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Initial Screening of Extrachromosomal Circular DNA Candidates for Pork Meat Quality Traits Using Circle-Seq and RNA-Seq Analysis
by
, , , , and
Liyao Bai
1,2,
Jiahao Wu
1,
Tengfei Dou
1,2,
Donghui Chu
1,
Xinjian Li
3,
Xuelei Han
1,
Ruimin Qiao
1,
Kejun Wang
1,
Feng Yang
1 and
Xiuling Li
1,2,* 1
College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
2
Henan Xunxian Pig Science and Technology Backyard, Hebi 456250, China
3
Sanya Institute, Hainan Academy of Agricultural Science, Sanya 572025, China
*
Author to whom correspondence should be addressed.
Animals 2025, 15(11), 1590; https://doi.org/10.3390/ani15111590
Submission received: 6 March 2025
/
Revised: 20 May 2025
/
Accepted: 27 May 2025
/
Published: 29 May 2025
(This article belongs to the Section Pigs)
Simple Summary
The rising global demand for high-quality animal protein underscores the need for sustainable advancements in pork production. While meat quality traits are influenced by multiple genetic factors, their molecular regulatory mechanisms remain incompletely understood. Emerging evidence indicates that extrachromosomal circular DNA (eccDNA)—double-stranded circular DNA derived from chromosomal DNA—participates in muscle biology regulation, yet its functional relevance in swine remains uncharted. Here, we performed the first comprehensive analysis of eccDNA profiles in porcine longest dorsal muscle using Circle-seq technology, comparing two pig populations. Our preliminary analyses revealed significant differences in eccDNA abundance, size distribution patterns, and genomic locations. Through integrated RNA-seq analysis, we identified eccDNA-associated differentially expressed genes (eccDEGs) enriched in lipid metabolism pathways and uncovered potential regulatory networks linked to pork quality traits. These findings provide novel insights into the eccDNA-mediated genetic regulation of muscle development and offer new targets for breeding optimization.
Abstract
Yunong Black (YN) pigs and Yunong Black × Landrace (YL) hybrid pigs exhibit significant differences in meat quality characteristics. Studies have suggested that extrachromosomal circular DNA (eccDNA) may play a regulatory role in muscle development. In order to study the differences in eccDNA between two groups with different meat quality traits and their potential biological significance, this study used the Circle-seq method to detect eccDNA in the longest dorsal muscle (LDM) of Yunong Black pigs (YN) (n = 3) and Yunong Black × Landrace hybrid pigs (YL) (n = 3). EccDNA-related differentially expressed genes (eccDEGs) were then analyzed in combination with RNA-seq to explore the mechanisms by which eccDNA affects meat quality. The results showed that 1325 and 1304 differentially expressed eccDNAs were identified in the YN and YL groups, varying in size and distributed across multiple genomic functional regions. These eccDNAs were also annotated according to several protein-coding genes. Combined analysis with RNA-seq results revealed 19 and 27 eccDEGs in the YN and YL groups. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analysis enriched many lipid-related pathways, such as chemokine signals and ADP metabolic processes. By constructing a regulatory network, several potential regulatory networks that might be related to pork quality, for example, ecc_sus_8665/ssc-miR-212/ADAMTS16, were identified. In summary, we identified several potential eccDNAs that may regulate pig muscle, offering insights into the regulation of pig muscle traits for breeding.
