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Pipeline publication

[…] Approximately 82.15% of the identified novel variants were considered sequence modifiers; the remaining (~17,85%) were inferred to produce high impact (2.52%), moderate impact (7.42%) or low impact (7.91%) changes in the corresponding transcriptional unit (Fig. ).Fig. 2 , Considering that the variants found within QTL regions may have been a consequence of selective pressures related to dairy production traits, we performed a functional enrichment analysis of the genes containing the variants with high and moderate functional impacts. For this analysis, we considered the variants that were classified as high and moderate impact variants (Fig. ) by the two annotation software programs used, SnpEff [] and VEP []. However, based on the large number of moderate missense variants identified by both programs (Fig. ), we performed additional filtering to consider only the missense mutations predicted to be deleterious by SIFT [], an external tool implemented in the VEP software that predicts the effects of an amino acid substitution on protein function. Hence, after discarding those variants predicted to be tolerated, a final total of 371 unique genes containing relevant functional variants (Additional file ) were used to perform a functional enrichment analysis using the WEB-based Gene SeT AnaLysis Toolkit (WebGestalt) []. These genes were categorized by 14 enriched KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway terms (p adj < 0.05) (Additional file ). The highest enriched KEGG pathway was “protein processing in endoplasmic reticulum” with a p adj of 2.60e-05. Metabolic processes in endoplasmic reticulum (ER) are associated with the synthesis and folding of membrane and secretory proteins as well as lipid synthesis. Under certain stress conditions (such as high levels of carbon-based molecules, free fatty acids, cytokines, and hypoxia), the accumulation of unfolded/misfolded proteins activates the ER stress signaling response [, ]. The mammary gland faces high metabolic stress during […]

Pipeline specifications

Software tools SnpEff, VEP, WebGestalt