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Region","award":["2023-JSGG-2"],"award-info":[{"award-number":["2023-JSGG-2"]}]},{"name":"Sub-Project Fund of the National Dairy Technology Innovation Center","award":["2021ZD0009"],"award-info":[{"award-number":["2021ZD0009"]}]},{"name":"Sub-Project Fund of the National Dairy Technology Innovation Center","award":["CG202423"],"award-info":[{"award-number":["CG202423"]}]},{"name":"Sub-Project Fund of the National Dairy Technology Innovation Center","award":["CG202410"],"award-info":[{"award-number":["CG202410"]}]},{"name":"Sub-Project Fund of the National Dairy Technology Innovation Center","award":["NDYB2022-1"],"award-info":[{"award-number":["NDYB2022-1"]}]},{"name":"Sub-Project Fund of the National Dairy Technology Innovation Center","award":["32460817"],"award-info":[{"award-number":["32460817"]}]},{"name":"Sub-Project Fund of the National Dairy Technology Innovation Center","award":["BR251026"],"award-info":[{"award-number":["BR251026"]}]},{"name":"Sub-Project Fund of the National Dairy Technology Innovation Center","award":["2023-JSGG-2"],"award-info":[{"award-number":["2023-JSGG-2"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background: Against the backdrop of the large-scale and intensive development of the livestock industry, enhancing the reproductive efficiency of cattle has become a crucial factor in industrial development. Holstein cows, as the most predominant dairy cattle breed globally, are characterized by high milk yield and excellent milk quality. However, their reproductive efficiency is comprehensively influenced by a variety of complex factors, and improving their reproductive performance faces numerous challenges. The ovary, as the core organ of the female reproductive system, plays a decisive role in embryonic development and pregnancy maintenance. It is not only the site where eggs are produced and developed but it also regulates the cow\u2019s estrous cycle, ovulation process, and the establishment and maintenance of pregnancy by secreting various hormones. The normal functioning of the ovary is crucial for the smooth development of the embryo and the successful maintenance of pregnancy. Methods: Currently, traditional sequencing technologies have obvious limitations in deciphering ovarian function and reproductive regulatory mechanisms. To overcome the bottlenecks of traditional sequencing technologies, this study selected Holstein cows as the research subjects. Ovarian samples were collected from one pregnant and one non-pregnant Holstein cow, and single-nucleus transcriptome sequencing technology was used to conduct an in-depth study on the ovarian cells of Holstein cows. Results: By constructing a cell type-specific molecular atlas of the ovaries, nine different cell types were successfully identified. This study compared the proportions of ovarian cell types under different physiological states and found that the proportion of endothelial cells decreased during pregnancy, while the proportions of granulosa cells and luteal cells increased significantly. In terms of functional enrichment analysis, oocytes during both pregnancy and non-pregnancy play roles in the \u201ccell cycle\u201d and \u201chomologous recombination\u201d pathways. However, non-pregnant oocytes are also involved in the \u201cprogesterone-mediated oocyte maturation\u201d pathway. Luteal cells during pregnancy mainly function in the \u201ccortisol synthesis and secretion\u201d and \u201covarian steroidogenesis\u201d pathways; non-pregnant luteal cells are mainly enriched in pathway processes such as the \u201cAMPK signaling pathway\u201d, \u201cpyrimidine metabolism\u201d, and \u201cnucleotide metabolism\u201d. Cell communication analysis reveals that there are 51 signaling pathways involved in the pregnant ovary, with endothelial cells, granulosa cells, and luteal cells serving as the core communication hubs. In the non-pregnant ovary, there are 48 pathways, and the interaction between endothelial cells and stromal cells is the dominant mode. Conclusions: This study provides new insights into the regulatory mechanisms of reproductive efficiency in Holstein cows. The differences in the proportions of ovarian cell types, functional pathways, and cell communication patterns under different physiological states, especially the increase in the proportions of granulosa cells and luteal cells during pregnancy and the specificity of related functional pathways, indicate that these cells play a crucial role in the reproductive process of cows. These findings also highlight the importance of ovarian cells in pathways such as \u201ccell cycle\u201d, \u201chomologous recombination\u201d, and \u201cprogesterone-mediated oocyte maturation\u201d, as well as the cell communication mechanisms in regulating ovarian function and reproductive performance.<\/jats:p>","DOI":"10.3390\/genes16080931","type":"journal-article","created":{"date-parts":[[2025,8,7]],"date-time":"2025-08-07T10:58:26Z","timestamp":1754564306000},"page":"931","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Single-Nucleus Transcriptome Sequencing Unravels Physiological Differences in Holstein Cows Under Different Physiological States"],"prefix":"10.3390","volume":"16","author":[{"given":"Peipei","family":"Li","sequence":"first","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010010, China"},{"name":"Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-9892-6158","authenticated-orcid":false,"given":"Yaqiang","family":"Guo","sequence":"additional","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010010, China"},{"name":"Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanchun","family":"Bao","sequence":"additional","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010010, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caixia","family":"Shi","sequence":"additional","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010010, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lin","family":"Zhu","sequence":"additional","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010010, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8244-9519","authenticated-orcid":false,"given":"Mingjuan","family":"Gu","sequence":"additional","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010010, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Risu","family":"Na","sequence":"additional","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010010, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenguang","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010010, China"},{"name":"Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,8,3]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"911","DOI":"10.1016\/S0140-6736(10)60355-8","article-title":"Primary ovarian insufficiency","volume":"376","author":"Devroey","year":"2010","journal-title":"Lancet"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1016\/j.gpb.2014.08.002","article-title":"A comprehensive transcriptomic analysis of infant and adult mouse ovary","volume":"12","author":"Pan","year":"2014","journal-title":"Genom. 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