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| Status |
Public on Dec 30, 2023 |
| Title |
Muscle transcriptome analysis of Duroc x Luchuan crossed pigs with extreme phenotypes of intramuscular fat content using RNA sequencing |
| Organism |
Sus scrofa |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Intramuscular fat (IMF) content is the determining factor for meat taste. To reveal the genetic basis of IMF content, genetic studies have made some progress in lean-type pig breeds, but fewer studies have been conducted in Chinese fat-type pigs. The Luchuan pig is a fat-type local breed in southern China that is famous for its desirable meat quality. In the present study, we measured the IMF content for 265 crossed pigs of Duroc x Luchuan pigs, from which individuals with extremely high (6.03% ± 0.58%, n = 12) and low (1.67% ± 0.42%, n = 12) IMF contents were selected to identify differentially expressed genes (DEGs) related to IMF content in the longissimus dorsi. RNA sequencing for 24 samples in total identified 312 differentially expressed transcripts that were significantly enriched in triglyceride biosynthesis- and metabolism-related processes (p-value ≤ 0.05 and fold change ≥ 1.5). Functional enrichment analysis revealed that the PPAR signaling pathway was the most significantly enriched pathway (p-value = 0.024, represented by ADIPOQ, FABP3, FABP4, LPL, PLIN4 and SCD). When a more stringent condition was applied (gene-based q-value ≤ 0.2 and fold change ≥ 1.5), only 17 transcripts remained to be differentially expressed, including LEP, ATP6V1F, SDR16C5, TUSC5, MPZ, PRX, PTPN4, BEX1, MVB12B, ZFP62, P4HA2, IDH2, THOC7, KRT14, FCGRT, MYPN and LPL. Among these DEGs, TUSC5 was significantly upregulated in the group of high IMF contents (log2FC = 1.114, p-value = 3.02E-5) and was suspected as a strong new candidate gene affecting porcine IMF content since it was the target gene of PPAR-gamma. The present study provided new data and candidate genes for the genetic study of porcine IMF content.
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| Overall design |
Transcriptome sequencing in longissimus dorsi muscle of 24 pigs from the crossing of 8 Duroc boars and 112 Luchuan sows
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| Contributor(s) |
Long H, Ma T |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jul 20, 2018 |
| Last update date |
Dec 30, 2023 |
| Contact name |
xuewen xu |
| E-mail(s) |
xuewen_xu@mail.hzau.edu.cn
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| Organization name |
Huazhong Agricultural University
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| Street address |
Shizishan street, No.1
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| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
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| Platforms (1) |
| GPL22475 |
Illumina HiSeq 4000 (Sus scrofa) |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA482050 |
| SRA |
SRP154522 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE117414_Complete_data.txt.gz |
2.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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