The quail genome: insights into social behaviour, seasonal biology and infectious disease response

Katrina M Morris,Andrew S Mason,Frédérique Pitel,Angela Danner ,Hanane Khoury,Tsuyoshi Shimmura,Francis Minvielle,Simone Meddle ,J Seiler ,Takashi Yoshimura,Wesley C Warren,Christine Leterrier,H S Forrest ,Thierry Jaffredo,David W Burt,Robert G Webster,Patrick Minx,David Gourichon,Matthew Hindle ,Jérôme Gros ,Simon Boitard,Ladeana W Hillier,Rusty Lansford,A S I Loudon ,Chad Tomlinson,Alain Vignal,Lél Eöry ,Jacqueline Smith

doi:10.1186/s12915-020-0743-4

Abstract

BackgroundThe Japanese quail (Coturnix japonica) is a popular domestic poultry species and an increasingly significant model species in avian developmental, behavioural and disease research.ResultsWe have produced a high-quality quail genome sequence, spanning 0.93 Gb assigned to 33 chromosomes. In terms of contiguity, assembly statistics, gene content and chromosomal organisation, the quail genome shows high similarity to the chicken genome. We demonstrate the utility of this genome through three diverse applications. First, we identify selection signatures and candidate genes associated with social behaviour in the quail genome, an important agricultural and domestication trait. Second, we investigate the effects and interaction of photoperiod and temperature on the transcriptome of the quail medial basal hypothalamus, revealing key mechanisms of photoperiodism. Finally, we investigate the response of quail to H5N1 influenza infection. In quail lung, many critical immune genes and pathways were downregulated after H5N1 infection, and this may be key to the susceptibility of quail to H5N1.ConclusionsWe have produced a high-quality genome of the quail which will facilitate further studies into diverse research questions using the quail as a model avian species.

Highlights

The Japanese quail (Coturnix japonica) is a popular domestic poultry species and an increasingly significant model species in avian developmental, behavioural and disease research
Coturnix japonica 2.0 assembly metrics were comparable to previous assemblies of Galliformes, and superior to other genomes of other quail species [38, 39] in ungapped sequence length metrics (Table 1)
We have demonstrated the utility of this genome in both infectious disease and behavioural research providing further confirmation of the importance of quail as a research model, and for its role in agricultural and animal health studies

Summary

Introduction

The Japanese quail (Coturnix japonica) is a popular domestic poultry species and an increasingly significant model species in avian developmental, behavioural and disease research. Quail have been used in genetics research since 1940 [1] and are an increasingly important model in developmental biology, behaviour and biomedical studies [2]. Quail belong to the same family as chickens (Phasianidae) but have several advantages over chickens as a research model. They are small and easy to raise, have a rapid growth rate and a. The avian embryo has long been a popular model for studying developmental biology due to the accessibility of the embryo, which permits fate mapping studies [5, 6] and dynamic imaging of embryogenesis [7,8,9]. Several transgenic lines that express fluorescent proteins exist, which greatly facilitates time-lapse imaging and tissue transplantation [7, 10,11,12,13]

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Discussion

Conclusion