Supporting data for "Whole-genome resequencing reveals signatures of selection and timing of duck domestication"

Dataset type: Genomic, Transcriptomic
Data released on March 15, 2018

Zhang Z; Jia Y; Almeida P; Mank JE; Tuinen Mv; Wang Q; Jiang Z; Chen Y; Zhan K; Hou S; Zhou Z; Li H; Yang F; He Y; Ning Z; Yang N; Qu L (2018): Supporting data for "Whole-genome resequencing reveals signatures of selection and timing of duck domestication" GigaScience Database. http://dx.doi.org/10.5524/100417

DOI10.5524/100417

The genetic basis of animal domestication remains poorly understood, and systems with substantial phenotypic differences between wild and domestic populations are useful for elucidating the genetic basis of adaptation to new environments as well as the genetic basis of rapid phenotypic change.
Here, we sequenced the whole genome of 78 individual ducks, from two wild and seven domesticated populations, with an average sequencing depth of 6.42X per individual.
Our population and demographic analyses indicate a complex history of domestication, with early selection for separate meat and egg lineages. Genomic comparison of wild to domesticated populations suggest that genes affecting brain and neuronal development have undergone strong positive selection during domestication. Our FST analysis also indicates that the duck white plumage is the result of selection at the melanogenesis associated transcription factor locus.
Our results advance the understanding of animal domestication and selection for complex phenotypic traits.

Additional details

Read the peer-reviewed publication(s):

(PubMed: 29635409)

Accessions (data generated as part of this study):

PROJECT: PRJNA419832
PROJECT: PRJNA419583
SRA: SRA633983
SRA: SRP125529





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMN080931728839Mallard duckmallardAnas platyrhynchos Alternative names:MDNM1_brain
Common name:mallard
Infra specific name:Mallard
...
+
SAMN080931738839Mallard duckmallardAnas platyrhynchos Alternative names:MDNM2_brain
Common name:mallard
Infra specific name:Mallard
...
+
SAMN080931748839Mallard duckmallardAnas platyrhynchos Alternative names:MDNM3_brain
Common name:mallard
Infra specific name:Mallard
...
+
SAMN080931758839Mallard duckmallardAnas platyrhynchos Alternative names:MDZM1_brain
Common name:mallard
Infra specific name:Mallard
...
+
SAMN080931768839Mallard duckmallardAnas platyrhynchos Alternative names:MDZM2_brain
Common name:mallard
Infra specific name:Mallard
...
+
SAMN080931778839Mallard duckmallardAnas platyrhynchos Alternative names:MDZM3_brain
Common name:mallard
Infra specific name:Mallard
...
+
SAMN080931788839Mallard duckmallardAnas platyrhynchos Alternative names:MDZM4_brain
Common name:mallard
Infra specific name:Mallard
...
+
SAMN080931798839Mallard duckmallardAnas platyrhynchos Alternative names:PKM1_brain
Common name:mallard
Infra specific name:Pekin
...
+
SAMN080931808839Mallard duckmallardAnas platyrhynchos Alternative names:CVM1_brain
Common name:mallard
Infra specific name:Cherry Valley
...
+
SAMN080931818839Mallard duckmallardAnas platyrhynchos Alternative names:MLM1_brain
Common name:mallard
Infra specific name:Maple Leaf
...
+
Displaying 1-10 of 120 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
ScriptUNKNOWN1.03 KB2018-03-13
Structural variationVCF67.32 MB2018-03-13
Structural variationVCF545.82 KB2018-03-13
SNPsVCF613.03 MB2018-03-13
SNPsVCF853.45 KB2018-03-13
ScriptPython4 KB2018-03-13
ScriptPython4.31 KB2018-03-13
ScriptUNKNOWN1 KB2018-03-13
AlignmentsFASTA1.12 MB2018-03-13
SNPsUNKNOWN4.17 MB2018-03-13
Displaying 1-10 of 69 File(s).
Funding body Awardee Award ID Comments
Modern Agro-industry Technology Research System Lujiang Qu BAIC04-2017
European Research Council Judith E Mank 680951
Royal Society Wolfson Research Merit Award Judith E Mank
Date Action
March 15, 2018 Dataset publish
July 4, 2018 Manuscript Link added : 10.1093/gigascience/giy027
November 10, 2022 Manuscript Link updated : 10.1093/gigascience/giy027