Candidate gene screening for lipid deposition using combined transcriptomic and proteomic data from Nanyang black pigs

Wang, Liyuan; Zhang, Yawen; Zhang, Bo; Zhong, Haian; Lu, Yao; Zhang, Hao

doi:10.1186/s12864-021-07764-2

Cited by 16 publications

(10 citation statements)

References 72 publications

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“…It has been shown that in animal organisms, the ACACA gene is highly expressed in tissues with strong fatty acid metabolic activity, and the acetyl coenzyme A carboxylase (ACACA) gene plays an important role in lipid metabolism by promoting fatty acid biosynthesis ( 26 ). The results of our study also showed extremely high expression in porcine dorsal lipid tissues, which is consistent with the findings of previous studies ( 27 , 28 ). Solute carrier family 2 member 4 (SLC2A4), also known as glucose transporter protein 4 (GLUT4), is an important transporter protein for cellular uptake of glucose, mainly expressed in muscle and adipose tissues, involved in active cellular uptake of glucose across membranes, and plays an important role in glucose metabolism, and was enriched in the present assay in AMPK signaling pathway, insulin signaling pathway and adipocyte factor signaling pathways.…”

Section: Discussionsupporting

confidence: 93%

Transcriptomics-Based Study of Differentially Expressed Genes Related to Fat Deposition in Tibetan and Yorkshire Pigs

Gong

Zheng²,

Zhang³

et al. 2022

Front. Vet. Sci.

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Fat deposition traits are one of the key factors in pig production and breeding. The fat deposition capacity of pigs mainly affects the quality of pork and pig productivity. The aim of this study was to analyze the differential expression of mRNA levels in dorsal adipose tissue of Tibetan and York pigs at different growth stages using transcriptomic data to estimate key genes that regulate fat deposition in pigs. The results showed that a total of 32,747 positively expressed genes were present in the dorsal adipose tissue of the two breeds. Differentially expressed gene (DEG) screening of multiple combinations between the two breeds yielded 324 DEGS. Gene ontology (GO) biofunctional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that these DEGS were mainly involved in lipid metabolic pathways, steroid biosynthetic pathways and lipid biosynthetic processes, sterol biosynthetic processes, brown adipocyte differentiation, and other pathways related to lipid deposition and metabolism. The results showed that ACACA, SLC2A4 and THRSP genes positively regulated the lipid deposition ability and CHPT1 gene negatively regulated the lipid deposition ability in pigs. The results of this experiment suggest a theoretical basis for further studies on the regulatory mechanisms of fat deposition in pigs.

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Section: Discussionsupporting

confidence: 93%

Transcriptomics-Based Study of Differentially Expressed Genes Related to Fat Deposition in Tibetan and Yorkshire Pigs

Gong

Zheng²,

Zhang³

et al. 2022

Front. Vet. Sci.

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“…Compared with western pig breeds, Chinese indigenous pigs have a slow growth rate and low lean meat rate but have excellent meat quality and superior lipid deposition. The population of Chinese indigenous pig breeds is small, the breeding method is relatively closed, and the selection intensity is low, resulting in obvious genetic and phenotypic differentiation [ 7 ]. The Wannanhua (WH) pig is an excellent indigenous pig breed from Anhui Province.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Profiling of Different Developmental Stages on Longissimus Dorsi to Identify Genes Underlying Intramuscular Fat Content in Wannanhua Pigs

Yang

et al. 2023

Genes

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Intramuscular fat (IMF) is a key index to measure the tenderness and flavor of pork. Wannanhua pig, a famous indigenous pig breed in Anhui Province, is renowned for its high lipid deposition and high genetic divergence, making it an ideal model for investigating the lipid position trait mechanisms in pigs. However, the regulatory mechanisms of lipid deposition and development in pigs remain unclear. Furthermore, the temporal differences in gene regulation are based on muscle growth and IMF deposition. The purpose of this study was to study the expression changes of longissimus dorsi (LD) at different growth stages of WH pigs at the molecular level, to screen the candidate genes and signaling pathways related to IMF during development by transcriptome sequencing technology, and to explore the transcriptional regulation mechanism of IMF deposition-related genes at different development stages. In total, 616, 485, and 1487 genes were differentially expressed between LD60 and LD120, LD120 and LD240, and LD60 and LD240, respectively. Numerous differentially expressed genes (DEGs) associated with lipid metabolism and muscle development were identified, and most of them were involved in IMF deposition and were significantly up-regulated in LD120 and LD240 compared to LD60. STEM (Short Time-series Expression Miner) analysis indicated significant variations in the mRNA expression across distinct muscle development stages. The differential expression of 12 selected DEGs was confirmed by RT-qPCR. The results of this study contribute to our understanding of the molecular mechanism of IMF deposition and provide a new way to accelerate the genetic improvement of pork quality.

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“… Zhang et al (2022a) considered FASN a candidate gene for fat deposition. Another study showed a strong correlation between FASN and intramuscular fat ( Wang et al, 2020 ), and FASN determined lipid deposition using transcriptome and proteome data ( Wang et al, 2021 ). The mRNA expression of FASN in the subcutaneous fat was higher than that in the perirenal fat.…”

Section: Discussionmentioning

confidence: 99%

Differences in histomorphology and expression of key lipid regulated genes of four adipose tissues from Tibetan pigs

Lin

Dong

Song

et al. 2023

PeerJ

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Tibetan pigs, an indigenous pig breed in China, have high overall fat deposition and flavorful and tasty meat. They are thus good models for studying adipogenesis. Few studies have been conducted focusing on expression of lipid regulated genes in different adipose tissues of Tibetan pigs. Therefore, we compared the difference of histomorphology and expression level of lipid regulated genes through qPCR and western blot in subcutaneous fat, perirenal fat, omental adipose tissue, and inguinal fat of Tibetan pigs. Our results showed that the area of subcutaneous adipocytes in Tibetan pigs was smaller, while the other three adipose tissues (perirenal fat, greater omentum fat, inguinal fat) had cell areas of similar size. The gene expression of FABP4, FASN, FABP3, and ME1 in subcutaneous fat was significantly higher than that in perirenal fat. Furthermore, the protein expression of FABP4 was significantly lower in subcutaneous fat than in perirenal fat (p < 0.05), and the expression of FASN was higher in greater omentum fat than in subcutaneous fat (p = 0.084). The difference in adipocyte cell size and expression of lipid-regulated genes in adipose tissues from the various parts of the pig body is likely due to the different cellular lipid metabolic processes. Specially, FABP4 and FASN may be involved in the regulation of fat deposition in different adipose tissues of Tibetan pigs.

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Candidate gene screening for lipid deposition using combined transcriptomic and proteomic data from Nanyang black pigs

Cited by 16 publications

References 72 publications

Transcriptomics-Based Study of Differentially Expressed Genes Related to Fat Deposition in Tibetan and Yorkshire Pigs

Transcriptomics-Based Study of Differentially Expressed Genes Related to Fat Deposition in Tibetan and Yorkshire Pigs

Transcriptome Profiling of Different Developmental Stages on Longissimus Dorsi to Identify Genes Underlying Intramuscular Fat Content in Wannanhua Pigs

Differences in histomorphology and expression of key lipid regulated genes of four adipose tissues from Tibetan pigs

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