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This study aims to identify endometrial genes and biological pathways involved in the maternal recognition of pregnancy. Caruncular endometrial tissues were collected from Day 15\u201317 of gestation (pregnant), non-pregnant (absence of conceptus), and cyclic (non-bred) heifers.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Total RNAs were isolated from the caruncular endometrial tissues of pregnant, non-pregnant, and cyclic heifers, and were subjected to high-throughput RNA-sequencing. The genes with at least two-fold change and Benjamini and Hochberg<jats:italic>p<\/jats:italic>-value\u2009\u2264\u20090.05 were considered differentially expressed genes and further confirmed with quantitative real-time PCR. A total of 107 genes (pregnant vs cyclic) and 98 genes (pregnant vs non-pregnant) were differentially expressed in the pregnant endometrium. The most highly up-regulated genes in the pregnant endometrium were<jats:italic>MRS2<\/jats:italic>,<jats:italic>CST6<\/jats:italic>,<jats:italic>FOS<\/jats:italic>,<jats:italic>VLDLR<\/jats:italic>,<jats:italic>ISG15, IFI6, MX2<\/jats:italic>,<jats:italic>C15H11ORF34<\/jats:italic>,<jats:italic>EIF3M<\/jats:italic>,<jats:italic>PRSS22<\/jats:italic>,<jats:italic>MS4A8<\/jats:italic>, and<jats:italic>TINAGL1<\/jats:italic>. Interferon signaling, immune response, nutrient transporter, synthesis, and secretion of proteins are crucial pathways during the maternal recognition of pregnancy.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>The study demonstrated that the presence of conceptus at Day 15\u201317 of gestation affects the endometrial gene expression related to endometrial remodeling, immune response, nutrients and ion transporters, and relevant signaling pathways in the caruncular region of bovine endometrium during the maternal recognition of pregnancy.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12864-022-08720-4","type":"journal-article","created":{"date-parts":[[2022,7,7]],"date-time":"2022-07-07T22:03:09Z","timestamp":1657231389000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":24,"title":["RNA-Sequencing based analysis of bovine endometrium during the maternal recognition of pregnancy"],"prefix":"10.1186","volume":"23","author":[{"given":"Bindu","family":"Adhikari","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chin N.","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vedbar S.","family":"Khadka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Youping","family":"Deng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Glen","family":"Fukumoto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Thorne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kyle","family":"Caires","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jenee","family":"Odani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Birendra","family":"Mishra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,7,7]]},"reference":[{"issue":"1\u20132","key":"8720_CR1","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.vetpar.2004.05.003","volume":"125","author":"H Steinfeld","year":"2004","unstructured":"Steinfeld H. 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