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

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 c DNA amplification have prevented further identification of MSRB3 allelic variants influencing pig ear size.Results： We cloned a full-length c DNA sequence of porcine MSRB3 by rapid-amplification of c DNA ends. The3,765-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 q RT-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.-735 C 〉 T in the 5＇ flanking region,c.2571 T 〉 C in the 3＇-UTR, and a synonymous mutation of c.484 T 〉 C in the coding region. The SNPs c.-735 C 〉 T and c.2571 T 〉 C were significantly associated with ear size in a Large White × Minzhu F2 population other than in Beijing Black pigs. Subsequently, at SNP c.-735 C 〉 T, the m RNA 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 c DNA 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 m RNA expression of MSRB3 have larger ear sizes. These results provide useful information for further functional analyses of MSRB3 influencing ear size in pigs.

Genome-wide search for candidate genes determining vertebrae number in pigs

Longer porcine carcasses may be expected to have more vertebrae. Therefore, vertebrae number in pigs is an economically important trait. To examine the genetic basis of this trait, we genotyped 578 F-2 Large White x Minzhu pigs using the Porcine SNP60K BeadChip. A genome-wide association study (GWAS) identified 36 significant single nucleotide polymorphisms (SNPs) on the chromosomes SSC1 (294.28-300.32 Mb) and SSC7 (102.22-109.39 Mb). A 6.04-Mb region that contained all 13 significant SNPs on SSC1 also contained the gene NR6A1, previously reported to influence the number of vertebrae in pigs. However, the reported putative casual mutation of NR6A1 c. 748C > T showed no genome-wide significant association with the trait, suggesting it was not a causal mutation in our population. The remaining 23 significant SNPs on SSC7 were concentrated in a 7.17-Mb region, which was within a quantitative trait locus interval for number of vertebrae. TMED10 was the closest gene to the most significant SNP and might be a candidate. Haplotype sharing and block analysis refined the QTL to an interval of about 3 Mb containing 29 candidate genes. Of these 29 genes, the previously reported possible casual mutation of VRTN g. 19034A > C was not found to be a causal mutation in our population. Exploration of these genes via additional genetic and functional studies in mammals revealed that TGF beta 3 could be a good candidate on SSC7. A mutation of TGF beta 3 c. 1749G > A was detected by GWAS and could be proposed as a candidate causal mutation, or as closely linked to a causal mutation, for the number of vertebrae in pigs.