQA基因exon 2、exon 3、exon 4分别检测出4种等位基因,5种基因型、6种等位基因,8种基因型、4种等位基因,7种基因型,包括3种新等位基因。SLA-DQA基因共编码255个氨基酸,编码区共发现32个核苷酸突变和13个氨基酸变异,exon 2多态性最为丰富。蛋白质结构预测结果显示二级结构中无规则卷曲和延伸链比例最高,α螺旋数量多且集中,β折叠最少。功能预测结果显示,SLA-DQA基因蛋白质在能量代谢、结构蛋白和生长因子等方面几率较高。本研究结果可为SLA-DQA基因在猪抗病分子育种中的应用提供理论依据。

The PCR-SSCP,cloning sequencing and bioinformatics methods were used to explore the Yantai black pig SLA-DQA gene coding polymorphisms,structural prediction and functional characteristics of the protein.The results showed that SLA-DQA gene exon 2,exon 3 and 4 were detected 4,6,4 alleles and 5,8,7 genotypes,respectively,and three new alleles were found for the first time. The SLA-DQA coding region encoded 255 amino acids,32 nucleotide mutations and 13 amino acid mutations were found,and exon 2 showed the most polymorphism.Protein prediction results showed that random coil and extended chain accounted for the highest level,alpha helix distribution concentrated,beta sheet appeared the least. The putative result of SLA-DQA gene protein function showed that the odds of energy metabolism,structural protein and growth factor were higher. These results could provide the theory foundation for the application of SLA-DQA gene to pig disease resistance molecular breeding.