English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Tools annual

Global: Zendy Free Plan

Global: Zendy Tools monthly

Global: Zendy Plus monthly

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 = 2.51 E  −7 ), and the nearest IMF-correlated gene  SFXN4  ( r  = 0.28, FDR = 4.00 E  −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.

Trait correlated expression combined with eQTL and ASE analyses identified novel candidate genes affecting intramuscular fat