Multi-omics analysis

GALLO 2.0: A toolkit for functional prioritization of positional candidate genes

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Abstract

The Genomic Annotation in Livestock for positional candidate LOci (GALLO) is an R package designed to provide an automatized and a straightforward environment for gene and quantitative trait loci (QTL) annotation. Currently, GALLO was downloaded more than 46,000 times from its official CRAN repository and the original published manuscript has been cited more than 200 times (since December 2020). Here, we present GALLO 2.0, the most substantial update since its original publication. The new version includes five major functionalities: 1) pleiotropic effect identification through multi-trait metanalysis; 2) estimation of the effective number of markers and independent segments within a chromosome; 3) gene-level p-value estimations based on squared cumulative normal distribution of the p-values mapped within a gene and the integration of eigenvalue obtained from linkage disequilibrium matrices of the respective single nucleotide polymorphisms; 4) network analysis for the representation of interaction between gene/markers and additional information, such as enriched QTL, Gene Ontology (GO) terms and metabolic pathways; 5) prioritization of functional candidate genes based on network-based machine learning (ML) models. This update has the potential to improve the detection of hidden patterns across datasets, facilitate data mining of previously reported associations, and improve efficiency in examining the genetic architecture of complex traits in livestock through the integration of results obtained in multi-omics studies. In particular, the network-based ML pipeline adds news possibilities of data integration by allowing users to combine the gene-level p-values with functional information from -OMICs studies and/or QTL, GO terms and metabolic pathway enrichment analysis through representative learning, and to estimate posterior probabilities of association between positional candidate genes and target phenotypes. In this context, GALLO 2.0 provides a comprehensive, end-to-end framework that delivers interpretable, decision-ready gene prioritizations, facilitating the identification of hidden biological patterns and the genetic characterization of key livestock traits.

Keywords: 2026

How to Cite:

Fonseca, P., Suárez-Vega, A. & Cánovas, Á., (2026) “GALLO 2.0: A toolkit for functional prioritization of positional candidate genes”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2273104. doi: https://doi.org/10.31274/wcgalp.23415

Rights: 1