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Genetic Mutation Analysis of High and Low IgY Chickens by Capture Sequencing

SIMPLE SUMMARY: Immunoglobulin Y (IgY) is the major antibody produced by hens and it endows their offspring with effective humoral immunity against the pathogens. In previous research, we identified 13 genomic regions that were significantly associated with the serum IgY level or antibody responses...

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Autores principales: Wang, Qiao, Wang, Fei, Liu, Lu, Li, Qinghe, Liu, Ranran, Zheng, Maiqing, Cui, Huanxian, Wen, Jie, Zhao, Guiping
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6562818/
https://www.ncbi.nlm.nih.gov/pubmed/31126132
http://dx.doi.org/10.3390/ani9050272
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author Wang, Qiao
Wang, Fei
Liu, Lu
Li, Qinghe
Liu, Ranran
Zheng, Maiqing
Cui, Huanxian
Wen, Jie
Zhao, Guiping
author_facet Wang, Qiao
Wang, Fei
Liu, Lu
Li, Qinghe
Liu, Ranran
Zheng, Maiqing
Cui, Huanxian
Wen, Jie
Zhao, Guiping
author_sort Wang, Qiao
collection PubMed
description SIMPLE SUMMARY: Immunoglobulin Y (IgY) is the major antibody produced by hens and it endows their offspring with effective humoral immunity against the pathogens. In previous research, we identified 13 genomic regions that were significantly associated with the serum IgY level or antibody responses to sheep red-blood-cells, but the specific mutations in these regions have not been reported. Therefore, we screened for variations in these regions in White Leghorn and Beijing-You chickens with high and low IgY. Our study identified 35,154 mutations and 829 Indels which were associated with IgY levels in both lines. Many non-synonymous mutations were located in crucial genes related to the host immune function, indicating the possible involvement of these genes in controlling IgY levels. ABSTRACT: Based on the results of our previous genome-wide association study (GWAS), a comprehensive analysis on single nucleotide polymorphisms (SNPs) was performed on White Leghorn and Beijing-You chickens with high and low IgY levels in defined genomic regions using the capture-sequencing approach. High and low IgY chickens showed substantial genetic variations. In total, more than 30,000 SNPs were found in all four chicken groups, among which 1045 were non-synonymous mutations resulting in amino acids alterations. In total, 23,309 Indels were identified. Among the 1169 Indels that were found only in Beijing-You chickens, 702 were shared between high and low IgY chickens compared with the reference genome. There were 1016 Indels specific to the White Leghorn chickens, among which 188 were high IgY-specific, 134 were low IgY-specific and 694 were shared between the high and low IgY chicken lines. Many genetic mutations were located in the regulatory regions of important immunomodulatory genes, including TAP1, TAP2 and BF1. Our findings provide an in-depth understanding of genetic mutations in chicken microchromosomes.
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spelling pubmed-65628182019-06-17 Genetic Mutation Analysis of High and Low IgY Chickens by Capture Sequencing Wang, Qiao Wang, Fei Liu, Lu Li, Qinghe Liu, Ranran Zheng, Maiqing Cui, Huanxian Wen, Jie Zhao, Guiping Animals (Basel) Article SIMPLE SUMMARY: Immunoglobulin Y (IgY) is the major antibody produced by hens and it endows their offspring with effective humoral immunity against the pathogens. In previous research, we identified 13 genomic regions that were significantly associated with the serum IgY level or antibody responses to sheep red-blood-cells, but the specific mutations in these regions have not been reported. Therefore, we screened for variations in these regions in White Leghorn and Beijing-You chickens with high and low IgY. Our study identified 35,154 mutations and 829 Indels which were associated with IgY levels in both lines. Many non-synonymous mutations were located in crucial genes related to the host immune function, indicating the possible involvement of these genes in controlling IgY levels. ABSTRACT: Based on the results of our previous genome-wide association study (GWAS), a comprehensive analysis on single nucleotide polymorphisms (SNPs) was performed on White Leghorn and Beijing-You chickens with high and low IgY levels in defined genomic regions using the capture-sequencing approach. High and low IgY chickens showed substantial genetic variations. In total, more than 30,000 SNPs were found in all four chicken groups, among which 1045 were non-synonymous mutations resulting in amino acids alterations. In total, 23,309 Indels were identified. Among the 1169 Indels that were found only in Beijing-You chickens, 702 were shared between high and low IgY chickens compared with the reference genome. There were 1016 Indels specific to the White Leghorn chickens, among which 188 were high IgY-specific, 134 were low IgY-specific and 694 were shared between the high and low IgY chicken lines. Many genetic mutations were located in the regulatory regions of important immunomodulatory genes, including TAP1, TAP2 and BF1. Our findings provide an in-depth understanding of genetic mutations in chicken microchromosomes. MDPI 2019-05-23 /pmc/articles/PMC6562818/ /pubmed/31126132 http://dx.doi.org/10.3390/ani9050272 Text en © 2019 by the authors. 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 (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Wang, Qiao
Wang, Fei
Liu, Lu
Li, Qinghe
Liu, Ranran
Zheng, Maiqing
Cui, Huanxian
Wen, Jie
Zhao, Guiping
Genetic Mutation Analysis of High and Low IgY Chickens by Capture Sequencing
title Genetic Mutation Analysis of High and Low IgY Chickens by Capture Sequencing
title_full Genetic Mutation Analysis of High and Low IgY Chickens by Capture Sequencing
title_fullStr Genetic Mutation Analysis of High and Low IgY Chickens by Capture Sequencing
title_full_unstemmed Genetic Mutation Analysis of High and Low IgY Chickens by Capture Sequencing
title_short Genetic Mutation Analysis of High and Low IgY Chickens by Capture Sequencing
title_sort genetic mutation analysis of high and low igy chickens by capture sequencing
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6562818/
https://www.ncbi.nlm.nih.gov/pubmed/31126132
http://dx.doi.org/10.3390/ani9050272
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