Table 1.
Effect of photoperiod on differentially expressed genes in the mammary gland of dry cows
| Gene Symbol | Gene Name | Fold Change | P Value | Probe Set ID | IPA Biofunctions | GO Molecular Function | GO Biological Function |
|---|---|---|---|---|---|---|---|
| Expression Higher in Short Day Photoperiod | |||||||
| ADAM1B | A disintegrin and metalloproteinase 1B | −1.54 | 0.0382 | Bt.12799.1.S1_at | CI, CM | oxidoreductase activity | |
| AGA | aspartylglucosaminidase | −1.85 | < 0.0001 | Bt.3115.1.A1_at | |||
| ALDH5A1 | aldehyde dehydrogenase 5 member A1 | −1.91 | 0.0025 | Bt.2173.1.S1_at | CI, SMB | nucleic acid/amino acid metabolic process | |
| AKR1C3‡ | aldo-keto reductase family 1, member C3 | −1.61 | 0.0028 | Bt.23094.4.S1_at | SMB | proliferation, differentiation | |
| BCHE‡ | butyrylcholinesterase | −1.85 | 0.0494 | Bt.28385.1.A1_at | CI, SMB | hydrolase activity | |
| BoLA†‡ | major histocompatibility complex (MHC) I | −5.15 | 0.0001* | Bt.29823.1.S1_x_at | receptor activity | antigen processing/presentation, cellular defense | |
| BoLA-DQB1†‡ | MHC class II, DQ β1 | −3.48 | < 0.0001* | Bt.350.1.S1_at | CI, HSD, ICT | antigen processing/presentation, cellular defense response | |
| BoLA-DQA1† | MHC class II DQ α1 | −7.07 | < 0.0001* | Bt.22867.2.A1_at | CI, HSD, ICT | ||
| BoLA-DQA2† | MHC, class II, DQ α2 | −6.29 | < 0.0001* | Bt.4751.2.S1_at | |||
| BoLA-DQA3† | MHC, class II DQ α3 | −3.20 | < 0.0001 | Bt.4751.2.S1_at | |||
| BoLA-N† | MHC class I antigen | −7.95 | 0.0003 | Bt.5324.1.S1_s_at | |||
| BoLA-NC1 | MHC class I antigen | −3.72 | < 0.0001* | Bt.28022.1.A1_at | |||
| BTN3A2 | butyrophilin, subfamily 3A | −2.17 | 0.0021 | Bt.28475.1.A1_at | ubiquitin-protein ligase activity | immune system process | |
| DMP1 | dentin matrix acidic phosphoprotein 1 | −2.27 | 0.0284 | Bt.554.1.S1_at | CM | ||
| GBP1‡ | guanylate binding protein 1 | −1.54 | 0.0006 | Bt.24012.1.A1_at | invasion, tubulation, proliferation | ||
| gzmA | granzyme A | −1.58 | 0.0227 | Bt.29672.1.S1_at | serine-type peptidase activity | ||
| IgCgamma | IgG2a heavy chain constant region | −1.61 | 0.013 | Bt.12490.2.A1_x_at | |||
| KERA | Keratocan | −1.98 | 0.0022 | Bt.5391.1.S1_at | HSD | receptor activity | visual perception; GCPR/cytokine-mediated signaling |
| KIR2DS1 | killer cell immunoglobulin-like receptor 2DS1 | −1.56 | 0.0027 | Bt.11174.2.S1_at | |||
| MAL | mal, T-cell differentiation protein | −1.53 | 0.0100 | Bt.4060.1.S1_at | |||
| MAN1C1 | mannosidase, alpha, class 1C, member 1 | −1.52 | 0.0191 | Bt.10587.1.S1_at | hydrolase activity | metabolic process, glycosylation, proteolysis | |
| MAP1LC3C | microtubule-associated protein 1 light chain 3 γ | −1.63 | 0.0062 | Bt.3000.2.S1_a_at | cytoskeleton, microtubule binding | ||
| MCPH1 | microcephalin 1 | −1.56 | 0.0021 | Bt.11907.1.A1_at | |||
