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Open AccessArticle

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

by Qiao Wang 1,2,†, Fei Wang 1,2,†, Lu Liu 1,3, Qinghe Li 1,2, Ranran Liu 1,2, Maiqing Zheng 1,2, Huanxian Cui 1,2, Jie Wen 1,2 and Guiping Zhao 1,2,4,*
1
Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
2
State Key Laboratory of Animal Nutrition, Beijing 100193, China
3
College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
4
School of Life Science and Engineering, Foshan University, Foshan 528225, China
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Animals 2019, 9(5), 272; https://doi.org/10.3390/ani9050272
Received: 6 March 2019 / Revised: 19 May 2019 / Accepted: 20 May 2019 / Published: 23 May 2019
(This article belongs to the Collection Applications of Quantitative Genetics in Livestock Production)
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.
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. View Full-Text
Keywords: SNP; Indel; White Leghorn; Beijing-You; IgY level SNP; Indel; White Leghorn; Beijing-You; IgY level
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Wang, Q.; Wang, F.; Liu, L.; Li, Q.; Liu, R.; Zheng, M.; Cui, H.; Wen, J.; Zhao, G. Genetic Mutation Analysis of High and Low IgY Chickens by Capture Sequencing. Animals 2019, 9, 272.

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