{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,21]],"date-time":"2025-11-21T18:12:31Z","timestamp":1763748751431,"version":"build-2065373602"},"reference-count":43,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2022,9,19]],"date-time":"2022-09-19T00:00:00Z","timestamp":1663545600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Inner Mongolia Natural Science Foundation project","award":["2021ZD05","2021ZD0009","2021GG0008","2021GG0025","2019ZD016","2021YFD1200905"],"award-info":[{"award-number":["2021ZD05","2021ZD0009","2021GG0008","2021GG0025","2019ZD016","2021YFD1200905"]}]},{"name":"Inner Mongolia Natural Science Foundation project","award":["2021ZD05","2021ZD0009","2021GG0008","2021GG0025","2019ZD016","2021YFD1200905"],"award-info":[{"award-number":["2021ZD05","2021ZD0009","2021GG0008","2021GG0025","2019ZD016","2021YFD1200905"]}]},{"name":"Inner Mongolia science and technology plan project","award":["2021ZD05","2021ZD0009","2021GG0008","2021GG0025","2019ZD016","2021YFD1200905"],"award-info":[{"award-number":["2021ZD05","2021ZD0009","2021GG0008","2021GG0025","2019ZD016","2021YFD1200905"]}]},{"name":"Inner Mongolia science and technology plan project","award":["2021ZD05","2021ZD0009","2021GG0008","2021GG0025","2019ZD016","2021YFD1200905"],"award-info":[{"award-number":["2021ZD05","2021ZD0009","2021GG0008","2021GG0025","2019ZD016","2021YFD1200905"]}]},{"name":"Inner Mongolia science and technology plan project","award":["2021ZD05","2021ZD0009","2021GG0008","2021GG0025","2019ZD016","2021YFD1200905"],"award-info":[{"award-number":["2021ZD05","2021ZD0009","2021GG0008","2021GG0025","2019ZD016","2021YFD1200905"]}]},{"DOI":"10.13039\/501100012166","name":"National Key research and development Program","doi-asserted-by":"publisher","award":["2021ZD05","2021ZD0009","2021GG0008","2021GG0025","2019ZD016","2021YFD1200905"],"award-info":[{"award-number":["2021ZD05","2021ZD0009","2021GG0008","2021GG0025","2019ZD016","2021YFD1200905"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Maternal parity is an important physiological factor influencing beef cow reproductive performance. However, there are few studies on the influence of different calving periods on early growth and postpartum diseases. Here, we conducted blood transcriptomic analysis on cows of different parities for gene discovery. We used Short Time Series Expression Miner (STEM) analysis to determine gene expression levels in cows of various parities and divided multiple parities into three main periods (nulliparous, primiparous, and multiparous) for subsequent analysis. Furthermore, the top 15,000 genes with the lowest median absolute deviation (MAD) were used to build a co-expression network using weighted correlation network analysis (WGCNA), and six independent modules were identified. Combing with Exon Wide Selection Signature (EWSS) and protein-protein interaction (PPI) analysis revealed that TPCN2, KIF22, MICAL3, RUNX2, PDE4A, TESK2, GPM6A, POLR1A, and KLHL6 involved in early growth and postpartum diseases. The GO and KEGG enrichment showed that the Parathyroid hormone synthesis, secretion, and action pathway and stem cell differentiation function-related pathways were enriched. Collectively, our study revealed candidate genes and gene networks regulating the early growth and postpartum diseases and provided new insights into the potential mechanism of reproduction advantages of different parity selection.<\/jats:p>","DOI":"10.3390\/genes13091671","type":"journal-article","created":{"date-parts":[[2022,9,19]],"date-time":"2022-09-19T21:47:27Z","timestamp":1663624047000},"page":"1671","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Blood Transcriptome Analysis of Beef Cow with Different Parity Revealed Candidate Genes and Gene Networks Regulating the Postpartum Diseases"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1762-3461","authenticated-orcid":false,"given":"Yanda","family":"Yang","sequence":"first","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010010, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7146-2067","authenticated-orcid":false,"given":"Chencheng","family":"Chang","sequence":"additional","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010010, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Batu","family":"Baiyin","sequence":"additional","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010010, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zaixia","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010010, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lili","family":"Guo","sequence":"additional","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010010, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Le","family":"Zhou","sequence":"additional","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010010, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bin","family":"Liu","sequence":"additional","affiliation":[{"name":"Inner