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Background  The size and type of ears are important conformation characteristics that distinguish pig breeds. A significant quantitative trait locus (QTL) for ear size has been identified on SSC5 (SSC for  Sus scrofa  chromosome) but the underlying causative gene and mutation remain unknown. Thus, our aim was to identify the gene responsible for enlarged ears in pig.    Results  First, we narrowed down the QTL region on SSC5 to a 137.85-kb interval that harbors only the  methionine sulfoxide reductase B3  ( MSRB3 ) gene. Then, we identified a 38.7-kb copy number variation (CNV) that affects the last two exons of  MSRB3  and could be the candidate causative mutation for this QTL. This CNV showed complete concordance with genotype at the QTL of the founder animals in a white Duroc × Erhualian F 2  intercross and was found only in pigs from six Chinese indigenous breeds with large ears and from the Landrace breed with half-floppy ears. Moreover, it accounted for the significant association with ear size on SSC5 across the five pig populations tested. eQTL mapping revealed that this CNV was significantly associated with the expression of the microRNA (miRNA) miR-584-5p, which interacts with  MSRB3 , one of its target genes. In vivo and in vitro experiments confirmed that miR-584-5p inhibits the translation of MSRB3 mRNA. Taken together, these results led us to conclude that presence of the 38.7-kb CNV in the genome of some pig breeds affects ear size by altering the expression of miR-584-5p, which consequently hinders the expression of one of its target genes (e.g.  MSRB3 ).    Conclusions  Our findings shed insight into the underlying mechanism of development of external ears in mammals and contribute to a better understanding of how the presence of CNV can regulate gene expression.    Electronic supplementary material  The online version of this article (10.1186/s12711-018-0442-6) contains supplementary material, which is available to authorized users.

Copy number variation in the MSRB3 gene enlarges porcine ear size through a mechanism involving miR-584-5p