Characterization of Transcriptome-associated SNPs in the Chicken

Single nucleotide polymorphisms (SNP) are the most frequent type of genomic variation, accounting for phenotypic variation and disease susceptibility. A major area of SNP research is to understand their effect on gene expression. Leveraging on publicly available resources, a robust bioinformatics methodology for the identification and characterization of gene-associated SNPs is being constructed using high-throughput next generation sequencing data. The methodology consists of trimming, genome alignment, variant detection, and variant annotation and gene effect prediction. The resulting variants were filtered based on impact; causative and high impact SNPs were functionally annotated and connected to underlying pathways. Quality control procedures were carried out at each step of the pipeline to ensure data integrity. This methodology is being used to evaluate allelic differences in the transcriptome of distinct chicken lines.