Comparison of liver transcriptome from high- and low-intramuscular fat Chaohu ducks provided additional candidate genes for lipid selection

Abstract

The meat quality of ducks is closely related to the intramuscular fat (IMF) content. This study explored the candidate regulatory genes of IMF formation and lipid deposition in Chaohu ducks. The IMF of breast muscle in 100 ducks was determined and statistically analysed by normal distribution test. Duck liver samples with high IMF (CH, n = 3) and low IMF (CL, n = 3) were selected for transcriptome analysis by RNA sequencing (RNA-Seq). The IMF was in accordance with normal distribution (T = 0.001, P = 0.999). The IMF from two tails of the normal distribution was significantly different with 2.9983% ± 0.3296% in the CH group and 1.1960% ± 0.1481% in the CL group (P < 0.0001). RNA-Seq revealed 147 differentially expressed genes, including 78 up-regulated and 69 down-regulated genes in both groups. Validation by qRT-PCR was in agreement with RNA-Seq (R 2 = 0.838). Gene ontology analysis revealed that organophosphate catabolism, oxidation-reduction process, cellular lipid catabolism, lipid transport, lipid localisation, lipid biosynthesis and cellular lipid catabolism were involved in lipid metabolism. Meanwhile, Kyoto Encyclopedia of Genes and Genomes pathway analysis suggested that steroid hormone biosynthesis, ovarian steroidogenesis, alpha-linolenic acid metabolism, glycosylphosphatidylinositol anchor biosynthesis and linoleic acid metabolism were involved in lipid deposition, wherein the genes COMT,

Genome-Wide Detection and Analysis of Copy Number Variation in Anhui Indigenous and Western Commercial Pig Breeds Using Porcine 80K SNP BeadChip

“…The results showed that the heritability of IMP at seven days post-mortem decreased from 0.32 to 0.08 when the NT5E genotype was included in the model. Similarly, NT5E , which is involved in the biological process of lipid deposition, has been identified as a candidate gene for selecting markers to control IMF formation in Chaohu ducks [ 70 ]. In this study, we identified 22 QTLs, including those related to meat quality, such as marbling (ID = 38049), muscle movement percentage (ID = 38073), and drip loss (ID = 21947,), based on CNVs located in the NT5E gene and the QTL database in control pigs.…”

Comparative Transcriptomic Profiles of Differentiated Adipocytes Provide Insights into Adipogenesis Mechanisms of Subcutaneous and Intramuscular Fat Tissues in Pigs

“…GNAS plays multiple important roles in cell fate determination and differentiation during osteogenic differentiation [40]. NDUFA4L2 is considered to be a gene related to meat quality [41], and PPP1R3C is considered to be a candidate gene for intramuscular fat deposition in ducks [42].…”

Comparative transcriptome analysis of Indian domestic duck reveals candidate genes associated with egg production

“…KPNA7 (Karyopherin subunit alpha 7) which functions as a receptor for oocyte-specific protein that are important for oocyte and embryonic development 29 . HSD17B2 (Hydroxysteroid 17-beta dehydrogenase 2) a key regulator of steroid hormone metabolism 30 . LHX9 (LIM homeobox 9), which plays a key role in female reproductive tract development 31 .…”