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Identification of SNPs Related to Salmonella Resistance in Chickens Using RNA-Seq and Integrated Bioinformatics Approach
Potential single nucleotide polymorphisms (SNPs) were detected between two chicken breeds (Kashmir favorella and broiler) using deep RNA sequencing. This was carried out to comprehend the coding area alterations, which cause variances in the immunological response to Salmonella infection. In the pre...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10297900/ https://www.ncbi.nlm.nih.gov/pubmed/37372463 http://dx.doi.org/10.3390/genes14061283 |
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author | Dar, Mashooq Ahmad Bhat, Basharat Nazir, Junaid Saleem, Afnan Manzoor, Tasaduq Khan, Mahak Haq, Zulfqarul Bhat, Sahar Saleem Ahmad, Syed Mudasir |
author_facet | Dar, Mashooq Ahmad Bhat, Basharat Nazir, Junaid Saleem, Afnan Manzoor, Tasaduq Khan, Mahak Haq, Zulfqarul Bhat, Sahar Saleem Ahmad, Syed Mudasir |
author_sort | Dar, Mashooq Ahmad |
collection | PubMed |
description | Potential single nucleotide polymorphisms (SNPs) were detected between two chicken breeds (Kashmir favorella and broiler) using deep RNA sequencing. This was carried out to comprehend the coding area alterations, which cause variances in the immunological response to Salmonella infection. In the present study, we identified high impact SNPs from both chicken breeds in order to delineate different pathways that mediate disease resistant/susceptibility traits. Samples (liver and spleen) were collected from Salmonella resistant (K. favorella) and susceptible (broiler) chicken breeds. Salmonella resistance and susceptibility were checked by different pathological parameters post infection. To explore possible polymorphisms in genes linked with disease resistance, SNP identification analysis was performed utilizing RNA seq data from nine K. favorella and ten broiler chickens. A total of 1778 (1070 SNPs and 708 INDELs) and 1459 (859 SNPs and 600 INDELs) were found to be specific to K. favorella and broiler, respectively. Based on our results, we conclude that in broiler chickens the enriched pathways mostly included metabolic pathways like fatty acid metabolism, carbon metabolism and amino acid metabolism (Arginine and proline metabolism), while as in K. favorella genes with high impact SNPs were enriched in most of the immune-related pathways like MAPK signaling pathway, Wnt signaling pathway, NOD-like receptor signaling pathway, etc., which could be a possible resistance mechanism against salmonella infection. In K. favorella, protein–protein interaction analysis also shows some important hub nodes, which are important in providing defense against different infectious diseases. Phylogenomic analysis revealed that indigenous poultry breeds (resistant) are clearly separated from commercial breeds (susceptible). These findings will offer fresh perspectives on the genetic diversity in chicken breeds and will aid in the genomic selection of poultry birds. |
format | Online Article Text |
id | pubmed-10297900 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-102979002023-06-28 Identification of SNPs Related to Salmonella Resistance in Chickens Using RNA-Seq and Integrated Bioinformatics Approach Dar, Mashooq Ahmad Bhat, Basharat Nazir, Junaid Saleem, Afnan Manzoor, Tasaduq Khan, Mahak Haq, Zulfqarul Bhat, Sahar Saleem Ahmad, Syed Mudasir Genes (Basel) Article Potential single nucleotide polymorphisms (SNPs) were detected between two chicken breeds (Kashmir favorella and broiler) using deep RNA sequencing. This was carried out to comprehend the coding area alterations, which cause variances in the immunological response to Salmonella infection. In the present study, we identified high impact SNPs from both chicken breeds in order to delineate different pathways that mediate disease resistant/susceptibility traits. Samples (liver and spleen) were collected from Salmonella resistant (K. favorella) and susceptible (broiler) chicken breeds. Salmonella resistance and susceptibility were checked by different pathological parameters post infection. To explore possible polymorphisms in genes linked with disease resistance, SNP identification analysis was performed utilizing RNA seq data from nine K. favorella and ten broiler chickens. A total of 1778 (1070 SNPs and 708 INDELs) and 1459 (859 SNPs and 600 INDELs) were found to be specific to K. favorella and broiler, respectively. Based on our results, we conclude that in broiler chickens the enriched pathways mostly included metabolic pathways like fatty acid metabolism, carbon metabolism and amino acid metabolism (Arginine and proline metabolism), while as in K. favorella genes with high impact SNPs were enriched in most of the immune-related pathways like MAPK signaling pathway, Wnt signaling pathway, NOD-like receptor signaling pathway, etc., which could be a possible resistance mechanism against salmonella infection. In K. favorella, protein–protein interaction analysis also shows some important hub nodes, which are important in providing defense against different infectious diseases. Phylogenomic analysis revealed that indigenous poultry breeds (resistant) are clearly separated from commercial breeds (susceptible). These findings will offer fresh perspectives on the genetic diversity in chicken breeds and will aid in the genomic selection of poultry birds. MDPI 2023-06-17 /pmc/articles/PMC10297900/ /pubmed/37372463 http://dx.doi.org/10.3390/genes14061283 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Dar, Mashooq Ahmad Bhat, Basharat Nazir, Junaid Saleem, Afnan Manzoor, Tasaduq Khan, Mahak Haq, Zulfqarul Bhat, Sahar Saleem Ahmad, Syed Mudasir Identification of SNPs Related to Salmonella Resistance in Chickens Using RNA-Seq and Integrated Bioinformatics Approach |
title | Identification of SNPs Related to Salmonella Resistance in Chickens Using RNA-Seq and Integrated Bioinformatics Approach |
title_full | Identification of SNPs Related to Salmonella Resistance in Chickens Using RNA-Seq and Integrated Bioinformatics Approach |
title_fullStr | Identification of SNPs Related to Salmonella Resistance in Chickens Using RNA-Seq and Integrated Bioinformatics Approach |
title_full_unstemmed | Identification of SNPs Related to Salmonella Resistance in Chickens Using RNA-Seq and Integrated Bioinformatics Approach |
title_short | Identification of SNPs Related to Salmonella Resistance in Chickens Using RNA-Seq and Integrated Bioinformatics Approach |
title_sort | identification of snps related to salmonella resistance in chickens using rna-seq and integrated bioinformatics approach |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10297900/ https://www.ncbi.nlm.nih.gov/pubmed/37372463 http://dx.doi.org/10.3390/genes14061283 |
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