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

Dataset type: Genomic
Data released on May 14, 2018

Zhao P; Yu Y; Feng W; Du H; Yu J; Kang H; Zheng X; Wang Z; Liu GE; Ernst CW; 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

DOI10.5524/100429

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.

Additional details

Read the peer-reviewed publication(s):

Zhao, P., Yu, Y., Feng, W., Du, H., Yu, J., Kang, H., … Liu, J.-F. (2018). Evidence of evolutionary history and selective sweeps in the genome of Meishan pig reveals its genetic and phenotypic characterization. GigaScience, 7(5). doi:10.1093/gigascience/giy058

Accessions (data generated as part of this study):

BioProject: PRJNA378496





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Asian-wild-boar_19823PigpigSus scrofa Description:DNA extracted from Asian wild boar, fr...
Alternative accession-BioSample:SAMEA1557386
Infra specific rank:breed
...
+
Asian wild boar_29823PigpigSus scrofa Description:DNA extracted from Asian wild boar, fr...
Alternative accession-BioSample:SAMEA1557437
Infra specific rank:breed
...
+
Asian wild boar_39823PigpigSus scrofa Description:DNA extracted from Asian wild boar, fr...
Alternative accession-BioSample:SAMN06563372
Infra specific rank:breed
...
+
Bamaxiang9825 domestic pigSus scrofa domesticus Description:DNA extracted from Bamaxiang pig
Alternative accession-BioSample:SAMEA1557398
Infra specific rank:breed
...
+
bearded41807 bearded pigSus barbatus Description:DNA extracted from bearded pig
Alternative accession-BioSample:SAMEA1557429
Celebes273789  Sus celebensis Description:DNA extracted from Celebes wild boar
Alternative accession-BioSample:SAMEA1557393
Daweiz9825 domestic pigSus scrofa domesticus Description:DNA extracted from Daweiz pig
Alternative accession-BioSample:SAMN06562957
Infra specific rank:breed
...
+
Diannan9825 domestic pigSus scrofa domesticus Description:DNA extracted from Diannan small-ear p...
Alternative accession-BioSample:SAMN06560373
Infra specific rank:breed
...
+
Durocs_19825 domestic pigSus scrofa domesticus Description:DNA extracted from the ear of Durocs p...
Alternative accession-BioSample:SAMN06554454
Infra specific rank:breed
...
+
Durocs_1009825 domestic pigSus scrofa domesticus Description:DNA extracted from Durocs pig, sample ...
Alternative accession-BioSample:SAMEA1557407
Infra specific rank:breed
...
+
Displaying 1-10 of 118 Sample(s).




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).
Funding body Awardee Award ID Comments
National High Technology Research and Development Program of China Jian-Feng Liu 2013AA102503 863 Program
Program for Changjiang Scholar and Innovation Research Team in University Jian-Feng Liu IRT1191
The National Natural Science Foundations of China Jian-Feng Liu 31661146013
Kunming Bureau of Science and Technology Key Program Jian-Feng Lui 09H130302
Date Action
May 14, 2018 Dataset publish
July 4, 2018 Manuscript Link added : 10.1093/gigascience/giy058