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Background  In  Sus scrofa ,  methionine sulfoxide reductase B3  ( MSRB3 ) is a crucial candidate gene for ear size, and an important conformational trait of pig breeds. However, challenges in  MSRB3  cDNA amplification have prevented further identification of  MSRB3  allelic variants influencing pig ear size.    Results  We cloned a full-length cDNA sequence of porcine  MSRB3  by rapid-amplification of cDNA ends. The 3,765-bp gene contained a 5’-untranslated region (UTR) (190 bp), a coding region (552 bp), and a 3’-UTR (3,016 bp) and shared 84 %, 84 %, 87 %, 86 %, and 70 % sequence identities with human, orangutan, mouse, chicken, and zebrafish, respectively. The gene encoded a 183-amino acid protein, which shared 88 %, 91 %, 89 %, 86 %, and 67 % identities with human, orangutan, mouse, chicken, and zebrafish, respectively. Tissue expression analysis using qRT-PCR revealed that  MSRB3  was expressed in the heart, liver, lung, kidney, spleen, ear, muscle, fat, lymph, skeletal, and hypothalamic tissues. Three single nucleotide polymorphisms (SNPs) were identified in  MSRB3 : c.-735C &gt; T in the 5’ flanking region, c.2571 T &gt; C in the 3’-UTR, and a synonymous mutation of c.484 T &gt; C in the coding region. The SNPs c.-735C &gt; T and c.2571 T &gt; C were significantly associated with ear size in a Large White × Minzhu F2 population other than in Beijing Black pigs. Subsequently, at SNP c.-735C &gt; T, the mRNA of  MSRB3  was significantly higher expressed in ears of individuals with the TT genotype (Minzhu) than those with CC (Large White).    Conclusions  The porcine  MSRB3  owned a 3,765-bp full-length cDNA sequence and was detected to express in ear tissue. Two SNPs of this gene were shown to be significantly associated with ear size in a Large White × Minzhu intercross population instead of Beijing Black pig population. What’s more, the individuals with higher mRNA expression of  MSRB3  have larger ear sizes. These results provide useful information for further functional analyses of  MSRB3  influencing ear size in pigs.    Electronic supplementary material  The online version of this article (doi:10.1186/s40104-015-0060-x) contains supplementary material, which is available to authorized users.

journal of animal science and biotechnology/journal of animal science and biotechnology

Porcine methionine sulfoxide reductase B3: molecular cloning, tissue-specific expression profiles, and polymorphisms associated with ear size in Sus scrofa