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. https://doi.org/10.5524/100417
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):
- Zhang, Z., Jia, Y., Almeida, P., Mank, J. E., van Tuinen, M., 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). Whole-genome resequencing reveals signatures of selection and timing of duck domestication. GigaScience, 7(4). https://doi.org/10.1093/gigascience/giy027 (PubMed:29635409)
Accessions (data included in GigaDB):
PROJECT: PRJNA419832
PROJECT: PRJNA419583
SRA: SRA633983
SRA: SRP125529
Click on a table column to sort the results.
Table SettingsSample ID | Common Name | Scientific Name | Sample Attributes | Taxonomic ID | Genbank Name |
---|---|---|---|---|---|
SAMN08093172 | Mallard duck | Anas platyrhynchos | Analyte type:RNA Common name:mallard Sex:male ... |
8839 | mallard |
SAMN08093173 | Mallard duck | Anas platyrhynchos | Common name:mallard Sex:male Life stage:adult ... |
8839 | mallard |
SAMN08093174 | Mallard duck | Anas platyrhynchos | Common name:mallard Sex:male Life stage:adult ... |
8839 | mallard |
SAMN08093175 | Mallard duck | Anas platyrhynchos | Infra specific name:Mallard Common name:mallard Sex:male ... |
8839 | mallard |
SAMN08093176 | Mallard duck | Anas platyrhynchos | Common name:mallard Sex:male Life stage:adult ... |
8839 | mallard |
SAMN08093177 | Mallard duck | Anas platyrhynchos | Common name:mallard Sex:male Life stage:adult ... |
8839 | mallard |
SAMN08093178 | Mallard duck | Anas platyrhynchos | Common name:mallard Sex:male Life stage:adult ... |
8839 | mallard |
SAMN08093179 | Mallard duck | Anas platyrhynchos | Common name:mallard Sex:male Life stage:adult ... |
8839 | mallard |
SAMN08093180 | Mallard duck | Anas platyrhynchos | Common name:mallard Sex:male Life stage:adult ... |
8839 | mallard |
SAMN08093181 | Mallard duck | Anas platyrhynchos | Common name:mallard Sex:male Life stage:adult ... |
8839 | mallard |
Click on a table column to sort the results.
Table SettingsFile Name | Description | Sample ID | Data Type | File Format | Size | Release Date | File Attributes | Download |
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Readme | TEXT | 6.76 kB | 2018-03-13 | MD5 checksum: 74038904e07690c1d8cf7455e7fac228 |
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SNP information of 7 mallards from Ningxia province (MDN1-MDN8) | SNPs | VCF | 1.64 GB | 2018-03-13 | MD5 checksum: b42352dd8277a2d5a74a4f79082fd780 |
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SNP information of 14 mallards from Zhejiang province (MDZ1-MDZ14) | SNPs | VCF | 3.43 GB | 2018-03-13 | MD5 checksum: 7f833ec97190d799122051f0117678c3 |
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SNP information of 8 Pekin duck (PK1-PK8) | SNPs | VCF | 737.08 MB | 2018-03-13 | MD5 checksum: 9f78d3ad0265ae6f3c2e017a4946a360 |
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SNP information of 8 Cherry Valley duck (CV1-CV8) | SNPs | VCF | 642.81 MB | 2018-03-13 | MD5 checksum: fd18b6b8537d89593653368846866f06 |
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SNP information of 8 Maple Leaf duck (ML1-ML8) | SNPs | VCF | 830.18 MB | 2018-03-13 | MD5 checksum: 870ea40ee72c00509837467bcd4f31e2 |
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SNP information of 8 Jinding duck (JD1-JD8) | SNPs | VCF | 835.35 MB | 2018-03-13 | MD5 checksum: 6b46f9bcd5e923fc4c1aa98e6eab1dce |
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SNP information of 8 Shanma duck (SM1-SM8) | SNPs | VCF | 944.98 MB | 2018-03-13 | MD5 checksum: 05e5b4f7fcc02756f4b3fb868b51ce02 |
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SNP information of 8 Shaoxing duck (SX1-SX8) | SNPs | VCF | 983.40 MB | 2018-03-13 | MD5 checksum: b1fcb534faebabb9b415e23c9502be6f |
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SNP information of 8 Gaoyou duck (GY1-GY8) | SNPs | VCF | 837.31 MB | 2018-03-13 | MD5 checksum: afb2ee94a44e2ea2ca3aba3ae2f3cb7e |
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 |