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3 results on '"PCR for MAP detection"'

1. Identification of loci associated with susceptibility to Mycobacterium avium subsp. paratuberculosis infection in Holstein cattle using combinations of diagnostic tests and imputed whole-genome sequence data

Author

Canive, María, González Recio, Oscar, Fernández, Almudena, Vázquez, Patricia, Badia Bringué, Gerard, Lavín, José L., Garrido Urkullu, Joseba M., Juste Jordán, Ramón A., Alonso Hearn, Marta, Canive, María, González Recio, Oscar, Fernández, Almudena, Vázquez, Patricia, Badia Bringué, Gerard, Lavín, José L., Garrido Urkullu, Joseba M., Juste Jordán, Ramón A., and Alonso Hearn, Marta

Abstract

Bovine paratuberculosis (PTB) is a chronic inflammatory disease caused by Mycobacterium avium susbp. paratuberculosis (MAP). Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) significantly associated with susceptibility to bovine PTB. The main objective of this study was to identify quantitative trait loci (QTLs) associated with MAP infection in Spanish Holstein cows (N = 983) using combinations of diagnostic tests and imputed whole-genome sequence (WGS) data. The infection status of these animals was defined by three diagnostic methods including ELISA for MAP-antibodies detection, and tissue culture and PCR for MAP detection. The 983 cows included in this study were genotyped with the Bovine MD SNP50 Bead Chip, and the corresponding genotypes were imputed to WGS using the 1,000 Bull genomes reference population. In total, 33.77 million SNP variants per animal were identified across the genome. Linear mixed models were used to calculate the heritability (h2) estimates for each diagnostic test and test combinations. Next, we performed a case-control GWAS using the imputed WGS datasets and the phenotypes and combinations of phenotypes with h2 estimates > 0.080. After performing the GWAS, the test combinations that showed SNPs with a significant association (PFDR ≤ 0.05), were the ELISA-tissue PCR-tissue culture, ELISA-tissue culture, and ELISA-tissue PCR. A total of twelve quantitative trait loci (QTLs) highly associated with MAP infection status were identified on the Bos taurus autosomes (BTA) 4, BTA5, BTA11, BTA12, BTA14, BTA23, BTA24, and BTA28, and some of these QTLs were linked to immune-modulating genes. The identified QTLs on BTA23 spanning from 18.81 to 22.95 Mb of the Bos taurus genome overlapped with several QTLs previously found to be associated with PTB susceptibility, bovine tuberculosis susceptibility, and clinical mastitis. The results from this study provide more clues regarding the molecular mechanisms unde

Published
2021

2. Identification of loci associated with susceptibility to Mycobacterium avium subsp. paratuberculosis infection in Holstein cattle using combinations of diagnostic tests and imputed whole-genome sequence data

Author

Canive Ruiz, María, González Recio, Oscar, Fernández, Almudena, Vázquez, Patricia, Badia Bringué, Gerard, Lavín, José L., Garrido Urkullu, Joseba M., Juste Jordán, Ramón A., Alonso Hearn, Marta, Canive Ruiz, María, González Recio, Oscar, Fernández, Almudena, Vázquez, Patricia, Badia Bringué, Gerard, Lavín, José L., Garrido Urkullu, Joseba M., Juste Jordán, Ramón A., and Alonso Hearn, Marta

Abstract

Bovine paratuberculosis (PTB) is a chronic inflammatory disease caused by Mycobacterium avium susbp. paratuberculosis (MAP). Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) significantly associated with susceptibility to bovine PTB. The main objective of this study was to identify quantitative trait loci (QTLs) associated with MAP infection in Spanish Holstein cows (N = 983) using combinations of diagnostic tests and imputed whole-genome sequence (WGS) data. The infection status of these animals was defined by three diagnostic methods including ELISA for MAP-antibodies detection, and tissue culture and PCR for MAP detection. The 983 cows included in this study were genotyped with the Bovine MD SNP50 Bead Chip, and the corresponding genotypes were imputed to WGS using the 1,000 Bull genomes reference population. In total, 33.77 million SNP variants per animal were identified across the genome. Linear mixed models were used to calculate the heritability (h2) estimates for each diagnostic test and test combinations. Next, we performed a case-control GWAS using the imputed WGS datasets and the phenotypes and combinations of phenotypes with h2 estimates > 0.080. After performing the GWAS, the test combinations that showed SNPs with a significant association (PFDR ≤ 0.05), were the ELISA-tissue PCR-tissue culture, ELISA-tissue culture, and ELISA-tissue PCR. A total of twelve quantitative trait loci (QTLs) highly associated with MAP infection status were identified on the Bos taurus autosomes (BTA) 4, BTA5, BTA11, BTA12, BTA14, BTA23, BTA24, and BTA28, and some of these QTLs were linked to immune-modulating genes. The identified QTLs on BTA23 spanning from 18.81 to 22.95 Mb of the Bos taurus genome overlapped with several QTLs previously found to be associated with PTB susceptibility, bovine tuberculosis susceptibility, and clinical mastitis. The results from this study provide more clues regarding the molecular mechanisms unde

