Copy Number Variations Contribute to Intramuscular Fat Content Differences by Affecting the Expression of PELP1 Alternative Splices in Pigs

Abstract

Intramuscular fat (IMF) is a key meat quality trait. Research on the genetic mechanisms of IMF decomposition is valuable for both pork quality improvement and the treatment of obesity and type 2 diabetes. Copy number variations (CNVs) are a type of variant that may influence meat quality. In this study, a total of 1185 CNV regions (CNVRs) including 393 duplicated CNVRs, 432 deleted CNVRs, and 361 CNVRs with both duplicated and deleted status were identified in a pig F2 resource population using next-generation sequencing data. A genome-wide association study (GWAS) was then performed between CNVs and IMF, and a total of 19 CNVRs were found to be significantly associated with IMF. QTL colocation analysis indicated that 3 of the 19 CNVRs overlapped with known QTLs. RNA-seq and qPCR validation results indicated that CNV150, which is located on the 3′UTR end of the proline, as well as glutamate and the leucine rich protein 1 (PELP1) gene may affect the expression of PELP1 alternative splices. Sequence alignment and Alphafold2 structure prediction results indicated that the two alternative splices of PELP1 have a 23 AA sequence variation and a helix-fold structure variation. This region is located in the region of interaction between PELP1 and other proteins which have been reported to be significantly associated with fat deposition or insulin resistance. We infer that the CNVR may influence IMF content by regulating the alternative splicing of the PELP1 gene and ultimately affects the structure of the PELP1 protein. In conclusion, we found some CNVRs, especially CNV150, located in PELP1 that affect IMF. These findings suggest a novel mechanistic approach for meat quality improvement in animals and the potential treatment of insulin resistance in human beings.

Integration of ATAC-seq and RNA-seq analysis identifies key genes affecting intramuscular fat content in pigs

“…IMF content is a complex trait with moderate heritability (0.2–0.4) ( 3 ), and is regulated by multiple genes. In recent years, with the development of high-throughput sequencing and bioinformatics, an increasing number of studies have aimed to clarify the molecular mechanism involved in IMF trait.…”

“…To date, 890 QTLs related to IMF content have been identified and deposited in PigQTLdb (Release 47, Apr 25, 2022 1 ). Multiple candidate genes related to IMF content were identified in the pig, such as H-FABP ( 4 ), PLIN1 ( 1 ), PPAR γ ( 5 ), TCF7L2 ( 6 ) and PELP1 ( 3 ). However, whether these are the key genes affecting IMF content remains ambiguous.…”

Identification of Candidate Genes for Min Pig Villi Hair Traits by Genome-Wide Association of Copy Number Variation

“…After next-generation sequencing of the population, we used CNVcaller software (version 0.11) to investigate and to genotype all individual CNVs. All the details of resequencing, CNV calling, and genotyping were the same as described in the study of Wei et al [ 10 ].…”