Mongolia Mongol BioNew Technology Co., Ltd., Hohhot 010010, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Caixia","family":"Shi","sequence":"additional","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010010, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wenguang","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010010, China"},{"name":"College of Life Science, Inner Mongolia Agricultural University, Hohhot 010010, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,9,19]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1016\/j.tvjl.2012.07.031","article-title":"The Impact of Dystocia on Dairy Calf Health, Welfare, Performance and Survival","volume":"195","author":"Barrier","year":"2013","journal-title":"Vet. J."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1016\/j.meatsci.2017.04.019","article-title":"Animal breeding strategies can improve meat quality attributes within entire populations","volume":"132","author":"Berry","year":"2017","journal-title":"Meat Sci."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"6383","DOI":"10.3168\/jds.2019-17963","article-title":"Association of genomically enhanced and parent average breeding values with cow performance in Nordic dairy cattle","volume":"103","author":"Bengtsson","year":"2020","journal-title":"J. Dairy Sci."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"2523","DOI":"10.3168\/jds.2019-17431","article-title":"Observed progeny performance validates the benefit of mating genetically elite beef sires to dairy females","volume":"103","author":"Berry","year":"2020","journal-title":"J. Dairy Sci."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1016\/j.tvjl.2019.01.006","article-title":"Border disease in cattle","volume":"246","author":"Braun","year":"2019","journal-title":"Vet. J."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1412","DOI":"10.2527\/jas.2013-6723","article-title":"Genetics of reproductive performance in seasonal calving beef cows and its association with performance traits","volume":"92","author":"Berry","year":"2014","journal-title":"J. Anim. Sci."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"e13504","DOI":"10.1111\/asj.13504","article-title":"Genomic imprinting variances of beef carcass traits and physiochemical characteristics in Japanese Black cattle","volume":"92","author":"Inoue","year":"2021","journal-title":"Anim. Sci. J."},{"key":"ref_8","first-page":"218","article-title":"Relationship between reproductive management practices and fertility in primiparous and multiparous dairy cows","volume":"83","author":"Fodor","year":"2019","journal-title":"Can. J. Vet. Res. Rev. Can. Rech. Vet."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/j.prevetmed.2018.04.006","article-title":"On-farm mortality and related risk factors in Estonian dairy cows","volume":"155","author":"Reimus","year":"2018","journal-title":"Prev. Vet. Med."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1146\/annurev-animal-021815-111406","article-title":"Milk Production and Fertility in Cattle","volume":"4","author":"Berry","year":"2016","journal-title":"Annu. Rev. Anim. Biosci."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1016\/j.cvfa.2018.02.005","article-title":"Foreign Animal Disease Outbreaks","volume":"34","author":"Sanderson","year":"2018","journal-title":"Vet. Clin. N. Am. Food Anim. Pract."},{"key":"ref_12","first-page":"1913","article-title":"Economic Selection Index Development for Beefmaster Cattle Ii: General-Purpose Breeding Objective","volume":"95","author":"Ochsner","year":"2017","journal-title":"J. Anim. Sci."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"skaa322","DOI":"10.1093\/jas\/skaa322","article-title":"Validation of a beef cattle maternal breeding objective based on a cross-sectional analysis of a large national cattle database","volume":"98","author":"Twomey","year":"2020","journal-title":"J. Anim. Sci."