Published
2021

3. Identification of loci associated with susceptibility to Mycobacterium avium subsp. paratuberculosis infection in Holstein cattle using combinations of diagnostic tests and imputed whole-genome sequence data

Author

Maria Canive, Joseba M. Garrido, Almudena Fernández, José Luis Lavín, Gerard Badia-Bringué, Ramón A. Juste, Oscar González-Recio, Marta Alonso-Hearn, and Patricia Vázquez

Subjects
Male, bovine paratuberculosis, Jhones-disease, Single Nucleotide Polymorphisms, Resistance, Paratuberculosis, Genome-wide association study, clinical mastitis, Genome, Spanish Holstein cows, Package, Genotype, Enzyme-Linked Immunoassays, Oligonucleotide Array Sequence Analysis, Genetics, Mammals, Multidisciplinary, Eukaryota, Genomics, Ruminants, Mycobacterium avium subsp. paratuberculosis, Phenotype, Vertebrates, Medicine, Female, Antibody-response, Biological Cultures, MAP infection, Research Article, Science, Quantitative Trait Loci, Cattle Diseases, Single-nucleotide polymorphism, Enzyme-Linked Immunosorbent Assay, Biology, Quantitative trait locus, PCR for MAP detection, Research and Analysis Methods, Polymorphism, Single Nucleotide, Bovines, medicine, Genome-Wide Association Studies, Animals, Tuberculosis, Genetic Predisposition to Disease, tissue culture, Polymorphism, Dairy-cattle, Molecular Biology Techniques, Immunoassays, Molecular Biology, Tissue Cultures, Genetic association, SSP-paratuberculosis, Tissue, Whole Genome Sequencing, Diagnostic Tests, Routine, ELISA diagnostic method, Gene Mapping, Organisms, Biology and Life Sciences, Computational Biology, Human Genetics, Heritability, medicine.disease, Genome Analysis, Genetic Loci, Spain, Case-Control Studies, Amniotes, Immunologic Techniques, Linear Models, Cattle, Zoology, Genome-Wide Association Study, Mycobacterium avium
Abstract

Bovine paratuberculosis (PTB) is a chronic inflammatory disease caused by Mycobacterium avium susbp. paratuberculosis (MAP). Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) significantly associated with susceptibility to bovine PTB. The main objective of this study was to identify quantitative trait loci (QTLs) associated with MAP infection in Spanish Holstein cows (N = 983) using combinations of diagnostic tests and imputed whole-genome sequence (WGS) data. The infection status of these animals was defined by three diagnostic methods including ELISA for MAP-antibodies detection, and tissue culture and PCR for MAP detection. The 983 cows included in this study were genotyped with the Bovine MD SNP50 Bead Chip, and the corresponding genotypes were imputed to WGS using the 1,000 Bull genomes reference population. In total, 33.77 million SNP variants per animal were identified across the genome. Linear mixed models were used to calculate the heritability (h2) estimates for each diagnostic test and test combinations. Next, we performed a case-control GWAS using the imputed WGS datasets and the phenotypes and combinations of phenotypes with h2 estimates > 0.080. After performing the GWAS, the test combinations that showed SNPs with a significant association (PFDR ≤ 0.05), were the ELISA-tissue PCR-tissue culture, ELISA-tissue culture, and ELISA-tissue PCR. A total of twelve quantitative trait loci (QTLs) highly associated with MAP infection status were identified on the Bos taurus autosomes (BTA) 4, BTA5, BTA11, BTA12, BTA14, BTA23, BTA24, and BTA28, and some of these QTLs were linked to immune-modulating genes. The identified QTLs on BTA23 spanning from 18.81 to 22.95 Mb of the Bos taurus genome overlapped with several QTLs previously found to be associated with PTB susceptibility, bovine tuberculosis susceptibility, and clinical mastitis. The results from this study provide more clues regarding the molecular mechanisms underlying susceptibility to PTB infection in cattle and might be used to develop national genetic evaluations for PTB in Spain. Financial support for this study was provided by a grant from the Spanish Ministry of Science, Innovation, and Universities (MICINN, project code: RTI2018-094192-R-C21) and by European Regional Development Funds (FEDER) to MAH. MC and GBB have been awarded fellowships from the National Institute for Agricultural Research (INIA) and MICINN, respectively

Published
2021

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