Genes Involved in Feed Efficiency Identified in a Meta-Analysis of Rumen Tissue from Two Populations of Beef Steers
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Cattle Populations
2.2. Sample Preparation
2.3. RNA-Sequencing
2.4. Data Analysis
3. Results
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene Symbol | PNominal | PFDR | Consistent LFC 1 |
---|---|---|---|
LOC789569 | 6.71 × 10−9 | 9.52 × 10−5 | N |
LOC101904916 | 5.48 × 10−8 | 0.000389 | Y |
TECR | 1.44 × 10−7 | 0.000680 | Y |
ATP6AP1 | 2.96 × 10−7 | 0.000788 | N |
PAMR1 | 3.11 × 10−7 | 0.000788 | N |
EGLN3 | 7.51 × 10−7 | 0.00120 | N |
LOC100848775 | 7.60 × 10−7 | 0.00120 | N |
LYPD3 | 5.98 × 10−7 | 0.00120 | N |
KAT2B | 2.46 × 10−6 | 0.00234 | Y |
KLK13 | 2.22 × 10−6 | 0.00234 | N |
PLP2 | 2.43 × 10−6 | 0.00234 | N |
HTRA1 | 2.76 × 10−6 | 0.00245 | N |
RHOG | 3.97 × 10−6 | 0.00313 | N |
TUBA4A | 3.81 × 10−6 | 0.00313 | Y |
CD52 | 7.06 × 10−6 | 0.00501 | Y |
SH3BGRL3 | 7.81 × 10−6 | 0.00528 | N |
SESN3 | 1.02 × 10−5 | 0.00636 | Y |
ZDHHC5 | 1.07 × 10−5 | 0.00636 | Y |
ZNF750 | 1.07 × 10−5 | 0.00636 | N |
RPS15 | 1.85 × 10−5 | 0.0101 | Y |
ODF2L | 2.70 × 10−5 | 0.0137 | Y |
SH3GLB2 | 2.81 × 10−5 | 0.0138 | Y |
HGS | 3.63 × 10−5 | 0.0172 | Y |
MYL12A | 4.15 × 10−5 | 0.0190 | Y |
ZDHHC3 | 4.57 × 10−5 | 0.0203 | N |
ASB3 | 4.79 × 10−5 | 0.0205 | Y |
MYADM | 4.90 × 10−5 | 0.0205 | Y |
LOC104976804 | 5.56 × 10−5 | 0.0219 | Y |
LYPD2 | 5.45 × 10−5 | 0.0219 | N |
ASB2 | 5.90 × 10−5 | 0.0220 | N |
CBX2 | 5.75 × 10−5 | 0.0220 | N |
VARS | 6.67 × 10−5 | 0.0237 | Y |
GLULP | 7.17 × 10−5 | 0.0242 | Y |
RC3H1 | 7.02 × 10−5 | 0.0242 | Y |
HSPB1 | 7.77 × 10−5 | 0.0251 | N |
ZNF146 | 7.65 × 10−5 | 0.0251 | N |
LY6G6C | 8.04 × 10−5 | 0.0254 | N |
CYP1B1 | 9.02 × 10−5 | 0.0272 | N |
PSMB5 | 9.26 × 10−5 | 0.0274 | Y |
ALPK1 | 9.87 × 10−5 | 0.0277 | Y |
DNM2 | 9.94 × 10−5 | 0.0277 | N |
PSMB6 | 9.56 × 10−5 | 0.0277 | Y |
B3GNT3 | 0.000119 | 0.0294 | N |
C1QBP | 0.000117 | 0.0294 | Y |
NBEAL1 | 0.000120 | 0.0294 | Y |
SH3GL1 | 0.000110 | 0.0294 | Y |
IL1RN | 0.000130 | 0.0312 | N |
TUBB | 0.000135 | 0.0314 | Y |
SLC35D1 | 0.000149 | 0.0328 | N |
TMEM54 | 0.000152 | 0.0331 | N |
LOC104971374 | 0.000171 | 0.0357 | N |
CCDC66 | 0.000178 | 0.0367 | N |
MAN2B1 | 0.000189 | 0.0382 | N |
NDUFA9 | 0.000194 | 0.0382 | Y |
CFL1 | 0.000197 | 0.0383 | Y |
PIBF1 | 0.000199 | 0.0383 | N |
C7H5orf46 | 0.000208 | 0.0384 | N |
LOC100848030 | 0.000206 | 0.0384 | N |
YPEL3 | 0.000204 | 0.0384 | N |
MTERF2 | 0.000216 | 0.0392 | N |
FRK | 0.000219 | 0.0394 | Y |
ATR | 0.000239 | 0.0409 | N |
REXO5 | 0.000238 | 0.0409 | N |
RUVBL1 | 0.000251 | 0.0425 | Y |
LOC104973218 | 0.000257 | 0.0425 | N |
PRR5 | 0.000258 | 0.0425 | Y |
DNAJB1 | 0.000265 | 0.0432 | N |
MTAP | 0.000274 | 0.0438 | N |
