Using singleton densities to detect recent selection in Bos taurus

Area of Science:

• Population Genetics
• Genomics
• Animal Breeding

Background:

• Polygenic selection involves simultaneous changes in multiple genomic regions affecting quantitative traits.
• Advances in genomics and statistical methods facilitate the detection of recent selection events.
• Understanding selection is crucial for livestock improvement and conservation.

Purpose of the Study:

• To detect recent polygenic selection in the Holstein cattle breed (Bos taurus) using the Singleton Density Score (SDS).
• To identify candidate genes under recent selection.
• To evaluate the impact of population history on selection detection methods.

Main Methods:

• Application of the Singleton Density Score (SDS) method to Holstein cattle genomic data.
• Analysis of allele frequency changes over approximately the last 740 years.
• Simulations to assess the power of SDS methods in the context of population bottlenecks.

Main Results:

• Several candidate genes were identified as targets of recent selection, including those involved in cell regulation, catabolic processes, neural-cell adhesion, and immunity.
• No strong evidence for directional selection was found for milk protein content, milk fat content, or stature.
• Simulations indicated that a recent population bottleneck in Bos taurus reduces the power of SDS methods due to singleton depletion.

Conclusions:

• The study identifies specific genes underlying recent genetic changes in Holstein cattle.
• The findings highlight the importance of considering population history when investigating polygenic selection.
• Results provide insights into optimizing future studies of polygenic selection in livestock.