A large‐scale genome‐wide association analysis reveals QTL and candidate genes for intramuscular fat content in Duroc pigs

Zhuang, Zhanwei; Ding, Rongrong; Qiu, Yibin; Wu, Jie; Zhou, Shenping; Quan, Jianping; Zheng, Enqin; Li, Zhanbiao; Wu, Zhenfang; Yang, Jing

doi:10.1111/age.13069

Cited by 6 publications

(4 citation statements)

References 29 publications

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“…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.…”

Section: Introductionmentioning

confidence: 99%

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

Qiao

et al. 2022

Front. Nutr.

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Meat quality is one of the most important economic traits in pig breeding and production, and intramuscular fat (IMF) content is the major factor in improving meat quality. The IMF deposition in pigs is influenced by transcriptional regulation, which is dependent on chromatin accessibility. However, how chromatin accessibility plays a regulatory role in IMF deposition in pigs has not been reported. Xidu black is a composite pig breed with excellent meat quality, which is an ideal research object of this study. In this study, we used the assay for transposase-accessible chromatin using sequencing (ATAC-seq) and RNA sequencing (RNA-seq) analysis to identify the accessible chromatin regions and key genes affecting IMF content in Xidu black pig breed with extremely high and low IMF content. First, we identified 21,960 differential accessible chromatin peaks and 297 differentially expressed genes. The motif analysis of differential peaks revealed several potential cis-regulatory elements containing binding sites for transcription factors with potential roles in fat deposition, including Mef2c, CEBP, Fra1, and AP-1. Then, by integrating the ATAC-seq and RNA-seq analysis results, we found 47 genes in the extremely high IMF (IMF_H) group compared with the extremely low IMF (IMF_L) group. For these genes, we observed a significant positive correlation between the differential gene expression and differential ATAC-seq signal (r2 = 0.42). This suggests a causative relationship between chromatin remodeling and the resulting gene expression. We identified several candidate genes (PVALB, THRSP, HOXA9, EEPD1, HOXA10, and PDE4B) that might be associated with fat deposition. Through the PPI analysis, we found that PVALB gene was the top hub gene. In addition, some pathways that might regulate fat cell differentiation and lipid metabolism, such as the PI3K-Akt signaling pathway, MAPK signaling pathway, and calcium signaling pathway, were significantly enriched in the ATAC-seq and RNA-seq analysis. To the best of our knowledge, our study is the first to use ATAC-seq and RNA-seq to examine the mechanism of IMF deposition from a new perspective. Our results provide valuable information for understanding the regulation mechanism of IMF deposition and an important foundation for improving the quality of pork.

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Section: Introductionmentioning

confidence: 99%

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

Qiao

et al. 2022

Front. Nutr.

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“…Furthermore, on SSC12, the myosin heavy chain 3 ( MYH3 ) locus was displayed as a QTL for IMF in GWAS using the Large White × Minzhu F 2 , Landrace × KNP F 2 intercross, and Duroc × KNP F 2 intercross populations (Cho et al, 2019; Luo et al, 2012). However, two QTL (SSC7, 94.19–94.64 Mb; SSC14, 123.25–123.75 Mb) were newly identified as associated with IMF in Duroc pigs (Zhuang et al, 2021). Contrary to the above reports, two QTL signals for IMF were mapped on SSC13 and SSC15 by GWAS in Beijing Black pigs in this study.…”

Section: Discussionmentioning

confidence: 99%

“…On SSC15, previous research mapped the QTL for IMF in the region 25.45–25.97 Mb (Zhuang et al, 2021). Our study harbored three genome‐wide significant SNPs on 22.27–26.44 Mb, covering the previously reported QTL.…”

Section: Discussionmentioning

confidence: 99%

Integrating genome‐wide association study with RNA‐seq revealed DBI as a good candidate gene for intramuscular fat content in Beijing black pigs

et al. 2022

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Increasing intramuscular fat (IMF) content can enhance the sensory quality of meat, including tenderness, juiciness, flavor, and color. Genome‐wide association study and RNA‐sequencing (RNA‐seq) analysis were used to identify candidate IMF genes in Beijing Black pigs, a popular species among consumers in northern China. Two and three single nucleotide polymorphisms were significantly associated with IMF in SSC13 and SSC15 respectively. Solute carrier family 4 member 7 (SLC4A7) on SSC13 and insulin induced gene 2 (INSIG2), coiled‐coil domain containing 93 (CCDC93), and diazepam binding inhibitor acyl‐CoA binding protein (DBI) on SSC15 are good candidate genes in this population. Furthermore, RNA‐seq analysis was performed between high and low IMF groups, and 534 differentially expressed genes were identified. In addition, based on differentially expressed genes, Kyoto Encyclopedia of Genes and Genomes analysis revealed that peroxisome proliferator‐activated receptors and FoxO signaling pathway pathways might contribute to IMF. Moreover, the DBI gene was identified as a candidate for IMF both by genome‐wide association study and RNA‐seq analysis, suggesting that it might be a crucial candidate gene for influencing IMF in Beijing Black pigs.

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“…As stated in the PigQTLdb ( , accessed on 23 August 2021) a total of 842 IMF-related QTLs have been reported [ 6 ]. Although thousands of single-nucleotide polymorphisms (SNPs) have been reported to be associated with IMF in genome-wide association studies (GWAS), most of them only explain a small part of the total genetic variance [ 4 , 7 , 8 ].…”

Section: Introductionmentioning

confidence: 99%

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

Wei

Shu

Wang

et al. 2022

Animals

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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.

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A large‐scale genome‐wide association analysis reveals QTL and candidate genes for intramuscular fat content in Duroc pigs

Cited by 6 publications

References 29 publications

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

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

Integrating genome‐wide association study with RNA‐seq revealed DBI as a good candidate gene for intramuscular fat content in Beijing black pigs

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

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