Detection of genomic structural variations in Guizhou indigenous pigs and the comparison with other breeds

Abstract

Genomic structural variation (SV) is noticed for the contribution to genetic diversity and phenotypic changes. Guizhou indigenous pig (GZP) has been raised for hundreds of years with many special characteristics. The present paper aimed to uncover the influence of SV on gene polymorphism and the genetic mechanisms of phenotypic traits for GZP. Eighteen GZPs were chosen for resequencing by Illumina sequencing platform. The confident SVs of GZP were called out by both programs of pindel and softSV simultaneously and compared with the SVs deduced from the genomic data of European pig (EUP) and the native pig outside of Guizhou, China (NPOG). A total of 39,166 SVs were detected and covered 27.37 Mb of pig genome. All of 76 SVs were confirmed in GZP pig population by PCR method. The SVs numbers in NPOG and GZP were about 1.8 to 1.9 times higher than that in EUP. And a SV hotspot was found out from the 20 Mb of chromosome X of GZP, which harbored 29 genes and focused on histone modification. More than half of SVs was positioned in the intergenic regions and about one third of SVs in the introns of genes. And we found that SVs tended to locate in genes produced multi-transcripts, in which a positive correlation was found out between the numbers of SV and the gene transcripts. It illustrated that the primary mode of SVs might function on the regulation of gene expression or the transcripts splicing process. A total of 1,628 protein-coding genes were disturbed by 1,956 SVs specific in GZP, in which 93 GZP-specific SV-related genes would lose their functions due to the SV interference and gathered in reproduction ability. Interestingly, the 1,628 protein-coding genes were mainly enriched in estrogen receptor binding, steroid hormone receptor binding, retinoic acid receptor binding, oxytocin signaling pathway, mTOR signaling pathway, axon guidance and cholinergic synapse pathways. It suggested that SV might be a reason for the strong adaptability and low fecundity of GZP, and 51 candidate genes would be useful for the configuration phenotype in Xiang pig breed.

Longitudinal Expression of Testicular TAS1R3 from Prepuberty to Sexual Maturity in Congjiang Xiang Pigs

“…The minipig is considered a convenient animal model for preclinical studies because they rapidly achieve sexual maturity (before the age of six months) and the duration of the spermatogenic cycle is short (i.e., 35 day) [36]. Although there are structural variations at the genome level between relatively large litter sizes (average litter size: 13 piglets) and small litter sizes (average litter size: 8 piglets) in Congjiang Xiang pigs for long-term grazing and inbreeding [37,38], the breed is clearly characterized by early sexual maturity [39,40]. According to our study, Congjiang Xiang pigs exhibit the onset of puberty at approximately 2 months [40], similar to Gottingen pigs, and earlier than Yucatan minipigs (3.6-4 months) and Yorkshire (around 6 months) [41].…”

Assessing the Effect of SNPs on Litter Traits in Pigs

“…Chen et al [33] demonstrated the gene polymorphism association with the components of muscle tissue in broilers. Liu et al [34] found three insertions in AKT3 gene associated with Xiang pig fattening traits.…”

Genetic Diversity and Population Structures in Chinese Miniature Pigs Revealed by SINE Retrotransposon Insertion Polymorphisms, a New Type of Genetic Markers

“…The national conservation farm located at Bama County of Guangxi Zhuang Autonomous Region has conserved one population, which was named as BM-cov, while one closed herd (BM-clo) and one highly inbred (BM-inb) line are kept at Guangxi University [ 4 ]. All these breeds are characterized by early sexual maturity, good disease resistance, and strong adaptability in local environments [ 4 , 5 , 6 ]. In addition, because of isolation from the outside and the long time of natural and artificial selections, inbreeding has continuously increased in these populations, and the genetic diversities are expected to decrease significantly compared with the other Chinese local pig populations [ 4 , 7 ].…”