{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T10:29:04Z","timestamp":1776853744788,"version":"3.51.2"},"reference-count":42,"publisher":"MDPI AG","issue":"14","license":[{"start":{"date-parts":[[2025,7,11]],"date-time":"2025-07-11T00:00:00Z","timestamp":1752192000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Central Guidance for Local Science and Technology Development Fund","award":["ZYYD2025JD02"],"award-info":[{"award-number":["ZYYD2025JD02"]}]},{"name":"Central Guidance for Local Science and Technology Development Fund","award":["2024B02013-2"],"award-info":[{"award-number":["2024B02013-2"]}]},{"name":"Key Research and Development Project of Xinjiang Uygur Autonomous Region","award":["ZYYD2025JD02"],"award-info":[{"award-number":["ZYYD2025JD02"]}]},{"name":"Key Research and Development Project of Xinjiang Uygur Autonomous Region","award":["2024B02013-2"],"award-info":[{"award-number":["2024B02013-2"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>Kazakh mares have drawn significant attention for their outstanding lactation traits. Lactation, a complex physiological activity, is modulated by multiple factors. This study utilized high-throughput sequencing to conduct whole-transcriptome sequencing analysis on the mammary gland tissue of eight Kazakh mares, of which four were pregnant and four were non-pregnant, to systematically reveal the molecular regulatory mechanisms. The results showed differential expression in 2136 mRNAs, 180 lncRNAs, 104 miRNAs, and 1162 circRNAs. Gene ontology functional annotation indicates that these differentially expressed genes are involved in multiple key biological processes, such as the cellular process (BP), metabolic process, and biological regulation. Kyoto Encyclopedia of Genes and Genomes analysis suggests that the differentially expressed genes are significantly enriched in essential pathways such as cytokine\u2013cytokine receptor interaction, the chemokine signaling pathway, and the PI3K-Akt signaling pathway. Additionally, this study constructed a competing endogenous RNA (ceRNA) regulatory network based on the differentially expressed genes (|log2FC| &gt; 1, FDR &lt; 0.05), offering a novel perspective for revealing the functional regulation of the mammary gland. This study compared genomic differences in mammary gland tissue of pregnant and non-pregnant Kazakh mares and identified candidate genes that are closely related to lactation regulation. It found that various genes, such as PIK3CG, IL7R, and SOD2, play central regulatory roles in activating mammary gland functions. These findings provide theoretical support for explaining the molecular mechanisms underlying the mammary gland development of Kazakh mares.<\/jats:p>","DOI":"10.3390\/ani15142056","type":"journal-article","created":{"date-parts":[[2025,7,11]],"date-time":"2025-07-11T15:19:31Z","timestamp":1752247171000},"page":"2056","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Influence of Pregnancy on Whole-Transcriptome Sequencing in the Mammary Gland of Kazakh Mares"],"prefix":"10.3390","volume":"15","author":[{"given":"Zhenyu","family":"Zhang","sequence":"first","affiliation":[{"name":"College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-4804-7296","authenticated-orcid":false,"given":"Zhixin","family":"Lu","sequence":"additional","affiliation":[{"name":"College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinkui","family":"Yao","sequence":"additional","affiliation":[{"name":"College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China"},{"name":"Xinjiang Key Laboratory of Equine Breeding and Exercise Physiology, Urumqi 830052, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Linling","family":"Li","sequence":"additional","affiliation":[{"name":"College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jun","family":"Meng","sequence":"additional","affiliation":[{"name":"College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China"},{"name":"Xinjiang Key Laboratory of Equine Breeding and Exercise Physiology, Urumqi 830052, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7148-4557","authenticated-orcid":false,"given":"Jianwen","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China"},{"name":"Xinjiang Key Laboratory of Equine Breeding and Exercise Physiology, Urumqi 830052, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-1881-1221","authenticated-orcid":false,"given":"Yaqi","family":"Zeng","sequence":"additional","affiliation":[{"name":"College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China"},{"name":"Xinjiang Key Laboratory of Equine Breeding and Exercise Physiology, Urumqi 830052, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-5822-8366","authenticated-orcid":false,"given":"Wanlu","family":"Ren","sequence":"additional","affiliation":[{"name":"College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China"},{"name":"Xinjiang Key Laboratory of Equine Breeding and Exercise Physiology, Urumqi 830052, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,7,11]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"148483","DOI":"10.1016\/j.gene.2024.148483","article-title":"Investigating age-related differences in muscles of Kazakh horse through transcriptome analysis","volume":"919","author":"Ren","year":"2024","journal-title":"Gene"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"100926","DOI":"10.1016\/j.animal.2023.100926","article-title":"Genetic structure and genome-wide association study of the traditional Kazakh