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In silico genome-wide miRNA-QTL-SNPs analyses identify a functional SNP associated with mastitis in Holsteins

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 significa...

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Autores principales: Jiang, Qiang, Zhao, Han, Li, Rongling, Zhang, Yaran, Liu, Yong, Wang, Jinpeng, Wang, Xiuge, Ju, Zhihua, Liu, Wenhao, Hou, Minghai, Huang, Jinming
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6524300/
https://www.ncbi.nlm.nih.gov/pubmed/31096910
http://dx.doi.org/10.1186/s12863-019-0749-5
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author Jiang, Qiang
Zhao, Han
Li, Rongling
Zhang, Yaran
Liu, Yong
Wang, Jinpeng
Wang, Xiuge
Ju, Zhihua
Liu, Wenhao
Hou, Minghai
Huang, Jinming
author_facet Jiang, Qiang
Zhao, Han
Li, Rongling
Zhang, Yaran
Liu, Yong
Wang, Jinpeng
Wang, Xiuge
Ju, Zhihua
Liu, Wenhao
Hou, Minghai
Huang, Jinming
author_sort Jiang, Qiang
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12863-019-0749-5) contains supplementary material, which is available to authorized users.
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spelling pubmed-65243002019-05-24 In silico genome-wide miRNA-QTL-SNPs analyses identify a functional SNP associated with mastitis in Holsteins Jiang, Qiang Zhao, Han Li, Rongling Zhang, Yaran Liu, Yong Wang, Jinpeng Wang, Xiuge Ju, Zhihua Liu, Wenhao Hou, Minghai Huang, Jinming BMC Genet Research Article 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12863-019-0749-5) contains supplementary material, which is available to authorized users. BioMed Central 2019-05-16 /pmc/articles/PMC6524300/ /pubmed/31096910 http://dx.doi.org/10.1186/s12863-019-0749-5 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Jiang, Qiang
Zhao, Han
Li, Rongling
Zhang, Yaran
Liu, Yong
Wang, Jinpeng
Wang, Xiuge
Ju, Zhihua
Liu, Wenhao
Hou, Minghai
Huang, Jinming
In silico genome-wide miRNA-QTL-SNPs analyses identify a functional SNP associated with mastitis in Holsteins
title In silico genome-wide miRNA-QTL-SNPs analyses identify a functional SNP associated with mastitis in Holsteins
title_full In silico genome-wide miRNA-QTL-SNPs analyses identify a functional SNP associated with mastitis in Holsteins
title_fullStr In silico genome-wide miRNA-QTL-SNPs analyses identify a functional SNP associated with mastitis in Holsteins
title_full_unstemmed In silico genome-wide miRNA-QTL-SNPs analyses identify a functional SNP associated with mastitis in Holsteins
title_short In silico genome-wide miRNA-QTL-SNPs analyses identify a functional SNP associated with mastitis in Holsteins
title_sort in silico genome-wide mirna-qtl-snps analyses identify a functional snp associated with mastitis in holsteins
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6524300/
https://www.ncbi.nlm.nih.gov/pubmed/31096910
http://dx.doi.org/10.1186/s12863-019-0749-5
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