State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
Institute of Animal Husbandry and Veterinary, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China.
Genet Sel Evol. 2018 Dec 27;50(1):72. doi: 10.1186/s12711-018-0442-6.
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.
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 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).
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.
耳朵的大小和形状是区分猪品种的重要形态特征。在 SSC5（猪的 Sus scrofa 染色体）上已经确定了一个与耳朵大小相关的显著数量性状位点（QTL），但潜在的致病基因和突变仍然未知。因此，我们的目标是鉴定导致猪耳朵增大的基因。
首先，我们将 SSC5 上的 QTL 区域缩小到一个仅包含蛋氨酸亚砜还原酶 B3（MSRB3）基因的 137.85-kb 区间。然后，我们发现了一个影响 MSRB3 最后两个外显子的 38.7-kb 拷贝数变异（CNV），它可能是该 QTL 的候选致病突变。该 CNV 与大白杜洛克×二花脸杂种猪的创始动物 QTL 基因型完全一致，仅存在于六个大耳中国本土品种和半垂耳长白猪中。此外，它与五个测试猪群体的 SSC5 上的耳朵大小显著相关。eQTL 图谱显示，该 CNV 与 miRNA（miR-584-5p）的表达显著相关，miR-584-5p 与 MSRB3 相互作用，MSRB3 是其一个靶基因。体内和体外实验证实 miR-584-5p 抑制 MSRB3 mRNA 的翻译。综上所述，这些结果表明，一些猪品种基因组中存在 38.7-kb CNV 会通过改变 miR-584-5p 的表达来影响耳朵大小，进而影响其靶基因（如 MSRB3）的表达。
我们的研究结果深入了解了哺乳动物外耳发育的潜在机制，并有助于更好地理解 CNV 如何调节基因表达。
