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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
Meishan_89825 domestic pigSus scrofa domesticus Description:DNA extracted from the ear of Meisham ...
Alternative accession-BioSample:SAMN06562956
Infra specific rank:breed
...
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Meishan_99825 domestic pigSus scrofa domesticus Description:DNA extracted from the ear of Meisham ...
Alternative accession-BioSample:SAMN06562959
Infra specific rank:breed
...
+
Min9823PigpigSus scrofa Description:DNA extracted from Min pig
Alternative accession-BioSample:SAMN06610257
Infra specific rank:breed
...
+
Rongchang9825 domestic pigSus scrofa domesticus Description:DNA extracted from Rongchang pig
Alternative accession-BioSample:SAMN06560025
Infra specific rank:breed
...
+
Sumatran9825 domestic pigSus scrofa domesticus Description:DNA extracted from Sumatran pig
Alternative accession-BioSample:SAMEA1557414
Infra specific rank:breed
...
+
Tibetan-wild-boar_19823PigpigSus scrofa Description:DNA extracted from Tibetan wild boar
Alternative accession-BioSample:SAMN01894345
Infra specific rank:breed
...
+
Tibetan-wild-boar_109823PigpigSus scrofa Description:DNA extracted from Tibetan wild boar
Alternative accession-BioSample:SAMN01894386
Infra specific rank:breed
...
+
Tibetan-wild-boar_119823PigpigSus scrofa Description:DNA extracted from Tibetan wild boar
Alternative accession-BioSample:SAMN01894387
Infra specific rank:breed
...
+
Tibetan-wild-boar_129823PigpigSus scrofa Description:DNA extracted from Tibetan wild boar
Alternative accession-BioSample:SAMN01894388
Infra specific rank:breed
...
+
Tibetan-wild-boar_139823PigpigSus scrofa Description:DNA extracted from Tibetan wild boar
Alternative accession-BioSample:SAMN01894389
Infra specific rank:breed
...
+
Displaying 81-90 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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