SMARTER-database: a tool to integrate SNP array datasets for sheep and goat breeds.

Area of Science:

• Animal genetics
• Genomics
• Bioinformatics

Background:

• Underutilized sheep and goat breeds possess unique genetic adaptations to challenging environments.
• Integrating diverse genomic datasets is crucial for analyzing genetic diversity but is hindered by data inconsistencies.
• Standardization is needed to harmonize SNP chip array data from global small ruminant populations.

Purpose of the Study:

• To present the SMARTER-database, a suite of tools and scripts for standardizing genomic data and metadata.
• To facilitate reproducible genetic diversity analyses in sheep and goats.
• To support research on livestock adaptation and promote animal genetic resources sustainability.

Main Methods:

• Developed a collection of tools and scripts to standardize genomic data and metadata.
• Harmonized genotype data for approximately 12,000 sheep and 6,000 goats to a uniform coding and assembly version.
• Implemented data access via File Transfer Protocol and a web interface for metadata interaction.

Main Results:

• The SMARTER-database provides standardized genotype data for a large cohort of sheep and goats.
• Metadata is accessible through a web interface and custom scripts, allowing efficient sample filtering.
• The database focuses on SNP chip array data from global small ruminant populations.

Conclusions:

• The SMARTER-database empowers researchers by providing harmonized genomic data and metadata.
• Facilitates in-depth analyses of genetic diversity and adaptation in small ruminants.
• Contributes to the sustainable management of livestock genetic resources.