Accession PRJCA000093
Title Whole-genome variations trace evolutionary footprints underlying chicken domestication based on next-generation sequencing
Relevance Evolution
Umbrella project

eGPS: evolutionary Genotype-Phenotype Systems biology

Key theories & Model

Network regulation of the evolution and stability of complex traits in model systems

Data types Whole genome sequencing
Organisms Gallus gallus
Description The evolutionary dynamics underlying domestication for animal and plant are of significance. Chicken, an important model organism, has been subjected to intensive human-driven selection, leading to remarkable phenotypic diversity in morphology and physiology. Identifying the genetic dynamics underlying domestication and divergence would provide promising insight into the mechanisms by which genetic variations shape phenotypic diversity. We sequenced 62 chickens from 6 breeds with divergent characteristics, consist of meat-production breeds (Xinghua, XH; Beijing You, YOU; Recessive White, RW), egg-production breed (White Leghorn, WL), ornamental breed (Luxi Dou, DOU), medical breed (Silkie, SILK), as well as Red Jungle Fowl, profiled the whole-genome genetic variations in terms of 15904909 SNPs, 1327453 INDELs, 10445 segmental duplications and 30732 deletions, which exhibit substantial power to distinguish chicken genealogy with distinct origination, selection purpose and geographical distribution. Putative selective sweeps analysis based on self-developed method revealed that all modern chickens have undertaken multiple pivotal systems involving nervous, cardiovascular, skeletal and muscular development, calibrating the distinguishing between wild and modern breeds. For meat-purpose breeds, several intriguing genes/regions potentially associated with lipid metabolism have been identified. For egg-purpose breed, the reproduction system has been subject to human-driven reconstruction. We creatively introduced the conception of entropy and accurately exploited species islands and breed specific islands, which hightlights the breed differentiation. Four significant copy number variations reflected the genomic differentiations in breeds, namely EDN3, TACR3, SOCS2, SMARCE1/KRT222. This study traced the genomic dynamics and functional changing patterns during breed divergence underlying intensive domestication, provided promising insight into the putative genetic architectures of complex traits.
Sample scope MultiBreeds
Release date 2020-02-04
Data provider
Data provider Data provider URL
Agency program Grant ID Grant title
External link
External link Link description
Submitter Xue    Bai  (
Organization Beijing Institute of Genomics, Chinese Academy of Sciences
Submission date 2015-11-16