MAPK1 | 0.000278 | 0.0439 | Y |
TMSB10 | 0.000298 | 0.0461 | N |
UACA | 0.000298 | 0.0461 | Y |
ARAF | 0.000305 | 0.0465 | N |
DCUN1D4 | 0.000317 | 0.0465 | Y |
GABARAP | 0.000315 | 0.0465 | N |
MALL | 0.000318 | 0.0465 | N |
RGS5 | 0.000316 | 0.0465 | Y |
FAM107B | 0.000335 | 0.0476 | Y |
LOC100139345 | 0.000345 | 0.0476 | N |
PNPT1 | 0.000346 | 0.0476 | N |
RWDD3 | 0.000334 | 0.0476 | N |
SNX15 | 0.000341 | 0.0476 | N |
ELF5 | 0.000354 | 0.0483 | Y |
S100A11 | 0.000360 | 0.0486 | Y |
Pathway | #DEG 1 | P | Genes |
---|---|---|---|
Renal Cell Carcinoma | 3 | 0.004 | ARAF, EGLN3, MAPK1 |
Salmonella Infection | 6 | 0.007 | DNM2, MAPK1, MYL12A, RHOG, TUBA4A, TUBB |
p53 Signaling Pathway | 2 | 0.012 | ATR, SESN3 |
Phagosome | 4 | 0.012 | ATP6AP1, HGS, TUBA4A, TUBB |
Prion Disease | 6 | 0.014 | MAPK1, NDUFA9, PSMB5, PSMB6, TUBA4A, TUBB |
Parkinson Disease | 5 | 0.016 | NDUFA9, PSMB5, PSMB6, TUBA4A, TUBB |
Alzheimer Disease | 5 | 0.017 | ARAF, MAPK1, NDUFA9, PSMB5, PSMB6, TUBA4A, TUBB |
Gap Junction | 3 | 0.019 | MAPK1, TUBA4A, TUBB |
Pathways of Neurodegeneration—Multiple Diseases | 7 | 0.019 | ARAF, MAPK1, NDUFA9, PSMB5, PSMB6, TUBA4A, TUBB |
Huntington Disease | 5 | 0.022 | NDUFA9, PSMB5, PSMB6, TUBA4A, TUBB |
Bladder Cancer | 2 | 0.023 | ARAF, MAPK1, NDUFA9, PSMB5, PSMB6, TUBA4A, TUBB |
Axon Guidance | 3 | 0.028 | CFL1, MAPK1, MYL12A |
Serotonergic Synapse | 2 | 0.029 | ARAF, MAPK1 |
Regulation of Actin Cytoskeleton | 4 | 0.031 | ARAF, CFL1, MAPK1, MYL12A |
Fc Gamma R-mediated Phagocytosis | 3 | 0.039 | CFL1, DNM2, MAPK1 |
Human T-cell Leukemia Virus 1 Infection | 3 | 0.041 | ATR, KAT2B, MAPK1 |
Amyotrophic Lateral Sclerosis | 5 | 0.041 | NDUFA9, PSMB5, PSMB6, TUBA4A, TUBB |
Bacterial Invasion of Epithelial Cells | 2 | 0.045 | DNM2, RHOG |
Parathyroid Hormone Synthesis, Secretion and Action | 2 | 0.047 | ARAF, MAPK1 |
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Lindholm-Perry, A.K.; Meyer, A.M.; Kern-Lunbery, R.J.; Cunningham-Hollinger, H.C.; Funk, T.H.; Keel, B.N. Genes Involved in Feed Efficiency Identified in a Meta-Analysis of Rumen Tissue from Two Populations of Beef Steers. Animals 2022, 12, 1514. https://doi.org/10.3390/ani12121514
Lindholm-Perry AK, Meyer AM, Kern-Lunbery RJ, Cunningham-Hollinger HC, Funk TH, Keel BN. Genes Involved in Feed Efficiency Identified in a Meta-Analysis of Rumen Tissue from Two Populations of Beef Steers. Animals. 2022; 12(12):1514. https://doi.org/10.3390/ani12121514
Chicago/Turabian StyleLindholm-Perry, Amanda K., Allison M. Meyer, Rebecca J. Kern-Lunbery, Hannah C. Cunningham-Hollinger, Taran H. Funk, and Brittney N. Keel. 2022. "Genes Involved in Feed Efficiency Identified in a Meta-Analysis of Rumen Tissue from Two Populations of Beef Steers" Animals 12, no. 12: 1514. https://doi.org/10.3390/ani12121514