horses","volume":"17","author":"Pozharskiy","year":"2023","journal-title":"Animal"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"147143","DOI":"10.1016\/j.gene.2022.147143","article-title":"Integrating genome-wide methylation and transcriptome-wide analyses to reveal the genetic mechanism of milk traits in Kazakh horses","volume":"856","author":"Liu","year":"2023","journal-title":"Gene"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Ulaangerel, T., Wang, M., Zhao, B., Yi, M., Shen, Y., Mengkh, Y., Wen, X., Dugarjav, M., and Bou, G. (2024). A Comparative Analysis of the Gene Expression Profiles in the Mammary Glands of Lactating and Nonlactating Mares at the Second Month of Gestation. Animals, 14.","DOI":"10.3390\/ani14162319"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"2090","DOI":"10.3168\/jds.2024-25279","article-title":"Systemic and mammary inflammation and mammary gland development of Holstein dairy cows around dry-off and calving","volume":"108","author":"Gao","year":"2025","journal-title":"J. Dairy Sci."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1007\/s10911-020-09471-2","article-title":"Development and pathology of the equine mammary gland","volume":"26","author":"Hughes","year":"2021","journal-title":"J. Mammary Gland. Biol. Neoplasia"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1042\/CBI20090023","article-title":"Transcriptome analysis of mammary tissues reveals complex patterns of transporter gene expression during pregnancy and lactation","volume":"34","author":"Anantamongkol","year":"2010","journal-title":"Cell Biol. Int."},{"key":"ref_8","first-page":"1191","article-title":"RNA-Seq and its applications: A new technology for transcriptomics","volume":"33","author":"Qi","year":"2011","journal-title":"Hereditas"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1111\/age.13422","article-title":"Identification of candidate genes associated with milk production and mastitis based on transcriptome-wide association study","volume":"55","author":"Hosseinzadeh","year":"2024","journal-title":"Anim. Genet."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Xia, W., Liu, Y., Loor, J.J., Bionaz, M., and Jiang, M. (2023). Dynamic profile of the yak mammary transcriptome during the lactation cycle. Animals, 13.","DOI":"10.3390\/ani13101710"},{"key":"ref_11","first-page":"193","article-title":"Application of whole transcriptomics in animal husbandry","volume":"41","author":"Shi","year":"2019","journal-title":"Hereditas"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"148189","DOI":"10.1016\/j.gene.2024.148189","article-title":"Transcriptome identification of differential mammary genes of Kazakh horses during early pregnancy","volume":"902","author":"Ren","year":"2024","journal-title":"Gene"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Roth, M.J., and Moorehead, R.A. (2021). The miR-200 family in normal mammary gland development. BMC Dev. Biol., 21.","DOI":"10.1186\/s12861-021-00243-7"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: An ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_15","unstructured":"Zhu, Y. (2024). Exploration of Key Regulators of Back Fat Deposition in Dahe Pigs Based on Whole Transcriptome Sequencing, Yunnan Agricultural University."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Love, M.I., Huber, W., and Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol., 15.","DOI":"10.1186\/s13059-014-0550-8"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/j.semcdb.2020.12.012","article-title":"Embryonic mammary gland development","volume":"Volume 114","author":"Spina","year":"2021","journal-title":"Seminars in Cell & Developmental Biology"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"7546","DOI":"10.1021\/acs.jafc.3c09647","article-title":"Protein Dynamic Landscape during Mouse Mammary Gland Development from Virgin to Pregnant, Lactating, and Involuting Stages","volume":"72","author":"Wang","year":"2024","journal-title":"J. Agric. Food Chem."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Martin, F., Stein, T., and Howlin, J. (2017). Overview of mammary gland development: A comparison of mouse and human. Mammary Gland Development: Methods and Protocols, Humana Press.","DOI":"10.1007\/978-1-4939-6475-8"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Wang, W., Zang, X., Liu, Y., Liang, Y., Cai, G., Wu, Z., and Li, Z. (2022). Dynamic miRNA landscape links mammary gland development to the regulation of milk protein expression in mice. Animals, 12.","DOI":"10.3390\/ani12060727"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/j.ydbio.2018.11.002","article-title":"Molecular mechanism of mammary gland involution: An update","volume":"445","author":"Jena","year":"2019","journal-title":"Dev. Biol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1002\/wdev.35","article-title":"Mammary gland development","volume":"1","author":"Macias","year":"2012","journal-title":"Wiley Interdiscip. Rev. Dev. Biol."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Alateyah, N., Gupta, I., Rusyniak, R.S., and Ouhtit, A. (2022). SOD2, a potential transcriptional target underpinning CD44-promoted breast cancer progression. Molecules, 27.","DOI":"10.3390\/molecules27030811"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Sun, L., Wang, F., Wu, Z., Ma, L., Baumrucker, C., and Bu, D. (2020). Comparison of selenium source in preventing oxidative stress in bovine mammary epithelial cells. Animals, 10.","DOI":"10.3390\/ani10050842"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"3213","DOI":"10.1128\/IAI.00320-15","article-title":"Interleukin-7 produced by intestinal epithelial cells in response to Citrobacter rodentium infection plays a major role in innate immunity against this pathogen","volume":"83","author":"Zhang","year":"2015","journal-title":"Infect. Immun."