Molecular Pathways for Muscle and Adipose Tissue Are Altered between Beef Steers Classed as Choice or Standard
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
3. Results and Discussion
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Item, % (DM Basis) | Diet Composition 1 |
---|---|
Beef Finishing Pellet | 6.3 |
Corn Dry Grain | 75.18 |
Grass Hay | 18.52 |
Nutrient Composition 2 | |
DM, % | 86 |
CP, % | 11.7 |
TDN, % | 83.72 |
NDF, % | 19.29 |
Ca, % | 0.68 |
P, % | 0.32 |
S, % | 0.18 |
K, % | 0.97 |
NEm, Mcal/kg | 1.75 |
NEg, Mcal/kg | 1.18 |
Choice (n = 6) | Select (n = 5) | Standard (n = 4) | |
---|---|---|---|
ADG (kg) | 1.85 | 1.81 | 1.52 |
Carcass Wt. (kg) | 339.3 a | 275.7 b | 243.1 b |
Fat Thickness (cm) | 1.4 a | 1.0 a | 0.5 b |
Ribeye Area (cm2) | 70.9 | 64.0 | 66.9 |
Marbling Score y | 510 a | 382 b | 285 c |
Quality Classification 1 | Shear Force (N) 3 | MFI | Shear Force (N) 3 | MFI |
---|---|---|---|---|
Choice | 84.34 b | 59.25 b | 84.34 b | 59.25 b |
Select | 79.20 b | 64.55 a | 79.20 b | 64.55 a |
Standard | 105.70 a | 55.24 b | 105.70 a | 55.24 b |
Days 2 | ||||
1 | 118.42 a | 49.78 b | 118.42 a | 49.78 b |
3 | 95.31 b | 59.51 a | 95.31 b | 59.51 a |
7 | 86.70 bc | 62.02 a | 86.70 bc | 62.02 a |
14 | 73.55 c | 64.18 a | 73.55 c | 64.18 a |
21 | 74.76 c | 62.94 a | 74.76 c | 62.94 a |
Adipose Tissue | ||||||
Raw 1 | Clean 2 | Error (%) | Q20(%) 3 | Q30(%) 4 | GC Content (%) 5 | |
Standard | 52,994,544 | 51,102,307 | 0.036 | 96.59 | 91.53 | 54.05 |
Select | 52,655,296 | 52,008,329 | 0.012 | 96.61 | 91.50 | 54.26 |
Choice | 68,918,968 | 66,800,801 | 0.031 | 97.10 | 92.70 | 54.63 |
Muscle Tissue | ||||||
Raw 1 | Clean 2 | Error (%) | Q20(%) 3 | Q30(%) 4 | GC Content (%) 5 | |
Standard | 51,324,601 | 49,558,730 | 0.034 | 96.19 | 90.55 | 52.86 |
Select | 57,170,688 | 55,292,644 | 0.033 | 96.46 | 91.12 | 54.16 |
Choice | 48,957,502 | 46,709,699 | 0.046 | 96.62 | 91.41 | 54.79 |
Standard to Select Adipose | ||||
Gene Code | Fold Change | p-adj | Gene Abbreviation | Gene Name |
Downregulated: | ||||
ENSBTAG00000008063 | −1.59 | 2.47 × 10−5 | PPARA | Peroxisome proliferator activated receptor alpha |
ENSBTAG00000014387 | −1.85 | 2.19 × 10−5 | PRKAB2 | Protein kinase AMP-activated non-catalytic subunit beta 2 |
ENSBTAG00000040128 | −1.24 | 5.96 × 10−5 | FZD4 | Frizzled class receptor 4 |
ENSBTAG00000006037 | −1.82 | 3.03 × 10−5 | WISP2 | WNT1 inducible signaling pathway protein 2 |
Upregulated: | ||||
ENSBTAG00000021077 | 446 | 3.70 × 10−8 | BOLA-DMB | Major histocompatibility complex, class II, DM beta |
Select to Choice Adipose | ||||
Gene Code | Fold Change | p-adj | Gene Abbreviation | Gene Name |
Downregulated: | ||||
ENSBTAG00000014911 | 3.65 | 2.46 × 10−5 | LEP | Leptin |
ENSBTAG00000018777 | 2.64 | 6.08 × 10−7 | ADCY5 | Adenylate cyclase type 5 |
Standard to Choice Adipose | ||||
Gene Code | Fold Change | p-adj | Gene Abbreviation | Gene Name |
Downregulated: | ||||
ENSBTAG00000034222 | 1.18 | 4.76 × 10−5 | CAB39L | Calcium binding protein 39 like |
ENSBTAG00000005198 | 1.80 | 2.62 × 10−7 | FGF1 | Fibroblast growth factor 1 |
