Trait correlated expression combined with eQTL and ASE analyses identified novel candidate genes affecting intramuscular fat
Abstract 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-pop...
Guardado en:
| Autores principales: | , , , , , , , , , , , |
|---|---|
| Formato: | article |
| Lenguaje: | EN |
| Publicado: |
BMC
2021
|
| Materias: | |
| Acceso en línea: | https://doaj.org/article/9b611426239446a7aba6adbb1fc639db |
| Etiquetas: |
Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
|
| id |
oai:doaj.org-article:9b611426239446a7aba6adbb1fc639db |
|---|---|
| record_format |
dspace |
| spelling |
oai:doaj.org-article:9b611426239446a7aba6adbb1fc639db2021-11-14T12:26:47ZTrait correlated expression combined with eQTL and ASE analyses identified novel candidate genes affecting intramuscular fat10.1186/s12864-021-08141-91471-2164https://doaj.org/article/9b611426239446a7aba6adbb1fc639db2021-11-01T00:00:00Zhttps://doi.org/10.1186/s12864-021-08141-9https://doaj.org/toc/1471-2164Abstract 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.Yan LiuHuan LongSimin FengTingting MaMufeng WangLizhu NiuXinyi ZhangLianni WangYu LeiYilong ChenQiankun WangXuewen XuBMCarticlePigIMFeQTLASEGWASAMPK/PPARBiotechnologyTP248.13-248.65GeneticsQH426-470ENBMC Genomics, Vol 22, Iss 1, Pp 1-14 (2021) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Pig IMF eQTL ASE GWAS AMPK/PPAR Biotechnology TP248.13-248.65 Genetics QH426-470 |
| spellingShingle |
Pig IMF eQTL ASE GWAS AMPK/PPAR Biotechnology TP248.13-248.65 Genetics QH426-470 Yan Liu Huan Long Simin Feng Tingting Ma Mufeng Wang Lizhu Niu Xinyi Zhang Lianni Wang Yu Lei Yilong Chen Qiankun Wang Xuewen Xu Trait correlated expression combined with eQTL and ASE analyses identified novel candidate genes affecting intramuscular fat |
| description |
Abstract 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. |
| format |
article |
| author |
Yan Liu Huan Long Simin Feng Tingting Ma Mufeng Wang Lizhu Niu Xinyi Zhang Lianni Wang Yu Lei Yilong Chen Qiankun Wang Xuewen Xu |
| author_facet |
Yan Liu Huan Long Simin Feng Tingting Ma Mufeng Wang Lizhu Niu Xinyi Zhang Lianni Wang Yu Lei Yilong Chen Qiankun Wang Xuewen Xu |
| author_sort |
Yan Liu |
| title |
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_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_sort |
trait correlated expression combined with eqtl and ase analyses identified novel candidate genes affecting intramuscular fat |
| publisher |
BMC |
| publishDate |
2021 |
| url |
https://doaj.org/article/9b611426239446a7aba6adbb1fc639db |
| work_keys_str_mv |
AT yanliu traitcorrelatedexpressioncombinedwitheqtlandaseanalysesidentifiednovelcandidategenesaffectingintramuscularfat AT huanlong traitcorrelatedexpressioncombinedwitheqtlandaseanalysesidentifiednovelcandidategenesaffectingintramuscularfat AT siminfeng traitcorrelatedexpressioncombinedwitheqtlandaseanalysesidentifiednovelcandidategenesaffectingintramuscularfat AT tingtingma traitcorrelatedexpressioncombinedwitheqtlandaseanalysesidentifiednovelcandidategenesaffectingintramuscularfat AT mufengwang traitcorrelatedexpressioncombinedwitheqtlandaseanalysesidentifiednovelcandidategenesaffectingintramuscularfat AT lizhuniu traitcorrelatedexpressioncombinedwitheqtlandaseanalysesidentifiednovelcandidategenesaffectingintramuscularfat AT xinyizhang traitcorrelatedexpressioncombinedwitheqtlandaseanalysesidentifiednovelcandidategenesaffectingintramuscularfat AT lianniwang traitcorrelatedexpressioncombinedwitheqtlandaseanalysesidentifiednovelcandidategenesaffectingintramuscularfat AT yulei traitcorrelatedexpressioncombinedwitheqtlandaseanalysesidentifiednovelcandidategenesaffectingintramuscularfat AT yilongchen traitcorrelatedexpressioncombinedwitheqtlandaseanalysesidentifiednovelcandidategenesaffectingintramuscularfat AT qiankunwang traitcorrelatedexpressioncombinedwitheqtlandaseanalysesidentifiednovelcandidategenesaffectingintramuscularfat AT xuewenxu traitcorrelatedexpressioncombinedwitheqtlandaseanalysesidentifiednovelcandidategenesaffectingintramuscularfat |
| _version_ |
1718429245241294848 |