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Trait correlated expression combined with eQTL and ASE analyses identified novel candidate genes affecting intramuscular fat
BACKGROUND: Intramuscular fat (IMF) content is a determining factor for meat taste. The Luchuan pig is a fat-type local breed in southern China that is famous for its desirable meat quality due to high IMF, however, the crossbred offspring of Luchuan sows and Duroc boars displayed within-population...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8577010/ https://www.ncbi.nlm.nih.gov/pubmed/34749647 http://dx.doi.org/10.1186/s12864-021-08141-9 |
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author | Liu, Yan Long, Huan Feng, Simin Ma, Tingting Wang, Mufeng Niu, Lizhu Zhang, Xinyi Wang, Lianni Lei, Yu Chen, Yilong Wang, Qiankun Xu, Xuewen |
author_facet | Liu, Yan Long, Huan Feng, Simin Ma, Tingting Wang, Mufeng Niu, Lizhu Zhang, Xinyi Wang, Lianni Lei, Yu Chen, Yilong Wang, Qiankun Xu, Xuewen |
author_sort | Liu, Yan |
collection | PubMed |
description | BACKGROUND: Intramuscular fat (IMF) content is a determining factor for meat taste. The Luchuan pig is a fat-type local breed in southern China that is famous for its desirable meat quality due to high IMF, however, the crossbred offspring of Luchuan sows and Duroc boars displayed within-population variation on meat quality, and the reason remains unknown. RESULTS: In the present study, we identified 212 IMF-correlated genes (FDR ≤ 0.01) using correlation analysis between gene expression level and the value of IMF content. The IMF-correlated genes were significantly enriched in the processes of lipid metabolism and mitochondrial energy metabolism, as well as the AMPK/PPAR signaling pathway. From the IMF-correlated genes, we identified 99 genes associated with expression quantitative trait locus (eQTL) or allele-specific expression (ASE) signals, including 21 genes identified by both cis-eQTL and ASE analyses and 12 genes identified by trans-eQTL analysis. Genome-wide association study (GWAS) of IMF identified a significant QTL on SSC14 (p-value = 2.51E(−7)), and the nearest IMF-correlated gene SFXN4 (r = 0.28, FDR = 4.00E(−4)) was proposed as the candidate gene. Furthermore, we highlighted another three novel IMF candidate genes, namely AGT, EMG1, and PCTP, by integrated analysis of GWAS, eQTL, and IMF-gene correlation analysis. CONCLUSIONS: The AMPK/PPAR signaling pathway together with the processes of lipid and mitochondrial energy metabolism plays a vital role in regulating porcine IMF content. Trait correlated expression combined with eQTL and ASE analysis highlighted a priority list of genes, which compensated for the shortcoming of GWAS, thereby accelerating the mining of causal genes of IMF. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-021-08141-9. |
format | Online Article Text |
id | pubmed-8577010 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-85770102021-11-10 Trait correlated expression combined with eQTL and ASE analyses identified novel candidate genes affecting intramuscular fat Liu, Yan Long, Huan Feng, Simin Ma, Tingting Wang, Mufeng Niu, Lizhu Zhang, Xinyi Wang, Lianni Lei, Yu Chen, Yilong Wang, Qiankun Xu, Xuewen BMC Genomics Research BACKGROUND: Intramuscular fat (IMF) content is a determining factor for meat taste. The Luchuan pig is a fat-type local breed in southern China that is famous for its desirable meat quality due to high IMF, however, the crossbred offspring of Luchuan sows and Duroc boars displayed within-population variation on meat quality, and the reason remains unknown. RESULTS: In the present study, we identified 212 IMF-correlated genes (FDR ≤ 0.01) using correlation analysis between gene expression level and the value of IMF content. The IMF-correlated genes were significantly enriched in the processes of lipid metabolism and mitochondrial energy metabolism, as well as the AMPK/PPAR signaling pathway. From the IMF-correlated genes, we identified 99 genes associated with expression quantitative trait locus (eQTL) or allele-specific expression (ASE) signals, including 21 genes identified by both cis-eQTL and ASE analyses and 12 genes identified by trans-eQTL analysis. Genome-wide association study (GWAS) of IMF identified a significant QTL on SSC14 (p-value = 2.51E(−7)), and the nearest IMF-correlated gene SFXN4 (r = 0.28, FDR = 4.00E(−4)) was proposed as the candidate gene. Furthermore, we highlighted another three novel IMF candidate genes, namely AGT, EMG1, and PCTP, by integrated analysis of GWAS, eQTL, and IMF-gene correlation analysis. CONCLUSIONS: The AMPK/PPAR signaling pathway together with the processes of lipid and mitochondrial energy metabolism plays a vital role in regulating porcine IMF content. Trait correlated expression combined with eQTL and ASE analysis highlighted a priority list of genes, which compensated for the shortcoming of GWAS, thereby accelerating the mining of causal genes of IMF. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-021-08141-9. BioMed Central 2021-11-08 /pmc/articles/PMC8577010/ /pubmed/34749647 http://dx.doi.org/10.1186/s12864-021-08141-9 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Liu, Yan Long, Huan Feng, Simin Ma, Tingting Wang, Mufeng Niu, Lizhu Zhang, Xinyi Wang, Lianni Lei, Yu Chen, Yilong Wang, Qiankun Xu, Xuewen Trait correlated expression combined with eQTL and ASE analyses identified novel candidate genes affecting intramuscular fat |
title | Trait correlated expression combined with eQTL and ASE analyses identified novel candidate genes affecting intramuscular fat |
title_full | Trait correlated expression combined with eQTL and ASE analyses identified novel candidate genes affecting intramuscular fat |
title_fullStr | Trait correlated expression combined with eQTL and ASE analyses identified novel candidate genes affecting intramuscular fat |
title_full_unstemmed | Trait correlated expression combined with eQTL and ASE analyses identified novel candidate genes affecting intramuscular fat |
title_short | Trait correlated expression combined with eQTL and ASE analyses identified novel candidate genes affecting intramuscular fat |
title_sort | trait correlated expression combined with eqtl and ase analyses identified novel candidate genes affecting intramuscular fat |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8577010/ https://www.ncbi.nlm.nih.gov/pubmed/34749647 http://dx.doi.org/10.1186/s12864-021-08141-9 |
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