ENSBTAG00000047202 | 1.37 | 8.74 × 10−6 | GRIN1 | Glutamate ionotropic receptor NMDA type subunit 1 |
ENSBTAG00000014911 | 1.35 | 0.000297 | LEP | Leptin |
ENSBTAG00000013108 | 2.19 | 9.91 × 10−5 | HK2 | Hexokinase 2 |
ENSBTAG00000017567 | 1.79 | 1.48 × 10−6 | ACC1 | Acetyl-CoA carboxylase alpha |
ENSBTAG00000045728 | 1.84 | 0.000115 | SCD1 | Stearoyl-CoA desaturase |
ENSBTAG00000008102 | 2.34 | 3.52 × 10−6 | CRTAC1 | Cartilage acidic protein 1 isoform 2 precursor |
ENSBTAG00000008153 | 1.03 | 0.032 | CAMSAP2 | Calmodulin regulated spectric associated protein family member 2 |
ENSBTAG00000011337 | 1.72 | 0.0037 | ANKRD33B | Ankyrin repeat domain 33B |
ENSBTAG00000013107 | 2.12 | 4.76 × 10−6 | SHANK1 | SH3 and multiple ankyrin repeat domains 1 |
ENSBTAG00000018473 | 3.70 | 0.039 | MARCO | Macrophage recptor with collagenous structure |
ENSBTAG00000026156 | 1.63 | 0.025 | VCL | Vinculin |
ENSBTAG00000015690 | 1.03 | 1.88 × 10−6 | PLIN4 | Perilipin 4 |
ENSBTAG00000003359 | 1.44 | 4.39 × 10−6 | ELOVL5 | ELOVL fatty acid elongase 5 |
Upregulated: | ||||
ENSBTAG00000027654 | −1.43 | 7.97 × 10−5 | EIF4EBP1 | Eukaryotic translation initiation factor 4E binding protein 1 |
ENSBTAG00000016071 | −1.56 | 0.000195 | HHIP | Hedgehog interacting protein |
ENSBTAG00000003658 | −1.23 | 4.50 × 10−5 | RELN | Reelin precursor |
ENSBTAG00000007446 | −1.49 | 8.45 × 10−5 | NGF | Nerve growth factor |
ENSBTAG00000007446 | −1.55 | 0.004 | SCART1 | Scavenger receptor family member expressed on T-cells |
ENSBTAG00000007554 | −1.26 | 0.022 | IFI6 | Interferon alpha inducible protein 6 |
ENSBTAG00000015182 | −1.58 | 0.0002 | STARD10 | StAR related lipid transfer domain containing 10 |
ENSBTAG00000039520 | −2.29 | 0.042 | SIRPB1 | Signal Regulatory Protein |
ENSBTAG00000009656 | −1.53 | 5.51 × 10−6 | BOLA-DQA2 | Major histocompatibility complex, class II, DQ alpha 2 |
ENSBTAG00000021077 | −11.68 | 1.40 × 10−6 | BOLA-DQB | Major histocompatibility complex, class II, DQ beta |
ENSBTAG00000038128 | −2.36 | 1.36 × 10−6 | BOLA-DQA5 | Major histocompatibility complex, class II, DQ alpha 5 |
Standard to Choice Muscle | ||||
Gene Code | Fold Change | p-adj | Gene Abbreviation | Gene Name |
Downregulated: | ||||
ENSBTAG00000017412 | −1.23 | 0.0.19 | SOCS6 | Suppressor of cytokine signaling 6 |
ENSBTAG00000021308 | −1.12 | 0.032 | IRS1 | Insulin receptor substrate 1 |
Upregulated: | ||||
ENSBTAG00000002362 | 1.69 | 0.0009 | APOLD1 | Apolipoprotein L domain containing 1 |
ENSBTAG00000032369 | 1.45 | 0.03 | NMI | N-myc and STAT interactor |
ENSBTAG00000009656 | 2.67 | 0.002 | BOLA-DQA2 | Major histocompatibility complex, class II, DQ alpha 2 |
ENSBTAG00000012451 | 1.36 | 0.041 | BOLA-DMB | Major histocompatibility complex, class II, DM beta |
Select Compared to Standard Adipose Tissues | ||||||
---|---|---|---|---|---|---|
GO Accession | Description | Category | p-Adj | Count | Up | Down |
GO:0006629 | Lipid metabolic process | Cellular | 0.042 | 956 | 4 | 0 |
GO:0010887 | Negative regulation of cholesterol storage | Cellular | 0.005 | 4 | 1 | 0 |
