{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T11:28:39Z","timestamp":1784892519200,"version":"3.55.0"},"reference-count":60,"publisher":"MDPI AG","issue":"24","license":[{"start":{"date-parts":[[2025,12,5]],"date-time":"2025-12-05T00:00:00Z","timestamp":1764892800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Biological Breeding-Major Projects","award":["2023ZD0405501"],"award-info":[{"award-number":["2023ZD0405501"]}]},{"name":"Taishan Scholar Youth Project of Shandong Province, China"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>Hypoxia is a critical environmental stressor in aquaculture, significantly affecting the survival and growth performance of cultured fish. To explore the genetic basis of hypoxia tolerance in grass carp (Ctenopharyngodon idella), we integrated genome-wide association analysis (GWAS) and multi-tissue transcriptome profiling. A total of 2000 grass carp were subjected to hypoxic stress, from which the 150 most hypoxia-intolerant (HI) and 150 most hypoxia-tolerant (HT) individuals were selected based on the time to loss of equilibrium (LOE). GWAS using 3,730,919 SNPs and 851,595 InDels identified 21 SNPs and 6 InDels associated with hypoxia tolerance. Two SNPs on chromosomes 10 and 13 reached genome-wide significance, accounting for 2.7% and 4.8% of the phenotypic variance explained (PVE), respectively. Validation of identified SNPs was performed using kompetitive allele-specific PCR (KASP) analysis. Candidate genes within \u00b150 kb of these variants were enriched in steroid biosynthesis, insulin signaling, and glycosphingolipid biosynthesis pathways. Transcriptomic analysis of six tissues (brain, gill, intestine, kidney, liver, and spleen) revealed 1620, 1221, 796, 246, 210, and 58 differentially expressed genes (DEGs) in the HT group compared to the HI group, respectively. DEGs in the brain were primarily enriched in steroid metabolic processes and angiogenesis regulation, while those in kidney and spleen DEGs were associated with oxygen transport and erythrocyte development. Integrated analysis of GWAS and transcriptome data identified 16 shared genes, including usf1 and trpv4. These findings reveal key genomic loci and molecular pathways underlying hypoxia tolerance in grass carp, providing valuable markers for future selective breeding programs.<\/jats:p>","DOI":"10.3390\/ani15243518","type":"journal-article","created":{"date-parts":[[2025,12,5]],"date-time":"2025-12-05T15:11:24Z","timestamp":1764947484000},"page":"3518","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Integrative Genomics and Multi-Tissue Transcriptomics Identify Key Loci and Pathways for Hypoxia Tolerance in Grass Carp"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0645-4201","authenticated-orcid":false,"given":"Wenwen","family":"Wang","sequence":"first","affiliation":[{"name":"Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao 266071, China"},{"name":"Shandong Center of Technology Innovation for Biological Breeding of Premium Fish (Preparatory), Yantai 261418, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengyang","family":"Chang","sequence":"additional","affiliation":[{"name":"Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao 266071, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9618-1472","authenticated-orcid":false,"given":"Suxu","family":"Tan","sequence":"additional","affiliation":[{"name":"Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao 266071, China"},{"name":"Shandong Center of Technology Innovation for Biological Breeding of Premium Fish (Preparatory), Yantai 261418, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yiming","family":"Hu","sequence":"additional","affiliation":[{"name":"Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao 266071, China"},{"name":"Shandong Center of Technology Innovation for Biological Breeding of Premium Fish (Preparatory), Yantai 261418, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinlu","family":"Ren","sequence":"additional","affiliation":[{"name":"Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao 266071, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongtao","family":"Xue","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lizheng","family":"Gao","sequence":"additional","affiliation":[{"name":"Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao 266071, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao","family":"Cao","sequence":"additional","affiliation":[{"name":"Weishan County Nansihu Fishery Co., Ltd., Jining 277600, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ya","family":"Wang","sequence":"additional","affiliation":[{"name":"Weishan County Nansihu Fishery Co., Ltd., Jining 277600, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiyu","family":"Li","sequence":"additional","affiliation":[{"name":"Weishan County Nansihu Fishery Co., Ltd., Jining 277600, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-8903-3737","authenticated-orcid":false,"given":"Zhenxia","family":"Sha","sequence":"additional","affiliation":[{"name":"Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao 266071, China"},{"name":"Shandong Center of Technology Innovation for Biological Breeding of Premium Fish (Preparatory), Yantai 261418, China"},{"name":"Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao 266237, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,12,5]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S1546-5098(08)00001-0","article-title":"The hypoxic environment","volume":"27","author":"Diaz","year":"2009","journal-title":"Fish Physiol."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Robertson, C.E., Wright, P.A., K\u00f6blitz, L., and Bernier, N.J. 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