Transcriptome analysis in comparing carcass and meat quality traits of Jiaxing Black Pig and Duroc × Duroc × Berkshire × Jiaxing Black Pig crosses

Chen, Qiangqiang; Zhang, Wei; Cai, Jianfeng; Ni, Yifan; Xiao, Lixia; Zhang, Jinzhi

doi:10.1016/j.gene.2021.145978

Cited by 21 publications

(20 citation statements)

References 71 publications

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“…In total, 341 DEMs were identified from the sequencing data, of which the expression levels of 207 DEMs were upregulated in the H group, including a series of lipogenic genes, such as ACACA , ACLY , PTGR1 , DGAT2 , and CYB5R1 . These differentially expressed genes are involved in various aspects of de novo fatty acid synthesis, including direct and indirect regulation, and play catalytic roles in fatty acid biosynthesis [ 18 , 26 , 27 , 28 ]. Moreover, the expression differences in ACACA , ACLY , PTGR1 , DGAT2 , and CYB5R1 between the H and L groups were consistent with the increasing IMF deposition trend ( Supplementary File S1 ), indicating that these genes might act as positive regulators of the IMF deposition process.…”

Section: Discussionmentioning

confidence: 99%

“…For example, it is typically higher in indigenous Chinese pig breeds than in Western pig breeds and commercial pigs [ 17 ]. Pig breeds in China have high contents of subcutaneous and intramuscular fat and good meat quality [ 18 ]. However, commercial pig breeds, such as Duroc, Landrace, and Yorkshire, are selected for better lean muscle growth, leading to a decrease in the deposition of fat, including IMF, resulting in reduced meat palatability [ 12 ].…”

Section: Introductionmentioning

confidence: 99%

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Identification of Candidate Genes and Regulatory Competitive Endogenous RNA (ceRNA) Networks Underlying Intramuscular Fat Content in Yorkshire Pigs with Extreme Fat Deposition Phenotypes

Ding

Hou

Ling

et al. 2022

IJMS

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Intramuscular fat (IMF) content is vital for pork quality, serving an important role in economic performance in pig industry. Non-coding RNAs, with mRNAs, are involved in IMF deposition; however, their functions and regulatory mechanisms in porcine IMF remain elusive. This study assessed the whole transcriptome expression profiles of the Longissimus dorsi muscle of pigs with high (H) and low (L) IMF content to identify genes implicated in porcine IMF adipogenesis and their regulatory functions. Hundreds of differentially expressed RNAs were found to be involved in fatty acid metabolic processes, lipid metabolism, and fat cell differentiation. Furthermore, combing co-differential expression analyses, we constructed competing endogenous RNAs (ceRNA) regulatory networks, showing crosstalk among 30 lncRNAs and 61 mRNAs through 20 miRNAs, five circRNAs and 11 mRNAs through four miRNAs, and potential IMF deposition-related ceRNA subnetworks. Functional lncRNAs and circRNAs (such as MSTRG.12440.1, ENSSSCT00000066779, novel_circ_011355, novel_circ_011355) were found to act as ceRNAs of important lipid metabolism-related mRNAs (LEP, IP6K1, FFAR4, CEBPA, etc.) by sponging functional miRNAs (such as ssc-miR-196a, ssc-miR-200b, ssc-miR10391, miR486-y). These findings provide potential regulators and molecular regulatory networks that can be utilized for research on IMF traits in pigs, which would aid in marker-assisted selection to improve pork quality.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Identification of Candidate Genes and Regulatory Competitive Endogenous RNA (ceRNA) Networks Underlying Intramuscular Fat Content in Yorkshire Pigs with Extreme Fat Deposition Phenotypes

Ding

Hou

Ling

et al. 2022

IJMS

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“…Presently, with improvements in consumer living standards, the demand for pork has changed from quantity to quality with IMF content representing an important determinant of meat quality [ 1 , 2 ]. Previous studies have indicated that [ 51 , 52 , 53 ] compared with Western commercial pigs (WECPs), Chinese indigenous pigs (CHIPs) displayed better pork quality traits in terms of IMF percentage, 24 h drip loss, meat colour and pH value while WECPs were better in terms of lean meat percentage (BFT and loin eye area) ( Table 3 ). Anqing Sixwhite pig (AQSW) is an excellent breed raised in China demonstrating resistance to coarse fodder and disease, superior meat quality and high prolificacy [ 34 , 35 ].…”

Section: Discussionmentioning

confidence: 99%

miR-381-3p Inhibits Intramuscular Fat Deposition through Targeting FABP3 by ceRNA Regulatory Network

