Metabolomics and Transcriptomics Reveal Age-Dependent Development of Meat Quality Traits in Jingyuan Chicken
Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Ethical Statement
2.2. Animal and Sample Collection
2.3. Meat Quality Traits Determination
2.4. Metabolomics Analysis by Untargeted HPLC-HRMS
2.5. Transcriptomics Analysis
2.6. Combined Analysis of Differential Genes and Differential Metabolites
2.7. Statistical Analysis
3. Results
3.1. Meat Quality Traits Performance of Jingyuan Hens at Different Developmental Stages
3.2. Metabolome QC and OPLS-DA Analysis
3.3. Differential Metabolite Analysis
3.4. Trend Analysis of Differential Metabolite Expression
3.5. KEGG Pathway Enrichment Analysis
3.6. Joint Analysis of Transcriptome and Metabolome
3.7. Identification of Meat Quality Traits Related Candidate Genes and Metabolites
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
MLC | Muscle lipid content. |
DEMs | Directory of open access journals. |
DEGs | Three-letter acronym. |
OPLS-DA | Linear dichroism. |
PCA | Principal component analysis. |
HMDB | Human Metabolome Database. |
FC | Fold change. |
dT | Dynabeads Oligo. |
QC | Quality traits control |
References
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Metabolites | Class | FC | VIP | p Value |
---|---|---|---|---|
Acylcarnitine 9:0 | Fatty acyls | 0.16 | 3.48 | 0.01 |
Caffeoylcholine | 0.23 | 3.19 | 0.01 | |
Acylcarnitine 20:4 | Fatty acyls | 0.22 | 2.66 | 0.01 |
Dihydroxyacetone phosphate | Organooxygen compounds | 0.24 | 2.76 | 0.01 |
2,6-Dihydroxybenzoic acid | Benzene and substituted derivatives | 0.35 | 2.47 | 0.01 |
2-Piperidinone | Piperidines | 0.44 | 2.24 | 0.01 |
Gallic acid | Benzene and substituted derivatives | 0.24 | 2.67 | 0.01 |
L-Glutathione, reduced | Carboxylic acids and derivatives | 0.55 | 1.76 | 0.01 |
Linoleoylcarnitine | Fatty acyls | 0.27 | 2.46 | 0.01 |
Acylcarnitine 18:3 | Fatty acyls | 0.20 | 2.84 | 0.01 |
N-Undecanoylglycine | Carboxylic acids and derivatives | 0.48 | 1.61 | 0.01 |
4-Hydroxyquinoline | Quinolines and derivatives | 0.18 | 2.85 | 0.01 |
3-Methylglutarylcarnitine | Fatty acyls | 0.34 | 2.13 | 0.01 |
Adenosine 5′-monophosphate | Purine nucleotides | 0.54 | 1.76 | 0.01 |
D-Mannose-6-phosphate | Organooxygen compounds | 0.30 | 2.08 | 0.01 |
Lauroyl-L-carnitine | Fatty acyls | 0.38 | 2.19 | 0.01 |
D-Mannose-6-phosphate | Organooxygen compounds | 0.39 | 1.85 | 0.01 |
(2R)-3-Hydroxyisovaleroylcarnitine | Fatty acyls | 0.62 | 1.66 | 0.01 |
(Z)-14-Methyl-6-pentadecenoic acid | Purine nucleosides | 0.55 | 1.42 | 0.01 |
Clofentezine | 0.63 | 1.70 | 0.01 | |
N-Acetylhistamine | Carboxylic acids and derivatives | 0.45 | 1.50 | 0.01 |
Eremopetasinorol | Alcohols and polyols | 0.56 | 1.39 | 0.01 |
L-Carnosine | Peptidomimetics | 0.58 | 1.77 | 0.01 |
2-Hydroxy-2-methylbutyric acid | Fatty acyls | 0.52 | 1.53 | 0.01 |
2-Fluoromethamphetamine | 0.39 | 1.96 | 0.01 | |
Dehydro-beta-Ionone | Prenol lipids | 0.62 | 1.12 | 0.01 |
Xanthine | Carboxylic acids and derivatives | 0.61 | 1.56 | 0.01 |
D-2-Phosphoglyceric acid | 0.14 | 2.05 | 0.01 | |
Succinic acid | Prenol lipids | 0.41 | 1.69 | 0.01 |
Metabolites | Class | FC | VIP | p Value |
---|---|---|---|---|
Taurodeoxycholic acid | Carboxylic acids and derivatives | 2.27 | 1.59 | 0.03 |
Choline | Fatty acyls | 1.75 | 1.51 | 0.01 |
1,2,5,6-Tetrahydro-4H-pyrrolo [3,2,1-ij] quinolin-4-one | Fatty acyls | 2.18 | 1.78 | 0.01 |
Prolyl-Valine | Purine nucleotides | 1.63 | 1.62 | 0.01 |
Methylglutaric acid | Fatty acyls | 2.24 | 2.06 | 0.01 |
5,8,11-Eicosatrienoic acid | Fatty acyls | 2.12 | 2.23 | 0.01 |
8Z,11Z-eicosadienoic acid | Fatty acyls | 2.04 | 2.07 | 0.01 |
Threonine | Carboxylic acids and derivatives | 2.08 | 2.03 | 0.01 |
L-Propionylcarnitine | Fatty acyls | 3.72 | 2.20 | 0.01 |
LysoPC 20:3 | Glycerophospholipids | 2.50 | 2.44 | 0.01 |
