Genetic architecture and selection of Anhui autochthonous pig population revealed by whole genome resequencing

Abstract

The genetic resources among pigs in Anhui Province are diverse, but their value and potential have yet to be discovered. To illustrate the genetic diversity and population structure of the Anhui pigs population, we resequenced the genome of 150 pigs from six representative Anhui pigs populations and analyzed this data together with the sequencing data from 40 Asian wild boars and commercial pigs. Our results showed that Anhui pigs were divided into two distinct types based on ancestral descent: Wannan Spotted pig (WSP) and Wannan Black pig (WBP) origins from the same ancestor and the other four populations origins from another ancestor. We also identified several potential selective sweep regions associated with domestication characteristics among Anhui pigs, including reproduction-associated genes (CABS1, INSL6, MAP3K12, IGF1R, INSR, LIMK2, PATZ1, MAPK1), lipid- and meat-related genes (SNX19, MSTN, MC5R, PRKG1, CREBBP, ADCY9), and ear size genes (MSRB3 and SOX5). Therefore, these findings expand the catalogue and how these genetic differences among pigs and this newly generated data will be a valuable resource for future genetic studies and for improving genome-assisted breeding of pigs and other domesticated animals.

Genome-wide single nucleotide polymorphism (SNP) data reveal potential candidate genes for litter traits in a Yorkshire pig population

“…In pigs, through selective sweep analysis, IGF1R was identified as the key gene for high-prolificacy traits in Meishan pigs (Zhao et al, 2018). Zhang et al (2022) also identified IGF1R as a candidate gene related to pig reproductive traits in a selective sweep analysis of Wannan black pigs and commercial pigs. The present result was consistent with the results reported.…”

Genome-wide detection of selection signatures in Jianli pigs reveals novel cis-regulatory haplotype in EDNRB associated with two-end black coat color

“…We detected a list of genes under selection that showed associations with meat quality, such as CREBBP , ADCY9 , EEPD1 and HDAC9 . CREBBP and ADCY9 , which were involved in cAMP signaling, were also detected in the selection region for meat quality in the Anhui autochthonous pig population [ 28 ]. Previous GWAS and post-GWAS studies found that CREBBP and ADCY9 are located within regions that were significantly associated with meat pH [ 29 ].…”

Identification of Copy Number Variations and Selection Signatures in Wannan Spotted Pigs by Whole Genome Sequencing Data: A Preliminary Study

“…cGMP-dependent kinase 1 (PRKG1) regulates lipolysis in adipocytes to release fatty acids and glycerol via the hydrolysis of triacylglycerol. The PRKG1 was found as selected in the pigs of our previous study [19]. In cattle, post-GWAS identified that PRKG1 has a positive effect on milk fatty acids, especially medium-chain saturated fatty acid traits [40].…”