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1016\/j.rvsc.2018.06.021","article-title":"Cow mortality as an indicator of animal welfare in dairy herds","volume":"119","author":"Thomsen","year":"2018","journal-title":"Res. Vet. Sci."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/jbg.12073","article-title":"Marbled Japanese Black cattle","volume":"131","author":"Hirooka","year":"2014","journal-title":"J. Anim. Breed. Genet."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1080\/09168451.2018.1528139","article-title":"Comparative metabolomics of Japanese Black cattle beef and other meats using gas chromatography\u2013mass spectrometry","volume":"83","author":"Ueda","year":"2019","journal-title":"Biosci. Biotechnol. Biochem."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"e13663","DOI":"10.1111\/asj.13663","article-title":"Development of DNA markers for improvement of meat quality in a Japanese Black cattle population in Hyogo Prefecture","volume":"92","author":"Sasazaki","year":"2021","journal-title":"Anim. Sci. J."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.3317","article-title":"HISAT: A fast spliced aligner with low memory requirements","volume":"12","author":"Kim","year":"2015","journal-title":"Nat. Methods"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"GigaScience"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1261\/rna.074922.120","article-title":"Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols","volume":"26","author":"Zhao","year":"2020","journal-title":"RNA"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Li, B., Gong, Y., Zhang, Y., Kim, K.S., Xiao, Y., Zeng, Q., Xu, K., Duan, Y., He, J., and Ma, H. (2022). Spatiotemporal Regulation of Circular RNA Expression During the Developmentof Skeletal Muscle, Subcutaneous Fat, and Liver in Ningxiang Pigs. Genes, 13.","DOI":"10.3390\/genes13050746"},{"key":"ref_22","unstructured":"Chen, C., Rui, X., Hao, C., and He, Y. (2018). Tbtools, a Toolkit for Biologists Integrating Various Hts-Data Handling Tools with a User-Friendly Interface. BioRxiv, 289660."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Zhang, T., Zhang, X., Han, K., Zhang, G., Wang, J., Xie, K., Xue, Q., and Fan, X. (2017). Analysis of long noncoding RNA and mRNA using RNA sequencing during the differentiation of intramuscular preadipocytes in chicken. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0172389"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"821406","DOI":"10.3389\/fgene.2022.821406","article-title":"Transcriptome Analysis of Bovine Rumen Tissue in Three Developmental Stages","volume":"13","author":"Zhang","year":"2022","journal-title":"Front. Genet."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1523","DOI":"10.1038\/s41467-019-09234-6","article-title":"Metascape provides a biologist-oriented resource for the analysis of systems-level datasets","volume":"10","author":"Zhou","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1186\/s12967-020-02698-x","article-title":"Identification of Key Biomarkers and Immune Infiltration in Systemic Lupus Erythematosus by Integrated Bioinformatics Analysis","volume":"19","author":"Zhao","year":"2021","journal-title":"J. Transl. Med."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Liu, B., Li, P., He, S., Xing, S., Cao, Z., Cao, X., Wang, X., and Li, Z.-H. (2022). Effects of short-term exposure to tralopyril on physiological indexes and endocrine function in turbot (Scophthalmus maximus). Aquat. Toxicol., 245.","DOI":"10.1016\/j.aquatox.2022.106118"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1007\/s00223-009-9246-6","article-title":"Association of a RUNX2 Promoter Polymorphism with Bone Mineral Density in Postmenopausal Korean Women","volume":"84","author":"Lee","year":"2009","journal-title":"Calcif. Tissue Int."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"4297","DOI":"10.1038\/s41598-019-40781-6","article-title":"Survey of allele specific expression in bovine muscle","volume":"9","author":"Guillocheau","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1159\/000492872","article-title":"RUNX2 Plays An Oncogenic Role in Esophageal Carcinoma by Activating the PI3K\/AKT and ERK Signaling Pathways","volume":"49","author":"Lu","year":"2018","journal-title":"Cell. Physiol. Biochem."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"S67","DOI":"10.1016\/j.clml.2016.02.026","article-title":"PDE4 Differential Expression Is a Potential Prognostic Factor and Therapeutic Target in Patients with Myelodysplastic Syndrome and Chronic Myelomonocytic Leukemia","volume":"16","author":"Chamseddine","year":"2016","journal-title":"Clin. Lymphoma Myeloma Leuk."