Groups | Kegg Pathway | Metabolites | FC | p Value | VIP | Regulate |
---|---|---|---|---|---|---|
42 and 126 days old | Glycerophospholipid metabolism (map00564) | LysoPC 16:0 | 0.57 | 0.02 | 1.34 | down |
LysoPC 18:2 | 2.32 | 0.00 | 2.33 | up | ||
LysoPC 20:4 | 0.49 | 0.00 | 2.29 | down | ||
PG 36:4; PG(18:2/18:2) | 1.86 | 0.00 | 2.08 | up | ||
PG 36:3; PG(18:1/18:2) | 1.61 | 0.00 | 1.73 | up | ||
PI 38:4; PI(18:0/20:4) | 0.56 | 0.04 | 1.12 | down | ||
Choline | 1.75 | 0.01 | 1.51 | up | ||
LysoPC 22:4 | 0.47 | 0.01 | 1.73 | down | ||
Longevity-regulating pathway (map04211) | AMP | 1.78 | 0.04 | 1.44 | up | |
beta-Nicotinamide adenine dinucleotide | 4.57 | 0.00 | 3.20 | up | ||
NADH | 4.39 | 0.00 | 3.09 | up | ||
42 and 180 days old | Glycerophospholipid metabolism (map00564) | Dihydroxyacetone phosphate | 0.24 | 0.00 | 2.76 | down |
LysoPS 18:1 | 0.41 | 0.02 | 1.40 | down | ||
LysoPI 20:3 | 3.00 | 0.00 | 2.58 | up | ||
PG 36:4; PG(18:2/18:2) | 1.87 | 0.00 | 1.83 | up | ||
PG 36:3; PG(18:1/18:2) | 1.67 | 0.00 | 1.62 | up | ||
LysoPE 18:2 | 1.57 | 0.02 | 1.66 | up | ||
LysoPC 18:2 | 3.34 | 0.00 | 2.93 | up | ||
LysoPC 20:3 | 2.50 | 0.00 | 2.44 | up | ||
beta-Alanine metabolism (map00410) | L-Carnosine | 0.53 | 0.03 | 1.24 | down | |
Pantothenic acid | 0.64 | 0.02 | 1.12 | down | ||
L-Anserine | 0.63 | 0.00 | 1.35 | down | ||
126 and 180 days old | Oxidative phosphorylation (map00190) | Succinic acid | 0.41 | 0.04 | 1.69 | down |
beta-Nicotinamide adenine dinucleotide | 0.29 | 0.00 | 2.62 | down | ||
NADH | 0.18 | 0.00 | 3.36 | down | ||
Longevity-regulating pathway (map04212) | AMP | 0.44 | 0.00 | 2.09 | down | |
beta-Nicotinamide adenine dinucleotide | 0.29 | 0.00 | 2.62 | down |
Metabolite | Groups | Regulate | Kegg Pathway | Genes |
---|---|---|---|---|
LysoPC 18:2 | 42 and 126 days old | up | Glycerophospholipid metabolism | CHRNG, ENSGALG00010006533, HYDIN, CAMK2A, ENSGALG00010012015, ENSGALG00010022550, C17orf58 |
PG 36:4; PG(18:2/18:2) | up | ENSGALG00010016390 | ||
LysoPC 22:4 | CD3E, IL7R, RASSF5, ENSGALG00010025331, TARP | |||
LysoPC 20:4 | down | ENSGALG00010025331, TARP, IL7R, CD3E, RASSF5 | ||
LysoPC 18:2 | 42 and 180 days old | up | Glycerophospholipid metabolism | ENSGALG00010009589, HACD1, GAMT, HSPB7, ENSGALG00010009112 |
L-Carnosine | down | beta-Alanine metabolism | GLRB, BLEC2 | |
L-Anserine | down | ENSGALG00010007664, ENSGALG00010006904 | ||
Dihydroxyacetone phosphate | down | HSPB7 | ||
NADH | 126 and 180 days old | down | Oxidative phosphorylation | ENSGALG00010022328, TAL2, PCSK1, SGSM1, HYDIN, ENSGALG00010014657, KLHL30, TGFB3, CSRP3 |
beta-Nicotinamide adenine dinucleotide | down | PIK3C2B |
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Hu, J.; Zhao, W.; Zhao, J.; Tian, J.; Yang, L.; Wang, H.; Chen, S.; Ma, R.; Gu, Y.; Wei, D.; et al. Metabolomics and Transcriptomics Reveal Age-Dependent Development of Meat Quality Traits in Jingyuan Chicken. Animals 2025, 15, 1938. https://doi.org/10.3390/ani15131938
Hu J, Zhao W, Zhao J, Tian J, Yang L, Wang H, Chen S, Ma R, Gu Y, Wei D, et al. Metabolomics and Transcriptomics Reveal Age-Dependent Development of Meat Quality Traits in Jingyuan Chicken. Animals. 2025; 15(13):1938. https://doi.org/10.3390/ani15131938
Chicago/Turabian StyleHu, Jiahuan, Wei Zhao, Jinyan Zhao, Jinli Tian, Lijuan Yang, Hua Wang, Siyu Chen, Ruimin Ma, Yaling Gu, Dawei Wei, and et al. 2025. "Metabolomics and Transcriptomics Reveal Age-Dependent Development of Meat Quality Traits in Jingyuan Chicken" Animals 15, no. 13: 1938. https://doi.org/10.3390/ani15131938
APA StyleHu, J., Zhao, W., Zhao, J., Tian, J., Yang, L., Wang, H., Chen, S., Ma, R., Gu, Y., Wei, D., & Zhang, J. (2025). Metabolomics and Transcriptomics Reveal Age-Dependent Development of Meat Quality Traits in Jingyuan Chicken. Animals, 15(13), 1938. https://doi.org/10.3390/ani15131938