Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle
Background: Bovine leukemia virus (BLV) infection is omnipresent in dairy herds causing direct economic losses due to trade restrictions and lymphosarcoma-related deaths. Milk production drops and increase in the culling rate are also relevant and usually neglected. The BLV provirus persists throu...
| Autores principales: | , , , , , , , , , , |
|---|---|
| Formato: | Artículo |
| Lenguaje: | Inglés |
| Publicado: |
2018
|
| Materias: | |
| Acceso en línea: | http://hdl.handle.net/20.500.12123/2150 https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4523-2 https://doi.org/10.1186/s12864-018-4523-2 |
| _version_ | 1855483003761852416 |
|---|---|
| author | Carignano, Hugo Adrian Roldan, Dana Leticia Beribe, Maria Jose Raschia, Maria Agustina Amadio, Ariel Nani, Juan Pablo Gutierrez, Gerónimo Alvarez, Irene Trono, Karina Gabriela Poli, Mario Andres Miretti, Marcos Mateo |
| author_browse | Alvarez, Irene Amadio, Ariel Beribe, Maria Jose Carignano, Hugo Adrian Gutierrez, Gerónimo Miretti, Marcos Mateo Nani, Juan Pablo Poli, Mario Andres Raschia, Maria Agustina Roldan, Dana Leticia Trono, Karina Gabriela |
| author_facet | Carignano, Hugo Adrian Roldan, Dana Leticia Beribe, Maria Jose Raschia, Maria Agustina Amadio, Ariel Nani, Juan Pablo Gutierrez, Gerónimo Alvarez, Irene Trono, Karina Gabriela Poli, Mario Andres Miretti, Marcos Mateo |
| author_sort | Carignano, Hugo Adrian |
| collection | INTA Digital |
| description | Background: Bovine leukemia virus (BLV) infection is omnipresent in dairy herds causing direct economic losses
due to trade restrictions and lymphosarcoma-related deaths. Milk production drops and increase in the culling rate
are also relevant and usually neglected. The BLV provirus persists throughout a lifetime and an inter-individual
variation is observed in the level of infection (LI) in vivo. High LI is strongly correlated with disease progression and
BLV transmission among herd mates. In a context of high prevalence, classical control strategies are economically
prohibitive. Alternatively, host genomics studies aiming to dissect loci associated with LI are potentially useful tools
for genetic selection programs tending to abrogate the viral spreading. The LI was measured through the proviral
load (PVL) set–point and white blood cells (WBC) counts. The goals of this work were to gain insight into the
contribution of SNPs (bovine 50KSNP panel) on LI variability and to identify genomics regions underlying this trait.
Results: We quantified anti–p24 response and total leukocytes count in peripheral blood from 1800 cows and used
these to select 800 individuals with extreme phenotypes in WBCs and PVL. Two case-control genomic association
studies using linear mixed models (LMMs) considering population stratification were performed. The proportion of
the variance captured by all QC-passed SNPs represented 0.63 (SE ± 0.14) of the phenotypic variance for PVL and 0.
56 (SE ± 0.15) for WBCs. Overall, significant associations (Bonferroni’s corrected -log10p > 5.94) were shared for both
phenotypes by 24 SNPs within the Bovine MHC. Founder haplotypes were used to measure the linkage disequilibrium
(LD) extent (r2 = 0.22 ± 0.27 at inter-SNP distance of 25−50 kb). The SNPs and LD blocks indicated genes potentially
associated with LI in infected cows: i.e. relevant immune response related genes (DQA1, DRB3, BOLA-A, LTA, LTB, TNF,
IER3, GRP111, CRISP1), several genes involved in cell cytoskeletal reorganization (CD2AP, PKHD1, FLOT1, TUBB5) and
modelling of the extracellular matrix (TRAM2, TNXB). Host transcription factors (TFs) were also highlighted (TFAP2D;
ABT1, GCM1, PRRC2A).
