Optimal sequencing depth design for whole genome re-sequencing in pigs

Area of Science:

• Genomics
• Animal Genetics
• Bioinformatics

Background:

• Whole-genome sequencing (WGS) is increasingly common, necessitating cost-effective strategies.
• Optimal sequencing depth for pig WGS regarding coverage, variant discovery, and accuracy remains unclear.

Purpose of the Study:

• To determine the ideal sequencing depth for pig WGS.
• To evaluate the impact of sequencing depth on genome coverage, variant discovery power, and genotyping accuracy.

Main Methods:

• Sequenced three Yorkshire boars at ~20X depth.
• Downloaded ~20X WGS data for Duroc and Landrace pigs.
• Downsampled data to simulate various sequencing depths (1X to 22X).
• Compared single-sample and multi-sample variant calling algorithms using SNP chip data for validation.

Main Results:

• 10X sequencing depth achieves >99% genome coverage and optimal variant discovery.
• Sequencing depth below 4X significantly increases false-positive variants and reduces genome coverage to 95%.
• Multi-sample calling is more sensitive than single-sample calling, especially at lower depths, but yields more false positives.

Conclusions:

• 10X sequencing depth is recommended as a practical standard for pig WGS.
• Findings aid in designing cost-effective WGS studies with sufficient power.
• Understanding depth-dependent accuracy is crucial for genomic research under budget constraints.