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A Homeostasis Hypothesis of Avian Influenza Resistance in Chickens

by 1,2, 2,†, 3, 2, 2, 3, 2,*,†, 1,2,*,† and 2
1
Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
2
State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
3
Department of Animal Science, University of California, Davis, CA 95616, USA
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Genes 2019, 10(7), 543; https://doi.org/10.3390/genes10070543
Received: 8 May 2019 / Revised: 4 July 2019 / Accepted: 11 July 2019 / Published: 17 July 2019
(This article belongs to the Special Issue Genomics of Avian Viral Infections)
Avian influenza has caused significant damage to the poultry industry globally. Consequently, efforts have been made to elucidate the disease mechanisms as well as the mechanisms of disease resistance. Here, by investigating two chicken breeds with distinct responses to avian influenza virus (AIV), Leghorn GB2 and Fayoumi M43, we compared their genome, methylation, and transcriptome differences. MX1, HSP90AB1, and HSP90B1 exhibited high degrees of genetic differentiation (FST) between the two species. Except for the MX1-involved direct anti-virus mechanism, we found that at the methylation and transcriptome levels, the more AIV-resistant breed, Fayoumi, exhibited less variation compared with Leghorn after AIV inoculation, which included change trends in differentially expressed regions, top-fold change genes with FDR-corrected p < 0.05, immune response related genes, and housekeeping genes. Fayoumi also showed better consistency regarding changes in methylation and changes at the transcriptome level. Our results suggest a homeostasis hypothesis for avian influenza resistance, with Fayoumi maintaining superior homeostasis at both the epigenetic and gene expression levels. Three candidate genes—MX1, HSP90AB1, and HSP90B1—showed genetic differentiation and altered gene expression, methylation, and protein expression, which merit attention in further functional studies. View Full-Text
Keywords: Fayoumi; Leghorn; difference degrees; fold change levels; methylation; FST; RNA-seq Fayoumi; Leghorn; difference degrees; fold change levels; methylation; FST; RNA-seq
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An, J.; Li, J.; Wang, Y.; Wang, J.; Li, Q.; Zhou, H.; Hu, X.; Zhao, Y.; Li, N. A Homeostasis Hypothesis of Avian Influenza Resistance in Chickens. Genes 2019, 10, 543.

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