Conclusions: Data obtained represent a step forward to understand the biology of BLV–bovine interaction, and provide
genetic information potentially applicable to selective breeding programs |
| format | Artículo |
| id | INTA2150 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2018 |
| publishDateRange | 2018 |
| publishDateSort | 2018 |
| record_format | dspace |
| spelling | INTA21502018-04-12T13:44:37Z Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle Carignano, Hugo Adrian Roldan, Dana Leticia Beribe, Maria Jose Raschia, Maria Agustina Amadio, Ariel Nani, Juan Pablo Gutierrez, Gerónimo Alvarez, Irene Trono, Karina Gabriela Poli, Mario Andres Miretti, Marcos Mateo Ganado de Leche Leucemia Bovina Genomas Virus Leucemia Bovina Genetic Polymorphism Bovine Leukaemia Virus Leukaemia Genomes Dairy Cattle SNP Polimorfismos de Nucleótido Unico Background: Bovine leukemia virus (BLV) infection is omnipresent in dairy herds causing direct economic losses due to trade restrictions and lymphosarcoma-related deaths. Milk production drops and increase in the culling rate are also relevant and usually neglected. The BLV provirus persists throughout a lifetime and an inter-individual variation is observed in the level of infection (LI) in vivo. High LI is strongly correlated with disease progression and BLV transmission among herd mates. In a context of high prevalence, classical control strategies are economically prohibitive. Alternatively, host genomics studies aiming to dissect loci associated with LI are potentially useful tools for genetic selection programs tending to abrogate the viral spreading. The LI was measured through the proviral load (PVL) set–point and white blood cells (WBC) counts. The goals of this work were to gain insight into the contribution of SNPs (bovine 50KSNP panel) on LI variability and to identify genomics regions underlying this trait. Results: We quantified anti–p24 response and total leukocytes count in peripheral blood from 1800 cows and used these to select 800 individuals with extreme phenotypes in WBCs and PVL. Two case-control genomic association studies using linear mixed models (LMMs) considering population stratification were performed. The proportion of the variance captured by all QC-passed SNPs represented 0.63 (SE ± 0.14) of the phenotypic variance for PVL and 0. 56 (SE ± 0.15) for WBCs. Overall, significant associations (Bonferroni’s corrected -log10p > 5.94) were shared for both phenotypes by 24 SNPs within the Bovine MHC. Founder haplotypes were used to measure the linkage disequilibrium (LD) extent (r2 = 0.22 ± 0.27 at inter-SNP distance of 25−50 kb). The SNPs and LD blocks indicated genes potentially associated with LI in infected cows: i.e. relevant immune response related genes (DQA1, DRB3, BOLA-A, LTA, LTB, TNF, IER3, GRP111, CRISP1), several genes involved in cell cytoskeletal reorganization (CD2AP, PKHD1, FLOT1, TUBB5) and modelling of the extracellular matrix (TRAM2, TNXB). Host transcription factors (TFs) were also highlighted (TFAP2D; ABT1, GCM1, PRRC2A). Conclusions: Data obtained represent a step forward to understand the biology of BLV–bovine interaction, and provide genetic information potentially applicable to selective breeding programs Fil: Carignano, Hugo Adrian. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina Fil: Roldan, Dana Leticia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina Fil: Beribe, Maria Jose. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Pergamino; Argentina Fil: Raschia, Maria Agustina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina Fil: Amadio, Ariel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Nani, Juan Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela; Argentina Fil: Gutierrez, Gerónimo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Virología; Argentina Fil: Alvarez, Irene. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Trono, Karina Gabriela. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Virología; Argentina Fil: Poli, Mario Andres. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; Argentina Fil: Miretti, Marcos Mateo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; Argentina. Universidad Nacional de Misiones. Instituto de Biología Subtropical - Nodo Posadas; Argentina 2018-03-28T18:48:57Z 2018-03-28T18:48:57Z 2018-02-13 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://hdl.handle.net/20.500.12123/2150 https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4523-2 1471-2164 https://doi.org/10.1186/s12864-018-4523-2 eng info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by-nc-sa/4.0/ Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) application/pdf BMC Genomics 19 :142. (2018) |
| spellingShingle | Ganado de Leche Leucemia Bovina Genomas Virus Leucemia Bovina Genetic Polymorphism Bovine Leukaemia Virus Leukaemia Genomes Dairy Cattle SNP Polimorfismos de Nucleótido Unico Carignano, Hugo Adrian Roldan, Dana Leticia Beribe, Maria Jose Raschia, Maria Agustina Amadio, Ariel Nani, Juan Pablo Gutierrez, Gerónimo Alvarez, Irene Trono, Karina Gabriela Poli, Mario Andres Miretti, Marcos Mateo Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle |
| title | Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle |
| title_full | Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle |
| title_fullStr | Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle |
| title_full_unstemmed | Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle |
| title_short | Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle |
| title_sort | genome wide scan for commons snps affecting bovine leukemia virus infection level in dairy cattle |
| topic | Ganado de Leche Leucemia Bovina Genomas Virus Leucemia Bovina Genetic Polymorphism Bovine Leukaemia Virus Leukaemia Genomes Dairy Cattle SNP Polimorfismos de Nucleótido Unico |
| url | http://hdl.handle.net/20.500.12123/2150 https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4523-2 https://doi.org/10.1186/s12864-018-4523-2 |
| work_keys_str_mv | AT carignanohugoadrian genomewidescanforcommonssnpsaffectingbovineleukemiavirusinfectionlevelindairycattle AT roldandanaleticia genomewidescanforcommonssnpsaffectingbovineleukemiavirusinfectionlevelindairycattle AT beribemariajose genomewidescanforcommonssnpsaffectingbovineleukemiavirusinfectionlevelindairycattle AT raschiamariaagustina genomewidescanforcommonssnpsaffectingbovineleukemiavirusinfectionlevelindairycattle AT amadioariel genomewidescanforcommonssnpsaffectingbovineleukemiavirusinfectionlevelindairycattle AT nanijuanpablo genomewidescanforcommonssnpsaffectingbovineleukemiavirusinfectionlevelindairycattle AT gutierrezgeronimo genomewidescanforcommonssnpsaffectingbovineleukemiavirusinfectionlevelindairycattle AT alvarezirene genomewidescanforcommonssnpsaffectingbovineleukemiavirusinfectionlevelindairycattle AT tronokarinagabriela genomewidescanforcommonssnpsaffectingbovineleukemiavirusinfectionlevelindairycattle AT polimarioandres genomewidescanforcommonssnpsaffectingbovineleukemiavirusinfectionlevelindairycattle AT mirettimarcosmateo genomewidescanforcommonssnpsaffectingbovineleukemiavirusinfectionlevelindairycattle |