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
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):
(PubMed: 29790964)
Accessions (data generated as part of this study):
BioProject:
PRJNA378496
Sample ID | Taxonomic ID | Common Name | Genbank Name | Scientific Name | Sample Attributes |
---|---|---|---|---|---|
Asian-wild-boar_1 | 9823 | Pig | pig | Sus scrofa | Description:DNA extracted from Asian wild boar, fr... Alternative accession-BioSample:SAMEA1557386 Infra specific rank:breed ... + |
Asian wild boar_2 | 9823 | Pig | pig | Sus scrofa | Description:DNA extracted from Asian wild boar, fr... Alternative accession-BioSample:SAMEA1557437 Infra specific rank:breed ... + |
Asian wild boar_3 | 9823 | Pig | pig | Sus scrofa | Description:DNA extracted from Asian wild boar, fr... Alternative accession-BioSample:SAMN06563372 Infra specific rank:breed ... + |
Bamaxiang | 9825 | domestic pig | Sus scrofa domesticus | Description:DNA extracted from Bamaxiang pig Alternative accession-BioSample:SAMEA1557398 Infra specific rank:breed ... + | |
bearded | 41807 | bearded pig | Sus barbatus | Description:DNA extracted from bearded pig Alternative accession-BioSample:SAMEA1557429 | |
Celebes | 273789 | Sus celebensis | Description:DNA extracted from Celebes wild boar Alternative accession-BioSample:SAMEA1557393 | ||
Daweiz | 9825 | domestic pig | Sus scrofa domesticus | Description:DNA extracted from Daweiz pig Alternative accession-BioSample:SAMN06562957 Infra specific rank:breed ... + | |
Diannan | 9825 | domestic pig | Sus scrofa domesticus | Description:DNA extracted from Diannan small-ear p... Alternative accession-BioSample:SAMN06560373 Infra specific rank:breed ... + | |
Durocs_1 | 9825 | domestic pig | Sus scrofa domesticus | Description:DNA extracted from the ear of Durocs p... Alternative accession-BioSample:SAMN06554454 Infra specific rank:breed ... + | |
Durocs_100 | 9825 | domestic pig | Sus scrofa domesticus | Description:DNA extracted from Durocs pig, sample ... Alternative accession-BioSample:SAMEA1557407 Infra specific rank:breed ... + |