{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T05:23:05Z","timestamp":1790572985758,"version":"4.1.0"},"reference-count":85,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2023,6,24]],"date-time":"2023-06-24T00:00:00Z","timestamp":1687564800000},"content-version":"vor","delay-in-days":178,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010661","name":"Horizon 2020","doi-asserted-by":"publisher","award":["817998"],"award-info":[{"award-number":["817998"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014440","name":"Ministry of Science, Innovation and Universities","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100014440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003030","name":"AGAUR","doi-asserted-by":"publisher","award":["2021-SGR-01552"],"award-info":[{"award-number":["2021-SGR-01552"]}],"id":[{"id":"10.13039\/501100003030","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,12,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>In humans and livestock species, genome-wide association studies (GWAS) have been applied to study the association between variants distributed across the genome and a phenotype of interest. To discover genetic polymorphisms affecting the duodenum, liver, and muscle transcriptomes of 300 pigs from 3 different breeds (Duroc, Landrace, and Large White), we performed expression GWAS between 25,315,878 polymorphisms and the expression of 13,891 genes in duodenum, 12,748 genes in liver, and 11,617 genes in muscle.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>More than 9.68 \u00d7 1011 association tests were performed, yielding 14,096,080 significantly associated variants, which were grouped in 26,414 expression quantitative trait locus (eQTL) regions. Over 56% of the variants were within 1 Mb of their associated gene. In addition to the 100-kb region upstream of the transcription start site, we identified the importance of the 100-kb region downstream of the 3\u2032UTR for gene regulation, as most of the cis-regulatory variants were located within these 2 regions. We also observed 39,874 hotspot regulatory polymorphisms associated with the expression of 10 or more genes that could modify the protein structure or the expression of a regulator gene. In addition, 2 motifs (5\u2032-GATCCNGYGTTGCYG-3\u2032 and a poly(A) sequence) were enriched across the 3 tissues within the neighboring sequences of the most significant single-nucleotide polymorphisms in each cis-eQTL region.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>The 14 million significant associations obtained in this study are publicly available and have enabled the identification of expression-associated cis-, trans-, and hotspot regulatory variants within and across tissues, thus shedding light on the molecular mechanisms of regulatory variations that shape end-trait phenotypes.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/gigascience\/giad042","type":"journal-article","created":{"date-parts":[[2023,6,25]],"date-time":"2023-06-25T00:36:14Z","timestamp":1687653374000},"source":"Crossref","is-referenced-by-count":23,"title":["Identification of transcriptional regulatory variants in pig duodenum, liver, and muscle tissues"],"prefix":"10.1093","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7896-2507","authenticated-orcid":false,"given":"Daniel","family":"Crespo-Piazuelo","sequence":"first","affiliation":[{"name":"Animal Breeding and Genetics Program, IRTA , Torre Marimon, Caldes de Montbui (08140),","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4761-1055","authenticated-orcid":false,"given":"Herv\u00e9","family":"Acloque","sequence":"additional","affiliation":[{"name":"GABI, Universit\u00e9 Paris-Saclay, INRAE, AgroParisTech , Jouy-en-Josas (78350),","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olga","family":"Gonz\u00e1lez-Rodr\u00edguez","sequence":"additional","affiliation":[{"name":"Animal Breeding and Genetics Program, IRTA , Torre Marimon, Caldes de Montbui (08140),","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mayrone","family":"Mongellaz","sequence":"additional","affiliation":[{"name":"GABI, Universit\u00e9 Paris-Saclay, INRAE, AgroParisTech , Jouy-en-Josas (78350),","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3087-082X","authenticated-orcid":false,"given":"Marie-Jos\u00e9","family":"Mercat","sequence":"additional","affiliation":[{"name":"IFIP-Institut du porc and Alliance R&D , Le Rheu (35651),","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1278-2092","authenticated-orcid":false,"given":"Marco C A M","family":"Bink","sequence":"additional","affiliation":[{"name":"Hendrix Genetics Research Technology & Services B.V. , Boxmeer (5830 AC),","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6572-1157","authenticated-orcid":false,"given":"Abe E","family":"Huisman","sequence":"additional","affiliation":[{"name":"Hypor B.V. , Boxmeer (5830 AC),","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8142-0159","authenticated-orcid":false,"given":"Yuliaxis","family":"Ramayo-Caldas","sequence":"additional","affiliation":[{"name":"Animal Breeding and Genetics Program, IRTA , Torre Marimon, Caldes de Montbui (08140),","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8639-6146","authenticated-orcid":false,"given":"Juan Pablo","family":"S\u00e1nchez","sequence":"additional","affiliation":[{"name":"Animal Breeding and Genetics Program, IRTA , Torre Marimon, Caldes de Montbui 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