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1790","DOI":"10.3389\/fimmu.2019.01790","article-title":"Overexpression of Pde4a Acts as Checkpoint Inhibitor against Camp-Mediated Immunosuppression in Vitro","volume":"10","author":"Schmetterer","year":"2019","journal-title":"Front. Immunol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1042\/bj3210165","article-title":"Challenge of human Jurkat T-cells with the adenylate cyclase activator forskolin elicits major changes in cAMP phosphodiesterase (PDE) expression by up-regulating PDE3 and inducing PDE4D1 and PDE4D2 splice variants as well as down-regulating a novel PDE4A splice variant","volume":"321","author":"Erdogan","year":"1997","journal-title":"Biochem. J."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1152\/physiolgenomics.00135.2017","article-title":"Genetics of Metabolic Syndrome: Tpcn2 Knockout Mice Have Improved Insulin Sensitivity and Are Protected against High-Fat Diet-Induced Weight Gain","volume":"50","author":"He","year":"2018","journal-title":"Physiol. Genom."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"e202101047","DOI":"10.26508\/lsa.202101047","article-title":"TPC2 promotes choroidal angiogenesis and inflammation in a mouse model of neovascular age-related macular degeneration","volume":"4","author":"Li","year":"2021","journal-title":"Life Sci. Alliance"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"eaay3051","DOI":"10.1126\/sciadv.aay3051","article-title":"miR-26a regulates extracellular vesicle secretion from prostate cancer cells via targeting SHC4, PFDN4, and CHORDC1","volume":"6","author":"Urabe","year":"2020","journal-title":"Sci. Adv."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"8515","DOI":"10.1038\/s41598-021-88196-6","article-title":"Flavonoids increase melanin production and reduce proliferation, migration and invasion of melanoma cells by blocking endolysosomal\/melanosomal TPC2","volume":"11","author":"Netcharoensirisuk","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"3841","DOI":"10.3892\/etm.2017.4942","article-title":"Microrna-22 May Promote Apoptosis and Inhibit the Proliferation of Hypertrophic Scar Fibroblasts by Regulating the Mitogen-Activated Protein Kinase Kinase\/Extracellular Signal-Regulated Kinase\/P21 Pathway","volume":"14","author":"Shihua","year":"2017","journal-title":"Experim. Therap. Med."},{"key":"ref_39","first-page":"50","article-title":"Suppression of KIF22 Inhibits Cell Proliferation and Xenograft Tumor Growth in Colon Cancer","volume":"35","author":"Li","year":"2020","journal-title":"Cancer Biother. Radiopharm."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"20617","DOI":"10.1074\/jbc.M116.748186","article-title":"MICAL3 Flavoprotein Monooxygenase Forms a Complex with Centralspindlin and Regulates Cytokinesis","volume":"291","author":"Liu","year":"2016","journal-title":"J. Biol. Chem."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Ehrlich, K., Baribault, C., and Ehrlich, M. (2020). Epigenetics of Muscle- and Brain-Specific Expression of KLHL Family Genes. Int. J. Mol. Sci., 21.","DOI":"10.20944\/preprints202010.0365.v1"},{"key":"ref_42","first-page":"274","article-title":"Phenytoin Induced Down Regulation of Tesk2 Gene in Albino Rat Testis Gene Qrt PCR Analysis","volume":"6","author":"Rajkumar","year":"2013","journal-title":"J. Chem. Pharma. Sci."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"2628","DOI":"10.1093\/hmg\/ddy172","article-title":"Tp53-Dependent and Independent Signaling Underlies the Pathogenesis and Possible Prevention of Acrofacial Dysostosis-Cincinnati Type","volume":"27","author":"Watt","year":"2018","journal-title":"Human Mol. Genetics"}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/13\/9\/1671\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T00:34:16Z","timestamp":1760142856000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/13\/9\/1671"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,9,19]]},"references-count":43,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2022,9]]}},"alternative-id":["genes13091671"],"URL":"https:\/\/doi.org\/10.3390\/genes13091671","relation":{},"ISSN":["2073-4425"],"issn-type":[{"type":"electronic","value":"2073-4425"}],"subject":[],"published":{"date-parts":[[2022,9,19]]}}}