| MOXD1 | monooxygenase, DBH-like 1 | −1.56 | 0.0253 | Bt.20519.1.A1_at | oxidoreductase activity | neurological system, metabolic process | |
| OAS1X | 2′,5′-oligoadenylate synthetase 1, 40/46 kDa | −1.75 | 0.0001 | Bt.20922.1.S1_at | |||
| PRSS2 | protease, serine, 2 | −11.1 | < 0.0001* | Bt.4404.1.A1_at | |||
| SEPT2 | septin 2 | −1.81 | 0.0001 | Bt.20352.1.S1_at | |||
| SLC27A6‡ | solute carrier family 27 (fatty acid transporter), member 6 | −1.63 | 0.0104 | Bt.26921.1.A1_at | SMB | ligase activity, transporter activity | immune system process, fatty acid metabolic process |
| SLPI | secretory leukocyte peptidase inhibitor | −1.61 | 0.0183 | Bt.9736.1.S1_at | protein binding, endopeptidase inhibitor | proteolysis | |
| Expression Lower in Short Day Photoperiod | |||||||
| ABCC4 | ATP-binding cassette, subfamily C 4 | 2.10 | 0.0001 | Bt.27292.1.S1_at | |||
| BEX4 | brain expressed, X-linked 4 | 1.65 | 0.0034 | Bt.3698.1.S1_at | |||
| BoLA-DQA5‡ | MHC class II, DQ α5 | 28.5 | < 0.0001* | Bt.215.1.S1_at | CI, HSD, ICT | ||
| BoLA-DRB3‡ | MHC class II, DRB3 | 8.38 | < 0.0027* | Bt.20925.1.S1_at | |||
| CCR1‡ | chemokine (C-C motif) receptor 1 | 1.58 | 0.0013 | Bt.1377.1.S1_at | CI,SMB, CM, HSD, ICT | G-protein coupled receptor activity | immune/stimulus response, cytokine-mediated signaling |
| CD68‡ | CD68 molecule | 1.65 | 0.0106 | Bt.2334.1.S1_at | CI | lysosomal transport, proteolysis | |
| CLEC4E | C-type lectin domain family 4, member E | 1.86 | 0.0156 | Bt.16271.2.A1_at | CI, CM, SD, ICT | ||
| CSTB | cystatin B (stefin B) | 1.54 | 0.0068 | Bt.24354.1.S1_at | protein binding, endopeptidase inhibitor activity | proteolysis | |
| DDC | dopa decarboxylase | 1.75 | 0.003 | Bt.115.1.S1_at | CI, SMB | ||
| DEFB1 | defensin, beta 1 | 2.14 | 0.0007 | Bt.13125.1.S1_s_at | immune system, metabolic process, response to stress | ||
| DEFB5† | defensin beta 5 | 4.53 | 0.0005 | Bt.13125.1.S1_at | immune system. metabolic process, response to stress | ||
| DRD1 | dopamine receptor D1 | 1.6 | 0.0173 | Bt.9029.1.S1_at | CI, SMB, CM | G protein-coupled receptor activity | neurological system, GPCR/cell-cell signaling |
| F13A1† | coagulation factor XIII, A1 polypeptide | 1.64 | 0.0123 | Bt.19845.2.A1_at | CI,CM, HSD, ICT | acyltransferase activity | immune system, protein modification, blood coagulation |
| FXYD3 | FXYD domain containing ion transport regulator 3 | 1.53 | 0.0272 | Bt.9573.1.S1_a_at | ion channel activity, protein binding | ion transport, signal transduction | |
| GIMAP8 | GTPase IMAP family member 8-like | 1.81 | 0.0001 | Bt.26769.1.S1_at | |||
| GPNMB†‡ | glycoprotein (transmembrane) nmb | 1.94 | 0.0108 | Bt.9807.1.S1_at | |||
| IGL@ | immunoglobulin light chain, λ gene cluster | 1.52 | 0.0078 | ||||
| IL17RB‡ | interleukin 17 receptor B | 1.64 | 0.0118 | Bt.24532.1.A1_at | CM, HSD, ICT | ||
