Characterizing structural variants based on graph-genotyping provides insights into pig domestication and local...

Area of Science:

• Genomics
• Animal Genetics
• Evolutionary Biology

Background:

• Structural variants (SVs), including deletions (DELs) and insertions (INSs), are key drivers of genetic diversity and phenotypic variation in domestic pigs.
• Understanding the impact of SVs is crucial for pig domestication and adaptation studies.

Purpose of the Study:

• To map and re-genotype structural variants across a large cohort of pig genomes.
• To investigate the role of SVs in pig domestication, local adaptation, and trait variation.
• To identify specific SVs and associated genes influencing economically important traits like meat quality.

Main Methods:

• Utilized a library of SVs from long-read and short-read sequencing data.
• Employed a graph-based method for SV re-genotyping in 402 pig genomes.
• Analyzed population-stratified SVs for their effects on gene transcription and regulatory elements.

Main Results:

• Successfully mapped numerous pig genomic SVs using a graph-based approach.
• Identified population-stratified SVs potentially altering gene transcription via regulatory elements.
• Discovered two deletions (296-bp DEL, chr7; 278-bp DEL, chr18) in muscle enhancers linked to meat quality (FSD2) and muscle fiber genes (LMOD2, WASL).

Conclusions:

• Structural variants play a significant role in the evolution of domestic pigs.
• Identified SVs and candidate genes provide valuable resources for pig genomic research and breeding programs.
• Functional characterization of SVs offers insights into genetic improvement for traits like meat quality.