Identification of SNPs and Candidate Genes Associated with Monocyte/Lymphocyte Ratio and Neutrophil/Lymphocyte Ratio in Duroc × Erhualian F2 Population
Abstract
:1. Introduction
2. Results
2.1. MLR and NLR of Duroc × Erhualian F2 Resource Population Exhibited High Heritability
2.2. GWAS Analysis Identified Five SNPs Associated with MLR Trait
2.3. GWAS Analysis Identified Four SNPs Associated with NLR Trait
2.4. Functional Enrichment Analysis Identified Multiple Candidate Genes for MLR and NLR
3. Discussion
4. Materials and Methods
4.1. Animals
4.2. Phenotype
4.3. Genotype
4.4. Estimation of Genetic Variance and Heritability
4.5. Genome-Wide Association Study
4.6. Identification and Functional Analysis of Candidate Genes
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Trait | 1 ± SE | 2 ± SE | 3 ± 4 SE |
---|---|---|---|
MLR | 0.008 ± 0.002 | 0.004 ± 0.001 | 0.649 ± 0.080 |
NLR | 1.384 ± 0.273 | 0.627 ± 0.118 | 0.688 ± 0.076 |
SNP | 1 Chr | Position | Model | 2 p-Value |
---|---|---|---|---|
INRA0058297 | 2 | 7110358 | MLMA-LOCO | 1.51 × 10−5 |
BLINK | 2.71 × 10−7 * | |||
ASGA0022554 | 4 | 116094650 | MLM | 9.41 × 10−6 |
MLMA-LOCO | 6.07 × 10−6 | |||
H3GA0032308 | 11 | 54602515 | FarmCPU | 8.25 × 10−7 * |
BLINK | 2.27 × 10−8 * | |||
DRGA0011794 | 12 | 25068363 | MLMA-LOCO | 2.28 × 10−5 |
BLINK | 6.92 × 10−7 * | |||
ALGA0075031 | 14 | 9571032 | MLMA-LOCO | 2.54 × 10−5 |
FarmCPU | 2.98 × 10−12 * |
SNP | 1 Chr | Position | Model | 2 p-Value |
---|---|---|---|---|
ASGA0006650 | 1 | 223397796 | MLM | 2.53 × 10−5 |
MLMA-LOCO | 1.08 × 10−5 | |||
FarmCPU | 2.21 × 10−6 | |||
ASGA0023911 | 5 | 2488153 | MLMA-LOCO | 2.47 × 10−5 |
FarmCPU | 4.67 × 10−6 | |||
BLINK | 3.50 × 10−8 * | |||
ASGA0057335 | 13 | 26494790 | MLMA-LOCO | 1.94 × 10−5 |
FarmCPU | 8.84 × 10−6 | |||
M1GA0023131 | 18 | 9230153 | MLM | 1.32 × 10−6 * |
MLMA-LOCO | 8.52 × 10−7 * | |||
FarmCPU | 2.52 × 10−8 * | |||
BLINK | 6.60 × 10−9 * |
Trait | Gene | 1 Chr | 2 Term | Database | ID | 3 p-Value |
---|---|---|---|---|---|---|
MLR | SYVN1 | 2 | Ubiquitin mediated proteolysis | KEGG PATHWAY | ssc04120 | 0.014 |
negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway | Gene Ontology | GO:1902236 | 0.016 | |||
TM7SF2 | 2 | Steroid biosynthesis | KEGG PATHWAY | ssc00100 | 0.027 | |
CDCA5 | 2 | MicroRNAs in cancer | KEGG PATHWAY | ssc05206 | 0.004 | |
BATF2 | 2 | Endocytosis | KEGG PATHWAY | ssc04144 | 0.041 | |
myeloid dendritic cell differentiation | Gene Ontology | GO:0043011 | 0.019 | |||
defense response to protozoan | Gene Ontology | GO:0042832 | 0.020 | |||
ATG2A | 2 | Autophagy—other | KEGG PATHWAY | ssc04136 | 0.043 | |
MIR192 | 2 | MicroRNAs in cancer | KEGG PATHWAY | ssc05206 | 0.004 | |
SLITRK1 | 11 | synaptic membrane adhesion | Gene Ontology | GO:0099560 | 0.027 | |
CALCOCO2 | 12 | response to interferon-gamma | Gene Ontology | GO:0034341 | 0.023 | |
SNF8 | 12 | positive regulation of exosomal secretion | Gene Ontology | GO:1903543 | 0.009 | |
IGF2BP1 | 12 | MicroRNAs in cancer | KEGG PATHWAY | ssc05206 | 0.004 | |
CDCA2 | 14 | positive regulation of protein dephosphorylation | Gene Ontology | GO:0035307 | 0.021 | |
NLR | KLF9 | 1 | cellular response to thyroid hormone stimulus | Gene Ontology | GO:0097067 | 0.006 |
negative regulation of keratinocyte proliferation | Gene Ontology | GO:0010839 | 0.006 | |||
TBC1D22A | 5 | 14-3-3 protein binding | Gene Ontology | GO:0071889 | 0.006 | |
CERK | 5 | sphingolipid metabolic process | Gene Ontology | GO:0006665 | 0.009 | |
GRAMD4 | 5 | positive regulation of cysteine-type endopeptidase activity involved in apoptotic process | Gene Ontology | GO:0043280 | 0.016 | |
POMGNT2 | 13 | Mannose type O-glycan biosynthesis | KEGG PATHWAY | ssc00515 | 0.013 | |
KDM7A | 18 | histone demethylase activity (H3-K27 specific) | Gene Ontology | GO:0071558 | 0.003 |
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Qiao, J.; Xu, M.; Xu, F.; Che, Z.; Han, P.; Dai, X.; Miao, N.; Zhu, M. Identification of SNPs and Candidate Genes Associated with Monocyte/Lymphocyte Ratio and Neutrophil/Lymphocyte Ratio in Duroc × Erhualian F2 Population. Int. J. Mol. Sci. 2024, 25, 9745. https://doi.org/10.3390/ijms25179745
Qiao J, Xu M, Xu F, Che Z, Han P, Dai X, Miao N, Zhu M. Identification of SNPs and Candidate Genes Associated with Monocyte/Lymphocyte Ratio and Neutrophil/Lymphocyte Ratio in Duroc × Erhualian F2 Population. International Journal of Molecular Sciences. 2024; 25(17):9745. https://doi.org/10.3390/ijms25179745
Chicago/Turabian StyleQiao, Jiakun, Minghang Xu, Fangjun Xu, Zhaoxuan Che, Pingping Han, Xiangyu Dai, Na Miao, and Mengjin Zhu. 2024. "Identification of SNPs and Candidate Genes Associated with Monocyte/Lymphocyte Ratio and Neutrophil/Lymphocyte Ratio in Duroc × Erhualian F2 Population" International Journal of Molecular Sciences 25, no. 17: 9745. https://doi.org/10.3390/ijms25179745