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In silico genome-wide miRNA-QTL-SNPs analyses identify a functional SNP associated with mastitis in Holsteins.
BMC Genetics Pub Date : 2019-05-16 , DOI: 10.1186/s12863-019-0749-5 Qiang Jiang 1 , Han Zhao 1, 2 , Rongling Li 1 , Yaran Zhang 1 , Yong Liu 1 , Jinpeng Wang 1 , Xiuge Wang 1 , Zhihua Ju 1 , Wenhao Liu 1 , Minghai Hou 1 , Jinming Huang 1, 2
BMC Genetics Pub Date : 2019-05-16 , DOI: 10.1186/s12863-019-0749-5 Qiang Jiang 1 , Han Zhao 1, 2 , Rongling Li 1 , Yaran Zhang 1 , Yong Liu 1 , Jinpeng Wang 1 , Xiuge Wang 1 , Zhihua Ju 1 , Wenhao Liu 1 , Minghai Hou 1 , Jinming Huang 1, 2
Affiliation
BACKGROUND
Single-nucleotide polymorphisms (SNPs) in microRNAs (miRNAs) and their target binding sites affect miRNA function and are involved in biological processes and diseases, including bovine mastitis, a frequent inflammatory disease. Our previous study has shown that bta-miR-2899 is significantly upregulated in the mammary gland tissue of mastitis-infected cow than that of healthy cows.
RESULTS
In the present study, we used a customized miRNAQTLsnp software and identified 5252 SNPs in 691 bovine pre-miRNAs, which are also located within the quantitative trait loci (QTLs) that are associated with mastitis and udder conformation-related traits. Using luciferase assay in the bovine mammary epithelial cells, we confirmed a candidate SNP (rs109462250, g. 42,198,087 G > A) in the seed region of bta-miR-2899 located in the somatic cell score (SCS)-related QTL (Chr.18: 33.9-43.9 Mbp), which affected the interaction of bta-miR-2899 and its putative target Spi-1 proto-oncogene (SPI1), a pivotal regulator in the innate and adaptive immune systems. Quantitative real-time polymerase chain reaction results showed that the relative expression of SPI1 in the mammary gland of AA genotype cows was significantly higher than that of GG genotype cows. The SNP genotypes were associated with SCS in Holstein cows.
CONCLUSIONS
Altogether, miRNA-related SNPs, which influence the susceptibility to mastitis, are one of the plausible mechanisms underlying mastitis via modulating the interaction of miRNAs and immune-related genes. These miRNA-QTL-SNPs, such as the SNP (rs109462250) of bta-miR-2899 may have implication for the mastitis resistance breeding program in Holstein cattle.
中文翻译：
在计算机全基因组的miRNA-QTL-SNPs分析中鉴定出与荷斯坦牛乳腺炎相关的功能性SNP。
背景技术微小RNA（miRNA）中的单核苷酸多态性（SNP）及其靶结合位点影响miRNA的功能，并参与生物学过程和疾病，包括牛乳腺炎（一种常见的炎症性疾病）。我们先前的研究表明，感染乳腺炎的奶牛的乳腺组织中的bta-miR-2899比健康奶牛的bta-miR-2899明显上调。结果在本研究中，我们使用了定制的miRNAQTLsnp软件，在691个牛pre-miRNA中鉴定了5252个SNP，它们也位于与乳腺炎和乳房构象相关性状相关的定量性状位点（QTL）内。在牛乳腺上皮细胞中使用萤光素酶测定，我们确认了候选SNP（rs109462250，g。42,198,087 G> A）位于与体细胞评分（SCS）相关的QTL中的bta-miR-2899的种子区域（Chr.18：33.9-43.9 Mbp），这影响了bta-miR-2899与推定靶标Spi的相互作用-1原癌基因（SPI1），先天性和适应性免疫系统中的关键调节剂。实时定量聚合酶链反应结果表明，SPI基因在AA基因型奶牛的乳腺中的相对表达明显高于GG基因型奶牛。SNP基因型与荷斯坦奶牛的SCS有关。结论总之，影响乳腺炎敏感性的与miRNA相关的SNP是通过调节miRNA与免疫相关基因的相互作用而成为乳腺炎潜在的合理机制之一。这些miRNA-QTL-SNP，
更新日期：2019-05-16
中文翻译：
在计算机全基因组的miRNA-QTL-SNPs分析中鉴定出与荷斯坦牛乳腺炎相关的功能性SNP。
背景技术微小RNA（miRNA）中的单核苷酸多态性（SNP）及其靶结合位点影响miRNA的功能，并参与生物学过程和疾病，包括牛乳腺炎（一种常见的炎症性疾病）。我们先前的研究表明，感染乳腺炎的奶牛的乳腺组织中的bta-miR-2899比健康奶牛的bta-miR-2899明显上调。结果在本研究中，我们使用了定制的miRNAQTLsnp软件，在691个牛pre-miRNA中鉴定了5252个SNP，它们也位于与乳腺炎和乳房构象相关性状相关的定量性状位点（QTL）内。在牛乳腺上皮细胞中使用萤光素酶测定，我们确认了候选SNP（rs109462250，g。42,198,087 G> A）位于与体细胞评分（SCS）相关的QTL中的bta-miR-2899的种子区域（Chr.18：33.9-43.9 Mbp），这影响了bta-miR-2899与推定靶标Spi的相互作用-1原癌基因（SPI1），先天性和适应性免疫系统中的关键调节剂。实时定量聚合酶链反应结果表明，SPI基因在AA基因型奶牛的乳腺中的相对表达明显高于GG基因型奶牛。SNP基因型与荷斯坦奶牛的SCS有关。结论总之，影响乳腺炎敏感性的与miRNA相关的SNP是通过调节miRNA与免疫相关基因的相互作用而成为乳腺炎潜在的合理机制之一。这些miRNA-QTL-SNP，
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