{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T15:03:55Z","timestamp":1789571035971,"version":"build-2803163510"},"reference-count":29,"publisher":"Wiley","issue":"5","license":[{"start":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T00:00:00Z","timestamp":1789516800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T00:00:00Z","timestamp":1789516800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100001407","name":"Department of Biotechnology, Ministry of Science and Technology, India","doi-asserted-by":"publisher","award":["BT\/AAQ\/3\/SP13797\/2017"],"award-info":[{"award-number":["BT\/AAQ\/3\/SP13797\/2017"]}],"id":[{"id":"10.13039\/501100001407","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Animal Genetics"],"published-print":{"date-parts":[[2026,10]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Single nucleotide polymorphisms (SNPs) are key markers for population and conservation genetics in aquaculture species. Using low\u2010depth whole\u2010genome resequencing of 35\n                    <jats:italic>Labeo catla<\/jats:italic>\n                    individuals from seven populations (three wild riverine, four hatchery), we generated the first genome\u2010wide SNP catalogue for this Indian major carp. Filtering against the\n                    <jats:italic>L.\u2009catla<\/jats:italic>\n                    reference genome (GCA_012976165.1) yielded 2.05\u2009million high\u2010quality bi\u2010allelic SNPs (467\u2009291\u20131\u2009221\u2009268 per population), with 27\u2009000 shared across all populations. Heterozygosity (He\u2009=\u20090.4477\u20130.4532) and nucleotide diversity (\n                    <jats:italic>\u03c0<\/jats:italic>\n                    \u2009=\u20090.4703\u20130.4816) were broadly comparable across populations. Pairwise\n                    <jats:italic>F<\/jats:italic>\n                    <jats:sub>ST<\/jats:sub>\n                    (0.079\u20130.106) and UPGMA clustering resolved Cauvery as most divergent population, grouping the remaining six into two clusters (PCA: PC1\u2009=\u200921.4%, PC2\u2009=\u200916.8%). A differentiation scan identified 270 candidate high\u2010differentiation SNPs (top 1%; score\u2009&gt;\u20090.222) enriched for missense variants (~2.05\u2010fold;\n                    <jats:italic>p<\/jats:italic>\n                    \u2009=\u20090.021), implicating cell\u2010adhesion, extracellular\u2010matrix and muscle\u2010development genes in population differentiation. An independent chi\u2010square test of allele\u2010frequency heterogeneity, corrected for multiple testing (\n                    <jats:italic>q<\/jats:italic>\n                    \u2009&lt;\u20090.05), retained 114 of these 270 SNPs, mapping to 30 genes whose GO profile (endosome, granule and endolysosome lumen) differed from the broader 270\u2010SNP set indicating exploratory, hypothesis generating candidates rather than confirmed selection targets. Genome\u2010wide annotation of 2\u2009521\u2009013 SNPs classified 108\u2009113 (1.14%) as moderate\u2010impact missense and 5266 (0.06%) as high\u2010impact variants. These findings align with prior genotyping\u2010by\u2010sequencing data but extend marker density ~200\u2010fold, providing the first genome\u2010wide diversity, differentiation and functional profile for\n                    <jats:italic>L.\u2009catla<\/jats:italic>\n                    . The dataset (BioProject PRJNA1441081; Figshare doi:\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/doi.org\/10.6084\/m9.figshare.31829770\">https:\/\/doi.org\/10.6084\/m9.figshare.31829770<\/jats:ext-link>\n                    ) supports SNP array design, GWAS and conservation monitoring of Catla riverine stocks.\n                  <\/jats:p>","DOI":"10.1002\/age.70207","type":"journal-article","created":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T12:45:23Z","timestamp":1789562723000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genome\u2010Wide\n                    <scp>SNP<\/scp>\n                    Discovery and Population Genomic Characterisation in Indian Major Carp\n                    <i>Labeo catla<\/i>\n                    (Hamilton, 1822) Through Low\u2010Depth Whole\u2010Genome Resequencing"],"prefix":"10.1002","volume":"57","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8304-4660","authenticated-orcid":false,"given":"B.","family":"Sahoo","sequence":"first","affiliation":[{"name":"Fish Genetics and Biotechnology Division ICAR\u2010Central Institute of Freshwater Aquaculture (ICAR\u2010CIFA)  Bhubaneswar Odisha India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"P.","family":"Nandanpawar","sequence":"additional","affiliation":[{"name":"Fish Genetics and Biotechnology Division ICAR\u2010Central Institute of Freshwater Aquaculture (ICAR\u2010CIFA)  Bhubaneswar Odisha India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5525-2430","authenticated-orcid":false,"given":"P.","family":"Das","sequence":"additional","affiliation":[{"name":"Fish Genetics and Biotechnology Division ICAR\u2010Central Institute of Freshwater Aquaculture (ICAR\u2010CIFA)  Bhubaneswar Odisha India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7054-1214","authenticated-orcid":false,"given":"L.","family":"Sahoo","sequence":"additional","affiliation":[{"name":"Fish Genetics and Biotechnology Division ICAR\u2010Central Institute of Freshwater Aquaculture (ICAR\u2010CIFA)  Bhubaneswar Odisha India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"K.","family":"Murmu","sequence":"additional","affiliation":[{"name":"Fish