Jiang

Liu

et al. 2022

Biology

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Intramuscular fat (IMF) deposition is an important determinant of pork quality and a complex process facilitated by non-coding ceRNAs. In this study, 52 Berkshire × Anqing Sixwhite crossbred pigs were slaughtered to measure eight carcass and pork quality traits. Whole-transcriptome sequencing analysis was performed using longissimus dorsi samples of six low- and high-IMF samples; 34 ceRNA networks, based on 881, 394, 158 differentially expressed (DE) lncRNAs, miRNAs, and mRNAs, were constructed. Following weighted gene co-expression network analysis between the low and high IMF, only one ceRNA, lncRNA4789/miR-381-3p/FABP3, that showed similar DE trend in longissimus dorsi tissue was retained. Dual-luciferase reporter assays further indicated that FABP3 was a direct, functional target of miR-381-3p, where miR-381-3p overexpression inhibited the mRNA and protein expression of FABP3. In addition, overexpressed lncRNA4789 attenuated the effect of miR-381-3p on FABP3 by sponging miR-381-3p. Cell function verification experiment demonstrated that miR-381-3p suppressed IMF deposition by inhibiting preadipocyte cell differentiation and lipid droplet deposition via the suppression of FABP3 expression in the peroxisome proliferator-activated receptor signalling pathway, whereas lncRNA4789 rescued FABP3 expression by sponging miR-381-3p. Our study may aid in identifying novel molecular markers for its optimization in IMF which is of importance in breeding for improving pork quality.

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“…The BFT of pig has been a research hotspot for a long time because of its significance in pig breeding and production. With the development of omics technology and the reduction in chip and sequencing costs, there have been many studies on the important economic traits of pigs using omics methods, including BFT, and many new and interesting genes or mutations have been discovered [ 21 , 22 , 23 ]. In our previous study on the transcriptome analysis of pig BFT, the GLIPR1 gene was identified as a candidate gene by analyzing the differentially expressed genes, comparing the high-BFT group with the low-BFT group, and finding its biological function related to adipogenesis [ 7 ].…”

Section: Discussionmentioning

confidence: 99%

Expression and Genetic Effects of GLI Pathogenesis-Related 1 Gene on Backfat Thickness in Pigs

Liu

Zhang

et al. 2022

Genes

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Backfat thickness (BFT) is an important carcass composition trait and regarded as a breeding focus. Our initial transcriptome analysis of pig BFT identified GLI pathogenesis-related 1 (GLIPR1) as one of the promising candidate genes. This study was conducted to identify the expression profiles, polymorphisms, and genetic effects of the GLIPR1 gene on BFT in pigs. The expression of the GLIPR1 gene existed in every detected tissue, and there was a significantly higher expression in spleen and adipose tissue than others (p < 0.05). At the different ages of pig, the expression of the GLIPR1 gene was low at an early age, increased with growth, and reached the highest level at 180 days. Genetic polymorphism analysis was detected in 553 individuals of the Large White × Minzhu F2 population. Four SNPs in the promoter significantly associated with 6–7 rib BFT (p < 0.05) were predicted to alter the transcription factor binding sites (TFBS), and the mutations of g.38758089 T > G and g.38758114 G > C were predicted to change the TFs associated with the regulation of adipogenesis. Haplotypes were formed by the detected SNPs, and one block showed a strong association with BFT (p < 0.05). In summary, our results indicate that the expression profiles and genetic variants of GLIPR1 affected the BFT of pigs. To our knowledge, this study is the first to demonstrate the biological function and genetic effects of the GLIPR1 gene on the BFT of pig and provide genetic markers to optimize breeding for BFT in pigs.

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Transcriptome analysis in comparing carcass and meat quality traits of Jiaxing Black Pig and Duroc × Duroc × Berkshire × Jiaxing Black Pig crosses

Cited by 21 publications

References 71 publications

Identification of Candidate Genes and Regulatory Competitive Endogenous RNA (ceRNA) Networks Underlying Intramuscular Fat Content in Yorkshire Pigs with Extreme Fat Deposition Phenotypes

Identification of Candidate Genes and Regulatory Competitive Endogenous RNA (ceRNA) Networks Underlying Intramuscular Fat Content in Yorkshire Pigs with Extreme Fat Deposition Phenotypes

miR-381-3p Inhibits Intramuscular Fat Deposition through Targeting FABP3 by ceRNA Regulatory Network

Expression and Genetic Effects of GLI Pathogenesis-Related 1 Gene on Backfat Thickness in Pigs

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