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dc.contributor.authorBraud, Martin
dc.contributor.authorMagee, David A.
dc.contributor.authorPark, Stephen D. E.
dc.contributor.authorSonstegard, Tad S.
dc.contributor.authorWaters, Sinead M.
dc.contributor.authorMacHugh, David E.
dc.contributor.authorSpillane, Charles
dc.date.accessioned2018-09-20T16:01:31Z
dc.date.available2018-09-20T16:01:31Z
dc.date.issued2017-01-31
dc.identifier.citationBraud, Martin; Magee, David A. Park, Stephen D. E.; Sonstegard, Tad S.; Waters, Sinead M.; MacHugh, David E.; Spillane, Charles (2017). Genome-wide microrna binding site variation between extinct wild aurochs and modern cattle identifies candidate microrna-regulated domestication genes. Frontiers in Genetics 8 ,
dc.identifier.issn1664-8021
dc.identifier.urihttp://hdl.handle.net/10379/10508
dc.description.abstractThe domestication of cattle from the now-extinct wild aurochs (Bos primigenius) involved selection for physiological and behavioral traits, with underlying genetic factors that remain largely unknown. Non coding microRNAs have emerged as key regulators of the spatio-temporal expression of target genes controlling mammalian growth and development, including in livestock species. During the domestication process, selection of mutational changes in miRNAs and/or miRNA binding sites could have provided a mechanism to generate some of the traits that differentiate domesticated cattle from wild aurochs. To investigate this, we analyzed the open reading frame DNA sequence of 19,994 orthologous protein-coding gene pairs from extant Bos taurus genomes and a single extinct B. primigenius genome. We identified miRNA binding site polymorphisms in the 3' UTRs of 1,620 of these orthologous genes. These 1,620 genes with altered miRNA binding sites between the B. taurus and B. primigenius lineages represent candidate domestication genes. Using a novel Score Site ratio metric we have ranked these miRNA-regulated genes according to the extent of divergence between miRNA binding site presence, frequency and copy number between the orthologous genes from B. taurus and B. primigenius. This provides an unbiased approach to identify cattle genes that have undergone the most changes in miRNA binding (i.e., regulation) between the wild aurochs and modern-day cattle breeds. In addition, we demonstrate that these 1,620 candidate domestication genes are enriched for roles in pigmentation, fertility, neurobiology, metabolism, immunity and production traits (including milk quality and feed efficiency). Our findings suggest that directional selection of miRNA regulatory variants was important in the domestication and subsequent artificial selection that gave rise to modern taurine cattle.
dc.publisherFrontiers Media SA
dc.relation.ispartofFrontiers in Genetics
dc.subjectmicrorna
dc.subjectpolymorphism
dc.subjectevolution
dc.subjectdomestication
dc.subjectagriculture
dc.subjectbos primigenius
dc.subjectbos taurus
dc.subjectancient DNA
dc.subjectannotated analysis
dc.subjectinnate immunity
dc.subjectDNA-sequences
dc.subjectmeat quality
dc.subjecttarget-site
dc.subjectbos-taurus
dc.subjectassociation
dc.subjectexpression
dc.subjectevolution
dc.subjectvariants
dc.titleGenome-wide microrna binding site variation between extinct wild aurochs and modern cattle identifies candidate microrna-regulated domestication genes
dc.typeArticle
dc.identifier.doi10.3389/fgene.2017.00003
dc.local.publishedsourcehttps://www.frontiersin.org/articles/10.3389/fgene.2017.00003/pdf
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