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Data released on May 14, 2018

Supporting data for "Evidence of Evolutionary History and Selective Sweeps in the Genome of Meishan Pig Reveals Its Genetic and Phenotypic Characteristics"

Zhao, P; Yu, Y; Feng, W; Du, H; Yu, J; Kang, H; Zheng, X; Wang, Z; Liu, G, E; Ernst, C, W; Ran, X; Wang, J; Liu, J (2018): Supporting data for "Evidence of Evolutionary History and Selective Sweeps in the Genome of Meishan Pig Reveals Its Genetic and Phenotypic Characteristics" GigaScience Database. http://dx.doi.org/10.5524/100429 RIS BibTeX Text

Meishan is a pig breed indigenous to China and famous for its high fecundity. The traits of Meishan strongly associated with its distinct evolutionary history and domestication. However, the genomic evidence linking the domestication of Meishan pigs with the unique features are still poorly understood. The goal of this study is to investigate the genomic signatures an d evolutionary evidence related to phenotypic traits of Meishan by large-scale sequencing.
We found the unique domestication of Meishan pigs happened at Taihu Basin area between the Majiabang and the Liangzhu culture, during which 300 protein-coding genes have undergone positive selection. Notably, the FoxO signaling pathway with significant enrichment signal and the harbored gene IGF1R were likely associated with high fertility of Meishan pig. Moreover, NFKB1 exhibited strong selective sweep signals and positively participated in hyaluronan biosynthesis as the key gene of KF-kB signaling, which might have resulted in the wrinkled skin and face of Meishan pig. Particularly, three population-specific synonymous single nucleotide variants (SNVs) occurred in PYROXD1, MC1R, and FAM83G genes, of which T305C substitution in the MCIR gene explained the black coat in Meishan pig well. In addition, the shared haplotypes between Meishan and Duroc breeds confirmed the previous Asian-derived introgression and demonstrated the specific contribution of Meishan pigs.
The findings will help us explain the unique genetic and phenotypic characteristics of Meishan pigs, and offer a plausible method for the utilization of Meishan pigs as valuable genetic resources in pig breeding, and as the model animal for human wrinkled skin disease research.

Contact Submitter

Accessions (data included in GigaDB):

BioProject: PRJNA378496

Keywords:

large-scale sequencing meishan pig selective sweep fecundity 

Genomic

http://gigadb.org/images/data/cropped/100429.png

Funding:

  • Funding body - National High Technology Research and Development Program of China
  • Award ID - 2013AA102503
  • Comment - 863 Program
  • Awardee - Jian-Feng Liu
  • Funding body - Program for Changjiang Scholar and Innovation Research Team in University
  • Award ID - IRT1191
  • Awardee - Jian-Feng Liu
  • Funding body - The National Natural Science Foundations of China
  • Award ID - 31661146013
  • Awardee - Jian-Feng Liu
  • Funding body - Kunming Bureau of Science and Technology Key Program
  • Award ID - 09H130302
  • Awardee - Jian-Feng Lui

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Durocs_599825 domestic pigSus scrofa domesticus Description:DNA extracted from the ear of Durocs p...
Alternative accession-BioSample:SAMN06578718
Infra specific rank:breed
...
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Durocs_69825 domestic pigSus scrofa domesticus Description:DNA extracted from the ear of Durocs p...
Alternative accession-BioSample:SAMN06562586
Infra specific rank:breed
...
+
Durocs_609825 domestic pigSus scrofa domesticus Description:DNA extracted from the ear of Durocs p...
Alternative accession-BioSample:SAMN06578935
Infra specific rank:breed
...
+
European-wild-boar_19823PigpigSus scrofa Description:DNA extracted from European wild boar ...
Alternative accession-BioSample:SAMEA1557424
Infra specific rank:breed
...
+
European-wild-boar_29823PigpigSus scrofa Description:DNA extracted from European wild boar ...
Alternative accession-BioSample:SAMEA1557394
Infra specific rank:breed
...
+
European-wild-boar_39823PigpigSus scrofa Description:DNA extracted from European wild boar ...
Alternative accession-BioSample:SAMEA1557403
Infra specific rank:breed
...
+
Jangquhai9825 domestic pigSus scrofa domesticus Description:DNA extracted from Jangquhai pig
Alternative accession-BioSample:SAMEA1557388
Infra specific rank:breed
...
+
Japan-wild-boar9823PigpigSus scrofa Description:DNA extracted from Japan wild boar
Alternative accession-BioSample:SAMEA1557411
Infra specific rank:breed
...
+
Java159856 Java warty pigSus verrucosus Description:DNA extracted from Java warty pig
Alternative accession-BioSample:SAMEA1557384
Landrace9825 domestic pigSus scrofa domesticus Description:DNA extracted from Landrace pig
Alternative accession-BioSample:SAMN06562968
Infra specific rank:breed
...
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Displaying 41-50 of 118 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
Data Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDData TypeFile FormatSizeRelease Date 
scriptUNKNOWN0.11 KB2018-05-08
scriptUNKNOWN1.17 KB2018-05-08
scriptUNKNOWN0.96 KB2018-05-08
scriptUNKNOWN1.21 KB2018-05-08
mixed archiveTAR1.55 KB2018-05-08
mixed archiveTAR229.14 MB2018-05-08
mixed archiveTAR360.32 MB2018-05-08
mixed archiveTAR141.87 MB2018-05-08
Tabular DataEXCEL30.98 KB2018-05-08
Tabular DataVCF272.02 KB2018-05-08
Displaying 1-10 of 30 File(s).

History:

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