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Waterfowl (e.g., duck and goose) are representatives of them, and the external genitalia development of male geese is directly related to mating ability. Notably, some male geese show abnormal external genitalia development during ontogenesis. However, until now little is known about the molecular mechanisms of the external genitalia development in goose. In the present study, comparative transcriptomic analyses were performed on the hypothalamus, pituitary gland, testis, and external genitalia isolated from the 245-day-old male Tianfu meat geese showing normal (NEGG,\n                      <jats:italic>n<\/jats:italic>\n                      = 3) and abnormal (AEGG,\n                      <jats:italic>n<\/jats:italic>\n                      = 3) external genitals in order to provide a better understanding of the mechanisms controlling the development of the external genitalia in aquatic bird species.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      There were 107, 284, 2192, and 1005 differentially expressed genes (DEGs) identified in the hypothalamus, pituitary gland, testis and external genitalia between NEGG and AEGG. Functional enrichment analysis indicated that the DEGs identified in the hypothalamus were mainly enriched in the ECM-receptor interaction pathway. The ECM-receptor interaction, focal adhesion, and neuroactive ligand-receptor interaction pathways were significantly enriched by the DEGs in the pituitary gland. In the testis, the DEGs were enriched in the neuroactive ligand-receptor interaction, cell cycle, oocyte meiosis, and purine metabolism. In the external genitalia, the DEGs were enriched in the metabolic, neuroactive ligand-receptor interaction, and WNT signaling pathways. Furthermore, through integrated analysis of protein-protein interaction (PPI) network and co-expression network, fifteen genes involved in the neuroactive ligand-receptor interaction and WNT signaling pathways were identified, including\n                      <jats:italic>KNG1<\/jats:italic>\n                      ,\n                      <jats:italic>LPAR2<\/jats:italic>\n                      ,\n                      <jats:italic>LPAR3<\/jats:italic>\n                      ,\n                      <jats:italic>NPY<\/jats:italic>\n                      ,\n                      <jats:italic>PLCB1<\/jats:italic>\n                      ,\n                      <jats:italic>AVPR1B<\/jats:italic>\n                      ,\n                      <jats:italic>GHSR<\/jats:italic>\n                      ,\n                      <jats:italic>GRM3<\/jats:italic>\n                      ,\n                      <jats:italic>HTR5A<\/jats:italic>\n                      ,\n                      <jats:italic>FSHB<\/jats:italic>\n                      ,\n                      <jats:italic>FSHR<\/jats:italic>\n                      ,\n                      <jats:italic>WNT11<\/jats:italic>\n                      ,\n                      <jats:italic>WNT5A<\/jats:italic>\n                      ,\n                      <jats:italic>WIF1<\/jats:italic>\n                      , and\n                      <jats:italic>WNT7B<\/jats:italic>\n                      , which could play crucial roles in the development of goose external genitalia.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      This study is the first systematically comparing the hypothalamus, pituitary gland, testis, and external genitalia transcriptomes of male geese exhibiting normal and abnormal external genitals. Both bioinformatic analysis and validation experiments indicated that the neuroactive ligand-receptor interaction pathway could regulate the WNT signaling pathway through\n                      <jats:italic>PLCB1<\/jats:italic>\n                      to control male goose external genitalia development.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12864-022-08374-2","type":"journal-article","created":{"date-parts":[[2022,2,15]],"date-time":"2022-02-15T15:02:29Z","timestamp":1644937349000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":24,"title":["Comparative transcriptome analysis identifies crucial candidate genes and pathways in the hypothalamic-pituitary-gonadal axis during external genitalia development of male geese"],"prefix":"10.1186","volume":"23","author":[{"given":"Bincheng","family":"Tang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shenqiang","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingyuan","family":"Ouyang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tianhao","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yao","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiwei","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bo","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liang","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiwen","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,2,15]]},"reference":[{"issue":"12","key":"8374_CR1","doi-asserted-by":"publisher","first-page":"1065","DOI":"10.1016\/j.cub.2013.04.062","volume":"23","author":"AM Herrera","year":"2013","unstructured":"Herrera AM, Shuster SG, Perriton CL, Cohn MJ. 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