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Integrative Multi-Omics Analysis Identifies Novel Enhancer Variants on SSC2 Associated With Backfat Thickness in
Xigang Feng1,2, Xiuqi Zhou1, Hao Liang1
1Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.
Animal Genetics
|June 9, 2026
Summary
Researchers identified genetic variants influencing pig backfat thickness using genome-wide association studies. A specific haplotype (GG) in a regulatory region on chromosome 2 was linked to reduced backfat, offering potential for genetic improvement in Landrace pigs.
Area of Science:
- Animal Genetics
- Genomics
- Molecular Biology
Background:
- Backfat thickness is crucial for pig production economics.
- Understanding the genetic basis of backfat thickness is vital for breeding programs.
- Previous research has not fully identified functional regulatory variants for backfat thickness.
Purpose of the Study:
- To identify and characterize functional regulatory variants associated with backfat thickness in Landrace pigs.
- To elucidate the regulatory architecture of identified quantitative trait loci (QTLs).
- To provide molecular markers for enhancing pig breeding for reduced backfat.
Main Methods:
- Genome-wide association study (GWAS) in a large Landrace pig population (n=5923).
- Integration of multi-omics data, including Hi-C, epigenomic marks, and enhancer/promoter annotations.
- Prioritization of functional non-coding variants and haplotype analysis.
- Dual-luciferase reporter assays to validate regulatory activity.
Main Results:
- Two significant QTLs for backfat thickness were identified on SSC2 and SSC12.
- The SSC2 QTL acts as a regulatory hub with multiple enhancer-promoter interactions.
- Two linked SNPs on SSC2 define haplotypes; the GG haplotype shows higher transcriptional activity and is associated with lower backfat thickness.
- The SSC12 QTL also exhibits long-range interactions with candidate genes.
Conclusions:
- The study decodes the regulatory mechanisms of two major backfat QTLs.
- Identified functional variants and regulatory elements provide insights into backfat deposition.
- The GG haplotype represents a valuable molecular marker for genetic selection to improve backfat traits in Landrace pigs.
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