GO:0046426 | Negative regulation of JAK-STAT cascade | Cellular | 0.057 | 45 | 1 | 0 |
GO:0010888 | Negative regulation of lipid storage | Cellular | 0.017 | 12 | 1 | 0 |
GO:0010891 | Negative regulation of sequestering of triglyceride | Cellular | 0.007 | 5 | 1 | 0 |
Select Compared to Choice Adipose Tissues | ||||||
---|---|---|---|---|---|---|
GO Accession | Description | Category | p-Adj | Count | Up | Down |
GO:0060612 | Adipose tissue development | Cellular | 0.031 | 28 | 0 | 1 |
GO:0046427 | Positive regulation of JAK-STAT cascade | Cellular | 0.045 | 48 | 0 | 1 |
GO:00045723 | Positive regulation of fatty acid biosynthetic process | Cellular | 0.013 | 14 | 0 | 1 |
GO:0045923 | Postive regulation of fatty acid metabolic process | Cellular | 0.026 | 26 | 0 | 1 |
GO:0046889 | Positive regulation of lipid biosynthetic process | Cellular | 0.043 | 44 | 0 | 1 |
Choice Compared to Standard Adipose Tissues | ||||||
---|---|---|---|---|---|---|
GO Accession | Description | Category | p-Adj | Count | Up | Down |
GO:0006633 | Fatty acid biosynthetic process | Cellular | 0.000 | 104 | 5 | 1 |
GO:0034625 | Fatty acid elongation, monounsaturated fatty acid | Cellular | 0.048 | 7 | 2 | 0 |
GO:0006631 | Fatty acid metabolic process | Cellular | 0.014 | 254 | 5 | 1 |
GO:0060612 | Adipose tissue development | Cellular | 0.024 | 28 | 2 | 0 |
GO:0045723 | Positive regulation of fatty acid biosynthetic process | Cellular | 0.004 | 14 | 2 | 0 |
GO:0045923 | Postive regulation of fatty acid metabolic process | Cellular | 0.016 | 26 | 2 | 0 |
GO:0004321 | Fatty-acyl-CoA synthase activity | Cellular | 0.033 | 4 | 0 | 1 |
Standard Compared to Choice Muscle Tissues | ||||||
---|---|---|---|---|---|---|
GO Accession | Description | Category | p-Adj | Count | Up | Down |
GO:0001578 | Microtubule bundle formation | Cellular | 0.006 | 75 | 1 | 1 |
GO:0046785 | Microtubule polymerization | Cellular | 0.073 | 51 | 0 | 1 |
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Haderlie, S.A.; Hieber, J.K.; Boles, J.A.; Berardinelli, J.G.; Thomson, J.M. Molecular Pathways for Muscle and Adipose Tissue Are Altered between Beef Steers Classed as Choice or Standard. Animals 2023, 13, 1947. https://doi.org/10.3390/ani13121947
Haderlie SA, Hieber JK, Boles JA, Berardinelli JG, Thomson JM. Molecular Pathways for Muscle and Adipose Tissue Are Altered between Beef Steers Classed as Choice or Standard. Animals. 2023; 13(12):1947. https://doi.org/10.3390/ani13121947
Chicago/Turabian StyleHaderlie, Sarah A., Jordan K. Hieber, Jane A. Boles, James G. Berardinelli, and Jennifer M. Thomson. 2023. "Molecular Pathways for Muscle and Adipose Tissue Are Altered between Beef Steers Classed as Choice or Standard" Animals 13, no. 12: 1947. https://doi.org/10.3390/ani13121947
APA StyleHaderlie, S. A., Hieber, J. K., Boles, J. A., Berardinelli, J. G., & Thomson, J. M. (2023). Molecular Pathways for Muscle and Adipose Tissue Are Altered between Beef Steers Classed as Choice or Standard. Animals, 13(12), 1947. https://doi.org/10.3390/ani13121947