2026-04-18T02:58:50Zhttps://recercat.cat/oai/request

oai:recercat.cat:20.500.12327/22902025-10-22T11:25:07Zcom_2072_4428com_2072_4427col_2072_487898

00925njm 22002777a 4500 dc Crespo-Piazuelo, Daniel author Acloque, Hervé author González-Rodríguez, Olga author Mongellaz, Mayrone author Mercat, Marie-José author Bink, Marco C A M author Huisman, Abe E author Ramayo-Caldas, Yuliaxis author Sanchez, Juan Pablo author Ballester Devis, Maria author 2023-06-24 Background 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. Results More than 9.68 × 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′UTR 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′-GATCCNGYGTTGCYG-3′ 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. Conclusions 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. Crespo-Piazuelo, Daniel, Hervé Acloque, Olga González-Rodríguez, Mayrone Mongellaz, Marie-José Mercat, Marco C A M Bink, Abe E Huisman, Yuliaxis Ramayo-Caldas, Juan Pablo Sánchez, and Maria Ballester. 2022. "Identification Of Transcriptional Regulatory Variants In Pig Duodenum, Liver, And Muscle Tissues". Gigascience 12. doi:10.1093/gigascience/giad042. 2047-217X http://hdl.handle.net/20.500.12327/2290 https://doi.org/10.1093/gigascience/giad042 Identification of transcriptional regulatory variants in pig duodenum, liver, and muscle tissues