| IL8 | interleukin 8 | 1.67 | 0.002 | Bt.155.1.S1_at | CI,SMB, CM,HSD, ICT | chemokine activity | macrophage activation, cytokine-mediated signaling |
| KIR2DL5A | killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 5A | 1.89 | 0.002 | Bt.11174.1.S1_at | |||
| NPL | N-acetylneuraminate pyruvate lyase | 1.64 | 0.0006 | Bt.26155.1.A1_at | lyase activity | cellular amino acid biosynthetic process | |
| PEBP4 | phosphatidylethanolamine-binding protein 4 | 2.93 | 0.0002 | Bt.14398.1.S1_at | kinase regulator activity | signal transduction | |
| PTI† | pancreatic trypsin inhibitor | 2.96 | 0.0111 | Bt.28518.1.S1_at | |||
| RARRES1 | retinoic acid receptor responder | 1.61 | 0.0386 | Bt.24933.1.S1_at | CM | ||
| S100A12‡ | S100 calcium binding protein A12 | 1.91 | 0.019 | Bt.357.1.S1_at | CI, ICT | calcium ion, calmodulin binding | immune response, cell cycle |
| S100A8 | S100 calcium binding protein A8 | 1.91 | 0.0142 | Bt.9360.1.S1_at | CI,CM, ICT | calcium ion/calmodulin binding | macrophage activation, cell cycle |
| SDS | serine dehydratase | 1.61 | 0.0391 | Bt.5878.1.A1_at | SMB | ||
| SERPINA3 | serpin peptidase inhibitor A3 | 1.56 | 0.0036 | Bt.5362.1.S1_at | CM, HSD, ICT | protein binding, endopeptidase inhibitor activity | proteolysis |
| SFRP1 | secreted frizzled-related protein 1 | 1.55 | 0.0276 | Bt.5226.1.S1_at | CI CM, HSD, ICT | ||
| SPADH1 | spermadhesin 1 | 2.24 | 0.0295 | Bt.457.1.S1_at | |||
| TMEM183A‡ | transmembrane protein 183A | 1.55 | 0.0004 | Bt.17595.3.A1_at | |||
| TRAF3IP3‡ | TRAF3 interacting protein 3 | 1.56 | 0.0242 | Bt.2266.3.S1_at | |||
| VNN1 | vanin 1 | 1.84 | 0.0446 | Bt.28243.1.S1_a_at | CI | hydrolase activity | signal transduction, adhesion, vitamin metab |
| VNN2 | vanin 2 | 1.72 | 0.0061 | Bt.19160.1.A1_at | |||
| VSTM1 | V-set and transmembrane domain 1 | 1.59 | 0.0071 | Bt.9131.1.S1_at | |||
Biopsies were obtained from cows exposed to long or short day photoperiod. Microarray analysis was conducted on purified RNA using Affymetrix GeneChip Bovine Genome Arrays. Genes identified in response to photoperiod treatment (long day-short day). Differential expression was attributed to genes meeting the criteria of P ≤ 0.05 and fold-change ≥ |1.5|.
†
Multiple probes were differentially expressed; average fold-change and P values are shown. Top 5 Ingenuity Pathway Analysis (IPA) biofunctions and corresponding genes identified as differentially expressed in response to photoperiod.
CI, cell-to-cell interactions; SMB, small molecule biochemistry; CM, cell movement; HSD, hematological system development; ICT, immune cell trafficking.
Gene Ontology (GO) molecular and biological functions were assigned using Affymetrix NetAffx Analysis Center (http://www.affymetrix.com).
‡
Genes in common with the bovine lactation genome (35).
*
Genes meeting the criteria of false discovery rate ≤ 0.2.