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1899","DOI":"10.1111\/febs.15114","article-title":"Bovine milk transcriptome analysis reveals microRNAs and RNU2 involved in mastitis","volume":"287","author":"Lai","year":"2020","journal-title":"FEBS J."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1186\/s12864-017-4029-3","article-title":"Circular RNA expression profiles and features in human tissues: A study using RNA-seq data","volume":"18","author":"Xu","year":"2017","journal-title":"BMC Genom."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Wang, J., Ke, N., Wu, X., Zhen, H., Hu, J., Liu, X., Li, S., Zhao, F., Li, M., and Shi, B. (2024). MicroRNA-148a Targets DNMT1 and PPARGC1A to Regulate the Viability, Proliferation, and Milk Fat Synthesis of Ovine Mammary Epithelial Cells. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms25168558"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"7648","DOI":"10.3168\/jds.2017-12630","article-title":"Bovine miR-146a regulates inflammatory cytokines of bovine mammary epithelial cells via targeting the TRAF6 gene","volume":"100","author":"Wang","year":"2017","journal-title":"J. Dairy Sci."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1016\/j.jri.2010.11.006","article-title":"Cytokine signalling in mammary gland development","volume":"88","author":"Watson","year":"2011","journal-title":"J. Reprod. Immunol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1146\/annurev-immunol-032713-120211","article-title":"Insights into cytokine\u2013receptor interactions from cytokine engineering","volume":"33","author":"Spangler","year":"2015","journal-title":"Annu. Rev. Immunol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1007\/s10911-014-9319-7","article-title":"Cytokine networks that mediate epithelial cell-macrophage crosstalk in the mammary gland: Implications for development and cancer","volume":"19","author":"Sun","year":"2014","journal-title":"J. Mammary Gland. Biol. Neoplasia"},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Zhao, W., Shahzad, K., Jiang, M., Graugnard, D.E., Rodriguez-Zas, S.L., Luo, J., Loor, J.J., and Hurley, W.L. (2013). Bioinformatics and gene network analyses of the swine mammary gland transcriptome during late gestation. Bioinform. Biol. Insights, 7.","DOI":"10.4137\/BBI.S12205"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1016\/j.rvsc.2004.04.006","article-title":"The cytokines of bovine mammary gland: Prospects for diagnosis and therapy","volume":"77","author":"Alluwaimi","year":"2004","journal-title":"Res. Vet. Sci."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Zhu, C., Jiang, Y., Zhu, J., He, Y., Yin, H., Duan, Q., Zhang, L., Cao, B., and An, X. (2020). CircRNA8220 sponges MiR-8516 to regulate cell viability and milk synthesis via Ras\/MEK\/ERK and PI3K\/AKT\/mTOR pathways in goat mammary epithelial cells. Animals, 10.","DOI":"10.3390\/ani10081347"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1023\/A:1009568532177","article-title":"TGF-\u03b2 signaling in mammary gland development and tumorigenesis","volume":"6","author":"Wakefield","year":"2001","journal-title":"J. Mammary Gland. Biol. Neoplasia"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1016\/S1534-5807(02)00365-9","article-title":"IGF-2 is a mediator of prolactin-induced morphogenesis in the breast","volume":"3","author":"Brisken","year":"2002","journal-title":"Dev. Cell"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"740","DOI":"10.1111\/age.13249","article-title":"Identification of critical lncRNAs for milk fat metabolism in dairy cows using WGCNA and the construction of a ceRNAs network","volume":"53","author":"Mu","year":"2022","journal-title":"Anim. Genet."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1016\/j.omtn.2021.03.004","article-title":"Circular RNA circMYBPC1 promotes skeletal muscle differentiation by targeting MyHC","volume":"24","author":"Chen","year":"2021","journal-title":"Mol. Ther.-Nucleic Acids"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Lawless, N., Vegh, P., O\u2019Farrelly, C., and Lynn, D.J. (2014). The role of microRNAs in bovine infection and immunity. Front. Immunol., 5.","DOI":"10.3389\/fimmu.2014.00611"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"2128","DOI":"10.1038\/s41467-017-02001-5","article-title":"Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing","volume":"8","author":"Bach","year":"2017","journal-title":"Nat. Commun."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"810","DOI":"10.1093\/nsr\/nwz049","article-title":"Dog10K: An international sequencing effort to advance studies of canine domestication, phenotypes and health","volume":"6","author":"Ostrander","year":"2019","journal-title":"Natl. Sci. Rev."}],"container-title":["Animals"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2615\/15\/14\/2056\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T18:08:50Z","timestamp":1760033330000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2615\/15\/14\/2056"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7,11]]},"references-count":42,"journal-issue":{"issue":"14","published-online":{"date-parts":[[2025,7]]}},"alternative-id":["ani15142056"],"URL":"https:\/\/doi.org\/10.3390\/ani15142056","relation":{},"ISSN":["2076-2615"],"issn-type":[{"value":"2076-2615","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,7,11]]}}}