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This species is a valuable resource for both fisheries and aquaculture. Due to its cultural and economic importance, it has been prioritized for conservation in the Neotropical region. Population genomics studies supported two main lineages latitudinally distributed (North and South) in the Neotropical basins R\u00edo de la Plata and Laguna Mer\u00edn based on current genetic isolation and signals of local adaptation. In this study, we characterized the <jats:styled-content style=\"fixed-case\"><jats:italic>R. quelen<\/jats:italic><\/jats:styled-content> transcriptome in brain, head kidney, liver, skeletal muscle, testis, and ovary by RNAseq to target genes and associated markers involved in key adaptive traits. After filtering, a comprehensive catalog of 24,433 transcripts was annotated, providing insights into the immune function of head kidney and liver, the association of brain with the endocrine system, and the metabolic function of liver. Skeletal muscle and brain expressed genes associated with growth were also identified. Transcriptomic differences suggestive of adaptation to temperature and salinity were revealed between North and South genomic lineages. A total of 100,045 SNPs loci were identified within transcripts, most of them (78.8%) showing low genetic differentiation between lineages (F<jats:sub>ST<\/jats:sub> \u2264\u20090.100). However, 2504 loci (2.5%) showed high differentiation (F<jats:sub>ST<\/jats:sub> \u2265\u20090.800), some of them located within genes associated with putative adaptation of genomic lineages to environmental factors such as temperature and salinity. These SNPs represent useful gene markers for future functional and population genomic studies for sustainable management of wild populations and their application in breeding programs.<\/jats:p>","DOI":"10.1002\/ece3.71021","type":"journal-article","created":{"date-parts":[[2025,3,13]],"date-time":"2025-03-13T03:06:32Z","timestamp":1741835192000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Transcriptomic Divergence and Associated Markers Between Genomic Lineages of Silver Catfish (<scp><i>Rhamdia quelen<\/i><\/scp>)"],"prefix":"10.1002","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0669-7668","authenticated-orcid":false,"given":"N\u00e9stor","family":"R\u00edos","sequence":"first","affiliation":[{"name":"Secci\u00f3n Gen\u00e9tica Evolutiva, Facultad de Ciencias UdelaR  Montevideo Uruguay"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bel\u00e9n 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