Project Data

Resource name Description
BioSample (103) -
SAMC006352 Silkies_Optic Lobe_RNA-seq_1
SAMC006351 Recessive White Rock_Liver_RNA-seq_1
SAMC006350 White Leghorn_Liver_RNA-seq_1
SAMC006349 White Leghorn_Optic Lobe_RNA-seq_1
SAMC006348 White Leghorn_Cerebrum_RNA-seq_1
SAMC006347 Recessive White Rock_Liver_RNA-seq_2
SAMC006346 Luxi Cockfight_Striatum_RNA-seq_2
SAMC006345 Luxi Cockfight_Optic Lobe_RNA-seq_2
SAMC006344 Luxi Cockfight_Cerebellum_RNA-seq_2
SAMC006343 White Leghorn_Liver_RNA-seq_2
SAMC006342 Silkies_Cerebrum_RNA-seq_1
SAMC006341 Silkies_Striatum_RNA-seq_1
SAMC006340 Silkies_Liver_RNA-seq_1
SAMC006339 Silkies_Cerebellum_RNA-seq_1
SAMC006338 Recessive White Rock_Striatum_RNA-seq_3
SAMC006337 Recessive White Rock_Cerebrum_RNA-seq_3
SAMC006336 Recessive White Rock_Cerebrum_RNA-seq_2
SAMC006335 Recessive White Rock_Cerebellum_RNA-seq_2
SAMC006334 White Leghorn_Cerebellum_RNA-seq_3
SAMC006333 White Leghorn_Cerebellum_RNA-seq_2
SAMC006332 Silkies_Cerebrum_RNA-seq_2
SAMC006331 Recessive White Rock_Optic Lobe_RNA-seq_3
SAMC006330 Recessive White Rock_Cerebellum_RNA-seq_3
SAMC006329 Recessive White Rock_Striatum_RNA-seq_2
SAMC006328 Recessive White Rock_Optic Lobe_RNA-seq_2
SAMC006327 White Leghorn_Striatum_RNA-seq_3
SAMC006326 White Leghorn_Optic Lobe_RNA-seq_3
SAMC006325 White Leghorn_Cerebrum_RNA-seq_3
SAMC006324 White Leghorn_Liver_RNA-seq_3
SAMC006323 Silkies_Liver_RNA-seq_3
SAMC006322 Silkies_Striatum_RNA-seq_3
SAMC006321 Luxi Cockfight_Liver_RNA-seq_3
SAMC006320 Luxi Cockfight_Liver_RNA-seq_1
SAMC006319 Luxi Cockfight_Cerebellum_RNA-seq_1
SAMC006317 Luxi Cockfight_Cerebrum_RNA-seq_1
SAMC006316 Silkies_Optic Lobe_RNA-seq_3
SAMC006315 Silkies_Cerebellum_RNA-seq_3
SAMC006314 Silkies_Cerebrum_RNA-seq_3
SAMC006313 Luxi Cockfight_Striatum_RNA-seq_3
SAMC006312 Luxi Cockfight_Optic Lobe_RNA-seq_3
SAMC006311 Luxi Cockfight_Cerebrum_RNA-seq_3
SAMC000267 Red Jungle Fowl
SAMC000266 Red Jungle Fowl
SAMC000265 White Leghon
SAMC000264 White Leghon
SAMC000263 White Leghon
SAMC000262 White Leghon
SAMC000261 White Leghon
SAMC000260 White Leghon
SAMC000259 White Leghon
SAMC000258 White Leghon
SAMC000257 White Leghon
SAMC000256 White Leghon
SAMC000255 Recessive White Rock
SAMC000254 Recessive White Rock
SAMC000253 Recessive White Rock
SAMC000252 Recessive White Rock
SAMC000251 Recessive White Rock
SAMC000250 Recessive White Rock
SAMC000249 Recessive White Rock
SAMC000248 Recessive White Rock
SAMC000247 Recessive White Rock
SAMC000246 Recessive White Rock
SAMC000245 Silkie
SAMC000244 Silkie
SAMC000243 Silkie
SAMC000242 Silkie
SAMC000241 Silkie
SAMC000239 Silkie
SAMC000238 Silkie
SAMC000237 Silkie
SAMC000236 Silkie
SAMC000235 Silkie
SAMC000234 Beijing YOU
SAMC000233 Beijing YOU
SAMC000232 Beijing YOU
SAMC000231 Beijing YOU
SAMC000230 Beijing YOU
SAMC000229 Beijing YOU
SAMC000228 Beijing YOU
SAMC000227 Beijing YOU
SAMC000226 Beijing YOU
SAMC000225 Beijing YOU
SAMC000224 Luxi Dou
SAMC000223 Luxi Dou
SAMC000222 Luxi Dou
SAMC000221 Luxi Dou
SAMC000220 Luxi Dou
SAMC000219 Luxi Dou
SAMC000218 Luxi Dou
SAMC000217 Luxi Dou
SAMC000216 Luxi Dou
SAMC000215 Luxi Dou
SAMC000214 Guangxi Xinghua
SAMC000213 Guangxi Xinghua
SAMC000212 Guangxi Xinghua
SAMC000211 Guangxi Xinghua
SAMC000210 Guangxi Xinghua
SAMC000209 Guangxi Xinghua
SAMC000208 Guangxi Xinghua
SAMC000207 Guangxi Xinghua
SAMC000206 Guangxi Xinghua
SAMC000205 Guangxi Xinghua
GSA (1) -
CRA000005 Whole genome re-sequencing data and transcriptome data of chicken