GALLO: An R package for genomic annotation and integration of multiple data sources in livestock for positional candidate loci

Abstract

Background: The development of high-throughput sequencing and genotyping methodologies has enabled the identification of thousands of genomic regions associated with several complex traits. The integration of multiple sources of biological information is a crucial step required to better understand patterns regulating the development of these traits.

Findings: Genomic Annotation in Livestock for positional candidate LOci (GALLO) is an R package developed for the accurate annotation of genes and quantitative trait loci (QTLs) located in regions identified in common genomic analyses performed in livestock, such as genome-wide association studies and transcriptomics using RNA sequencing. Moreover, GALLO allows the graphical visualization of gene and QTL annotation results, data comparison among different grouping factors (e.g., methods, breeds, tissues, statistical models, studies), and QTL enrichment in different livestock species such as cattle, pigs, sheep, and chickens.

Conclusions: Consequently, GALLO is a useful package for annotation, identification of hidden patterns across datasets, and data mining previously reported associations, as well as the efficient examination of the genetic architecture of complex traits in livestock.

Keywords: QTL annotation; QTL enrichment analysis; data mining; gene annotation; livestock; multi-omics integration.