Journal
GIGASCIENCE
Volume 9, Issue 12, Pages -Publisher
OXFORD UNIV PRESS
DOI: 10.1093/gigascience/giaa149
Keywords
multi-omics integration; QTL annotation; gene annotation; data mining; QTL enrichment analysis; livestock
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Funding
- Sustainable Beef and Forage Science Cluster - Canadian Beef Cattle Check-Off [FDE.13.17]
- Beef Cattle Research Council
- Alberta Beef Producers
- Alberta Cattle Feeders' Association
- Beef Farmers of Ontario
- La Federation des Productuers de bovins du Quebec
- Agriculture and Agri-Food Canada's Canadian Agricultural Partnership
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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.
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