Genetics and Biotechnology Division ICAR\u2010Central Institute of Freshwater Aquaculture (ICAR\u2010CIFA)  Bhubaneswar Odisha India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6880-971X","authenticated-orcid":false,"given":"A.","family":"Rasal","sequence":"additional","affiliation":[{"name":"Fish Genetics and Biotechnology Division ICAR\u2010Central Institute of Freshwater Aquaculture (ICAR\u2010CIFA)  Bhubaneswar Odisha India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9311-0636","authenticated-orcid":false,"given":"J. K.","family":"Sundaray","sequence":"additional","affiliation":[{"name":"Fish Genetics and Biotechnology Division ICAR\u2010Central Institute of Freshwater Aquaculture (ICAR\u2010CIFA)  Bhubaneswar Odisha India"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,16]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.aquaculture.2005.02.012"},{"key":"e_1_2_10_3_1","unstructured":"Andrews S.2010.\u201cFastQC: A Quality Control Tool for High Throughput Sequence Data.\u201dhttp:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc."},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1038\/75556"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.1080\/24701394.2016.1253072"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msab293"},{"key":"e_1_2_10_7_1","first-page":"381","article-title":"Observations on the Spawning in Indian Carps by Hormone Injection","volume":"26","author":"Chaudhuri H.","year":"1957","journal-title":"Current Science"},{"key":"e_1_2_10_8_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty560"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.4161\/fly.19695"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btae508"},{"key":"e_1_2_10_11_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr330"},{"key":"e_1_2_10_12_1","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008"},{"key":"e_1_2_10_13_1","first-page":"1","article-title":"Fish Diversity, Community Structure and Ecological Integrity of River Brahmani","volume":"48","author":"Das M. K.","year":"2021","journal-title":"Journal of the Inland Fisheries Society of India"},{"key":"e_1_2_10_14_1","doi-asserted-by":"publisher","DOI":"10.1007\/s12041-018-1034-5"},{"key":"e_1_2_10_15_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu031"},{"key":"e_1_2_10_16_1","doi-asserted-by":"publisher","DOI":"10.1127\/0941-2948\/2006\/0130"},{"key":"e_1_2_10_17_1","first-page":"1935","article-title":"Molecular Markers for Genetic Characterization in Labeo catla","volume":"28","author":"Kumar S.","year":"2020","journal-title":"Aquaculture International"},{"key":"e_1_2_10_18_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp324"},{"key":"e_1_2_10_19_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"e_1_2_10_20_1","article-title":"Overview and Challenges of Aquaculture in Pakistan","volume":"8","author":"Qadeer M. A.","year":"2017","journal-title":"Fish and Aquaculture Journal"},{"key":"e_1_2_10_21_1","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2023.1166385"},{"key":"e_1_2_10_22_1","first-page":"1","article-title":"A Chromosome\u2010Level Assembly of the Catla (Labeo catla) Genome","volume":"13","author":"Sahoo B.","year":"2020","journal-title":"BMC Research Notes"},{"key":"e_1_2_10_23_1","volume-title":"Molecular Cloning: A Laboratory Manual","author":"Sambrook J.","year":"2001"},{"key":"e_1_2_10_24_1","first-page":"1","article-title":"Water Quality Assessment of Mahanadi River in Odisha, India","volume":"38","author":"Swain P.","year":"2017","journal-title":"Journal of Environmental Biology"},{"key":"e_1_2_10_25_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msu093"},{"key":"e_1_2_10_26_1","doi-asserted-by":"publisher","DOI":"10.1186\/1297-9686-34-3-275"},{"key":"e_1_2_10_27_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1558-5646.1984.tb05657.x"},{"key":"e_1_2_10_28_1","doi-asserted-by":"publisher","DOI":"10.1086\/682949"},{"key":"e_1_2_10_29_1","article-title":"Whole\u2010Genome Sequencing of Nile Tilapia (\n                     Oreochromis niloticus\n                  ) Provides a Major Impulse Towards Future Genomic Improvement Programs","volume":"514","author":"Yanez J. M.","year":"2020","journal-title":"Aquaculture"},{"key":"e_1_2_10_30_1","article-title":"Population Genomics Reveals Demographic History and Selection of Japanese Whiting (\n                     Sillago japonica\n                  )","volume":"10","author":"Yang Z.","year":"2020","journal-title":"Scientific Reports"}],"container-title":["Animal Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/age.70207","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/age.70207","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/age.70207","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T14:22:56Z","timestamp":1789568576000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/age.70207"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,16]]},"references-count":29,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2026,10]]}},"alternative-id":["10.1002\/age.70207"],"URL":"https:\/\/doi.org\/10.1002\/age.70207","archive":["Portico"],"relation":{},"ISSN":["0268-9146","1365-2052"],"issn-type":[{"value":"0268-9146","type":"print"},{"value":"1365-2052","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,16]]},"assertion":[{"value":"2026-05-20","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-09-05","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-09-16","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e70207"}}