Accuracy of Single Nucleotide Polymorphism Detection from Transcriptome Sequencing Data in Dairy Cattle
Transcriptome sequencing(RNA-Seq)can not only reveal gene expression profiles but also detect nucleotide polymorphisms in genes,making it an effective strategy for exploring functional mutations in protein-coding genes of dairy cows.In this study,we performed whole-genome sequencing(DNA-Seq)and transcriptome sequencing(RNA-Seq)on 20 Chinese Holstein cows.Using the SNPs detected by DNA-Seq as reference,we evaluated the accuracy of gene polymorphism detection based on RNA-Seq and its influencing factors.Results showed that the SNP consistency between DNA-Seq and RNA-Seq in the same individual ranged from 0.65 to 0.75,while the consistency between different individuals varied from 0.28 to 0.42.By optimizing the filtering parameters criteria for SNP detection in RNA-Seq,including SnpCluster,homopolymer,sequencing depth(DP＜5),and allele frequency(P＜0.13),the proportion of high-accuracy SNPs detected increased from 71.07％to 95.27％.Finally,through functional annotation,we identified a start codon mutation(BTA10:25435325 T/A)in the E1BHN1 gene on chromosome 10,which led to a change in the immunoglobulin domain-like protein from a heterotetramer to a heterodimer.This mutation might be a recessive lethal mutation.
万方数据
维普
