GALLO: An R package for Genomic Annotation and integration of multiple data source in livestock for positional candidate LOci

The development of high-throughput sequencing and genotyping methodologies allowed 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. 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, etc.), and QTL enrichment in different livestock species including cattle, pigs, sheep, and chickens, etc. Consequently, GALLO is a useful package for the annotation, identification of hidden patterns across datasets, datamining previously reported associations, as well as the efficient scrutinization of the genetic architecture of complex traits in livestock.

高通量测序与基因分型技术的发展，使研究者得以识别出与多种复杂性状相关的数千个基因组区域。整合多源生物学信息，是深入解析调控此类性状发育规律的关键环节。畜禽位置候选位点基因组注释工具（Genomic Annotation in Livestock for positional candidate LOci，GALLO）是一款专为精准注释畜禽常见基因组分析（如全基因组关联研究（Genome-Wide Association Studies）与基于RNA测序（RNA-Sequencing）的转录组学分析）所识别区域内的基因与数量性状位点（quantitative trait loci，QTLs）而开发的R语言软件包。此外，GALLO可实现基因与QTL注释结果的可视化绘图，支持针对不同分组因素（如分析方法、品种、组织、统计模型、研究等）开展数据对比，还可对牛、猪、绵羊、鸡等不同畜禽物种的QTL进行富集分析。综上，GALLO是一款实用的软件包，可用于基因与QTL注释、挖掘数据集内潜藏的规律、对已报道的关联信息开展数据挖掘，以及高效剖析畜禽复杂性状的遗传架构。