{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,22]],"date-time":"2026-01-22T22:19:49Z","timestamp":1769120389463,"version":"3.49.0"},"reference-count":43,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2026,1,20]],"date-time":"2026-01-20T00:00:00Z","timestamp":1768867200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Xizang Agricultural and Animal Husbandry University","award":["XZNMXYRXRC-2024-01"],"award-info":[{"award-number":["XZNMXYRXRC-2024-01"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>Significant differences in reproductive performance exist between meat-type ducks (e.g., Qiangying Duck, QD) and laying-type ducks (e.g., Shaoxing Duck, SD). The molecular mechanisms underlying these differences, particularly concerning ovarian development and function, remain incompletely understood. This study aimed to comprehensively characterize the ovarian transcriptomes of these two duck types, focusing on differential gene expression and post-transcriptional regulatory events. We performed an integrated full-length transcriptome analysis of ovarian tissues from these two breeds using PacBio SMRT and Illumina sequencing. Bioinformatic analyses, including functional annotation, differential expression analysis, and the identification of APA events, were used. We discovered substantial breed-specific differences in alternative polyadenylation (APA), with SD ducks exhibiting significant 3\u2032UTR shortening in 3799 genes and 3\u2032UTR lengthening in 1626 genes compared to QD. The integrated analysis of differential gene expression and APA events highlighted key genes related to steroid hormone synthesis (HMGCS1, DHCR24), lipid metabolism (SCD), signal transduction (HRAS), and antioxidant defense (SOD1). The functional enrichment implicated critical pathways such as mitochondrial energy metabolism, oxidative phosphorylation, and fatty acid degradation. Our study provides a comprehensive atlas of post-transcriptional regulation in the duck ovary and reveals APA as a crucial process of gene regulation. APA may contribute to the differential ovarian function and egg-laying capacity between meat and laying ducks, thus offering valuable targets for genetic selection.<\/jats:p>","DOI":"10.3390\/ani16020313","type":"journal-article","created":{"date-parts":[[2026,1,20]],"date-time":"2026-01-20T14:57:58Z","timestamp":1768921078000},"page":"313","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A Comparative Analysis of Transcriptome-Wide Differential Gene Expression and Alternative Polyadenylation in the Ovaries of Meat Ducks and Laying Ducks"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-8673-0174","authenticated-orcid":false,"given":"Sike","family":"Wang","sequence":"first","affiliation":[{"name":"College of Animal Science, Xizang Agricultural and Animal Husbandry University, Linzhi 860000, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yaomei","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Animal Science, Xizang Agricultural and Animal Husbandry University, Linzhi 860000, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-2514-964X","authenticated-orcid":false,"given":"Shiwei","family":"Li","sequence":"additional","affiliation":[{"name":"College of Animal Science, Xizang Agricultural and Animal Husbandry University, Linzhi 860000, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0635-2299","authenticated-orcid":false,"given":"Chao","family":"Jia","sequence":"additional","affiliation":[{"name":"Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4803-8580","authenticated-orcid":false,"given":"Debing","family":"Yu","sequence":"additional","affiliation":[{"name":"College of Animal Science, Xizang Agricultural and Animal Husbandry University, Linzhi 860000, China"},{"name":"Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9395-2200","authenticated-orcid":false,"given":"Weiling","family":"Huang","sequence":"additional","affiliation":[{"name":"Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2026,1,20]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"898","DOI":"10.1007\/s10528-012-9530-4","article-title":"An SNP in the MyoD1 Gene Intron 2 Associated with Growth and Carcass Traits in Three Duck Populations","volume":"50","author":"Wu","year":"2012","journal-title":"Biochem. 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