- 2 National Engineering Laboratory for Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, China Full list of author information is available at the end of the article. - Con- sidering that obesity poses an escalating health threat worldwide, a deeper understanding of the mechanisms underlying lipid deposition and metabolic changes would be beneficial. - Lipid deposition traits in the LD tissue of the Nanyang black pigs with high-and low-lipid-depositions are shown in Table 1 and Fig. - The backfat thickness of the live and slaughtered, TFA, and TFA/total dry matter showed the same trend between the high and low lipid de- position groups, although the difference was not signifi- cant. - It is of note that the significance level of the tissue slice was higher than that from the IMF measurements.. - Transcriptomic analysis between the high and low lipid deposition groups. - The cufflinks program identified a total of 342.8 million clean reads and approximately 94.94% of the clean reads were mapped to the Sus scrofa genome sequence. - To deter- mine the accuracy of the grouping, intra- and inter- group correlation analysis was performed for the gene expression of the six pigs, from the perspective of the FPKM values and count numbers, respectively. - Regardless of the FPKM value or the number of genes, the high lipid deposition group (HF01, HF02, and HF03) was clustered together first and was clearly separated from the low lipid depos- ition group (LF01, LF02, and LF03).. - Functional and clustering annotations of the DEGs To further utilize the DEG information, they were fur- ther interpreted using GO and KEGG analyses to iden- tify the related biological functions and pathways. - Among them were multiple sig- naling pathways that were involved in lipid formation and metabolism, including fatty acid biosynthesis, PPAR signaling pathway, steroid biosynthesis, fatty acid metab- olism, Notch signaling pathway, and the AMPK signaling pathway, which accounted for more than 50% of the sig- nificant enrichment pathways. - Overall, the results of the functional Table 1 Phenotypic data for the slaughter and meat quality of the Nanyang black pigs. - A: Oil red O staining using frozen LD samples from each of the 6 pigs, HF: high-fat deposition group, LF: low-fat deposition group. - B: Statistical analysis of the ratio of Oil red O-stained regions using students ’ T test. - B: Heat map of the DEGs in the different lipid deposition groups. - Validation of the transcriptome via qRT-PCR. - The expression trends for all 14 genes in the LD tissues were consistent with the results of the transcriptome analysis. - In addition to the ACACA gene, the expression of the 13 genes from the BF tissue were also consistent with the results of the transcriptome analysis (Fig. - 4 iRegulon analysis of the DEGs from the transcriptomic analysis. - D: 24 lipid deposition-related DEGs. - Most of the proteins were identified by 1–10 pep- tides (Additional file 4 B). - The KEGG functional enrichment analysis of the DEPs re- vealed that the TCA cycle, pyruvate metabolism, and. - Yellow: lipid deposition-related gene. - B: qRT-PCR of the 14 DEGs from the LD and backfat (BF) tissues. - Based on the functional analysis of the DEPs, 9 were screened for further analysis, including 3-hydroxybutyrate dehydro- genase 2 (BDH2), FASN, SLC25A20, eukaryotic transla- tion initiation factor 3 subunit E (EIF3E), CAT, periaxin (PRX), filamin A (FLNA), transferrin receptor (TFRC), and myelin protein zero (MPZ) (Table 3).. - they were identified as lipid deposition related genes (Fig. - Asian wild pigs were derived from ancient wild boars ap- proximately 1.2–0.8 million years ago and the domesti- cation of the pig in China occurred ∼9000 years ago [22, 23]. - Nanyang black pigs are one of the three main Chin- ese indigenous pig breeds in Henan Province and the quality of their meat is higher than that of Western commercial breeds (China National Commission of Ani- mal Genetic Resources 2011) [15]. - A: GO analysis of the DEPs. - B: KEGG analysis of the DEPs. - After database compari- sons, the number of positively expressed proteins identi- fied was 2036, which was lower than that of the transcriptome. - While the combined analysis of the tran- scriptome and proteome data can provide more accurate and comprehensive gene expression information than single omics data, some genes from the single omics re- sults were also discussed here to compliment the com- bined results [12, 19]. - 7 Venn plot of the candidate proteins and DEGs for lipid deposition. - how- ever, functional analysis of the DEGs involved in lipid deposition missed BDH2. - Upstream tran- scriptional factor analysis of the 24-lipid deposition- related genes showed that NR2F1, NR1H2, and DMRT2 were mainly clustered (NES >. - There have been many controversial studies of the multiple roles involving ACACA in mono- and poly-unsaturated fatty acid content and performance traits [54, 55]. - This indicates that ACACA might be involved in determining the direc- tional deposition of the lipids and this should be investi- gated further in the future.. - The Animal Welfare Committee of the State Key Laboratory for Agro- Biotechnology of the China Agricultural University ap- proved all procedures for animal care (approval number, SKLAB . - The relative humidity and temperature of the piglet houses were maintained at 60–65% and 25–. - Phenotype measurements and histological observations To evaluate the production performance of the sows, es- pecially their lipid deposition traits, we measured IMF using the Soxhlet extraction method, as previously de- scribed [18, 19]. - Measurements of the 6 indi- viduals were performed using three technical replicates.. - The number of fragments per kilobase of the transcripts per million mapped reads (FPKM) was used to determine the levels of gene expression with cufflinks (version . - Clustering of the STRI NG networks was performed using an embedded k- means algorithm, with a number of expected clusters de- termined empirically [65]. - Total RNA was extracted for qRT-PCR analysis in the LD and backfat tissues of the 12 pigs, which included the high lipid group (n = 6) and the low lipid group (n = 6). - The quantification level for the unique peptide was corrected as the proportion of the total. - intensity of the assigned peptides. - www.ebi.ac.uk/QuickGO/) was used to evaluate the sig- nificance level of the GO TERM after the DEP enrich- ment. - Student’s t-tests were performed using Statistical Analysis System software (SAS, version 9.2, SAS Institute Inc., Cary NC, USA) to examine the significance of the differential expression levels among the groups, and the differences among the groups were considered significant at P <. - org/10.1186/s . - Functional analysis of the 481 DEGs using GO and KEGG. - Results of the GO and KEGG analysis of the 481 DEGs from transcriptome with |log2 fold change| >. - TMT_based proteomic expression analysis of the Nanyang black pigs. - Expression analysis of the differentially expressed proteins identified in this investigation.. - Analysis of the 99 differentially expressed proteins identified in this investigation.. - Primers used for the qRT-PCR analysis of the DEGs. - A list of the primers used to assess the differentially expressed genes composing of ACACA, GK, SQLE, FASN, SCD, DHCR24, ACSL4, CAT, PPARA, UCP3, PDK4, CEBPA, SLC25A20, and EGFR.. - 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