Population genomic data reveal genes related to important traits of quail

GigaScience
Yan WuJinping Du

Abstract

Japanese quail (Coturnix japonica), a recently domesticated poultry species, is important not only as an agricultural product, but also as a model bird species for genetic research. However, most of the biological questions concerning genomics, phylogenetics, and genetics of some important economic traits have not been answered. It is thus necessary to complete a high-quality genome sequence as well as a series of comparative genomics, evolution, and functional studies. Here, we present a quail genome assembly spanning 1.04 Gb with 86.63% of sequences anchored to 30 chromosomes (28 autosomes and 2 sex chromosomes Z/W). Our genomic data have resolved the long-term debate of phylogeny among Perdicinae (Japanese quail), Meleagridinae (turkey), and Phasianinae (chicken). Comparative genomics and functional genomic data found that four candidate genes involved in early maturation had experienced positive selection, and one of them encodes follicle stimulating hormone beta (FSHβ), which is correlated with different FSHβ levels in quail and chicken. We re-sequenced 31 quails (10 wild, 11 egg-type, and 10 meat-type) and identified 18 and 26 candidate selective sweep regions in the egg-type and meat-type lines, respectively. That only o...Continue Reading

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Citations

Mar 12, 2020·Journal of Cardiovascular Development and Disease·Rusty Lansford, Sandra Rugonyi
Feb 14, 2020·Genome Biology and Evolution·George PachecoFilipe Garrett Vieira
Oct 5, 2018·Frontiers in Genetics·Shubham K JaiswalVineet K Sharma
Jan 18, 2021·Molecular Biology Reports·Fabiana Cristina Belchior de SousaKatiene Régia Silva Sousa
Jan 20, 2019·Journal of Cellular Biochemistry·Rongxing ShiTao Wang
Oct 18, 2019·Journal of Cellular Physiology·Dongling QuanLin Lv

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Datasets Mentioned

BETA
SRP104331

Methods Mentioned

BETA
RNA-Seq
PCA
ELISA
PCR

Key Resources (RRID) Mentioned

SCR_014986
SCR_015008
SCR_012954
SCR_011919
SCR_015054
SCR_008417
SCR_012902
SCR_013035
SCR_014597
SCR_012067

Software Mentioned

AUGUSTUS
GATK
MEGA
GENSCAN
II
Genome Analysis Toolkit
in
SMtools
SOAPdenovo2
SOAP denovo2

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