{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T03:14:06Z","timestamp":1788146046426,"version":"build-2803163510"},"reference-count":34,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,8,30]],"date-time":"2026-08-30T00:00:00Z","timestamp":1788048000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Hainan Provincial Key R&D Program","award":["ZDYF2025XDNY080"],"award-info":[{"award-number":["ZDYF2025XDNY080"]}]},{"name":"Zhejiang Province \u201cSNJF\u201d Science and Technology Collaboration Project","award":["2025SNJF040"],"award-info":[{"award-number":["2025SNJF040"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background\/Objectives: Shiqi and Dabao pigeons are two Chinese meat-pigeon breeds with distinct breeding backgrounds and production-related phenotypes, but whether these differences extend to ovarian physiology and molecular profiles remains unclear. This study compared ovarian physiological traits and multi-omics profiles between the breeds. Methods: Seven-month-old reproductively mature females were studied. Flock-level laying and fertilization records were obtained from 456 breeding pairs per breed and recorded every 2 days. Serum reproductive hormones were measured in 10 females per breed. Follicle numbers, atresia, and mature follicle diameter were evaluated in three females per breed. Ovarian samples from six females per breed were analyzed by paired-end RNA sequencing and untargeted LC\u2013MS\/MS metabolomics in positive- and negative-ion modes. Results: Dabao pigeons had higher serum progesterone concentrations than Shiqi pigeons (1.35 \u00b1 0.49 vs. 0.32 \u00b1 0.19 ng\/mL, p &lt; 0.001) and larger mature follicles (2.25 \u00b1 0.31 vs. 1.08 \u00b1 0.56 mm, p = 0.034), whereas follicle numbers were not significantly different. Transcriptomic analysis identified 761 DEGs (FC &gt; 2 or &lt; 0.5; adjusted p &lt; 0.05), mainly involving extracellular-matrix, cholesterol-, estrogen-, PI3K\u2013Akt-, and TGF-\u03b2-related processes. Metabolomic analysis identified five differential metabolites (VIP &gt; 1, FC &gt; 2 or &lt; 0.5; adjusted p &lt; 0.05), including three taurine-conjugated bile acids. Integrated analysis revealed exploratory gene\u2013metabolite associations related to lipid metabolism, follicular signaling, and extracellular-matrix remodeling. Conclusions: Shiqi and Dabao pigeons differed mainly in ovarian physiological and molecular characteristics, whereas short-term flock-level reproductive records were broadly similar. Metabolomic differences were limited but concentrated in bile-acid- and lipid-related features.<\/jats:p>","DOI":"10.3390\/genes17091049","type":"journal-article","created":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T02:08:58Z","timestamp":1788142138000},"page":"1049","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Differences in Reproductive Performance Between Shiqi and Dabao Pigeons: Insights from Multi-Omics Analysis"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-5347-0087","authenticated-orcid":false,"given":"Xingyu","family":"Tang","sequence":"first","affiliation":[{"name":"Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"}]},{"given":"Chenbo","family":"Zhao","sequence":"additional","affiliation":[{"name":"Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"}]},{"given":"Jinquan","family":"Xi","sequence":"additional","affiliation":[{"name":"Haikou Coconut Pigeon Food Breeding Co., Ltd., Haikou 571133, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"}]},{"given":"Tieshan","family":"Xu","sequence":"additional","affiliation":[{"name":"Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"given":"Tiantian","family":"Gu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Jindong","family":"Ren","sequence":"additional","affiliation":[{"name":"Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"investigation","vocabulary":"credit"}]},{"given":"Shihong","family":"Liu","sequence":"additional","affiliation":[{"name":"Haikou Coconut Pigeon Food Breeding Co., Ltd., Haikou 571133, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"resources","vocabulary":"credit"}]},{"given":"Lihong","family":"Gu","sequence":"additional","affiliation":[{"name":"Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571199, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"}]},{"given":"Lizhi","family":"Lu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Livestock and Poultry Resources (Poultry) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,30]]},"reference":[{"key":"ref_1","first-page":"436","article-title":"Investigation and analysis of the production scale and marketing situation of meat pigeons in China","volume":"61","author":"Liang","year":"2025","journal-title":"Chin. 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