Detection of genomic structure variants associated with wrinkled skin in Xiang pig by next generation sequencing

Abstract

Wrinkling is prominent manifestation of aging skin. A mutant phenotype characterized by systemic wrinkles and thickened skin was discovered in Xiang pig populations with incidence about 1-3%. The feature in histological structure was epidermal hyperplasia and thickening, collagen fibers disorder. To uncover genetic mechanisms for the mutant phenotype of Xiang pigs with systemic wrinkle (WXP), a genome-wide of structural variations (SVs) in WXP was described by next generation resequencing, taking Xiang pigs (XP) and European pigs (EUP) as compares. Total of 32,308 SVs were detected from three pig groups and 965 SVs were identified specifically from WXP, involving 481 protein-coding genes. These genes were mainly enriched in nuclear structure, ECM components and immunomodulatory pathways. According to gene function and enrichment analysis, we found that 65 candidate SVs in 59 protein genes were probably related with the systemic wrinkle of WXP. Of these, several genes are reported to be associate with aging, such as EIF4G2 , NOLC1 , XYLT1 , FUT8, MDM2 and so on. The insertion/deletion and duplication variations of SVs in these genes resulted in the loss of stop-codon or frameshift mutation, and aberrant alternative splicing of transcripts. These genes are involved in cell lamin filament, intermediate filament cytoskeleton, supramolecular complex, cell differentiation and regulation of macromolecule metabolic process etc. Our study suggested that the loss of function or aberrant expression of these genes lead to structural disorder of nuclear and the extracellular matrix (ECM) in skin cells, which probably was the genetic mechanisms for the mutant phenotype of systemic skin wrinkle of Xiang pig.

Poly‐L‐Lactic acid increases collagen gene expression and synthesis in cultured dermal fibroblast (Hs68) through the TGF‐β/Smad pathway

“…Economic growth and increased longevity have given rise to the pursuit of beauty and the active search for new bioactive substances that can fight age and promote health 1 . Skin aging is mainly characterized by structural and functional changes put into the epidermis and dermis 2 . Collagen, a major component of the extracellular matrix (ECM), is synthesized by dermal fibroblasts to maintain the skin's strength and elasticity 3 .…”

“…1 Skin aging is mainly characterized by structural and functional changes put into the epidermis and dermis. 2 Collagen, a major component of the extracellular matrix (ECM), is synthesized by dermal fibroblasts to maintain the skin's strength and elasticity. 3 However, UV rays, skin inflammation, intracellular metabolites, and aging can inhibit collagen synthesis, leading to skin aging occurrences such as wrinkle formation, sagging, and laxity.…”

Comparative transcriptome analysis of longissimus dorsi muscle reveal potential genes affecting meat trait in Chinese indigenous Xiang pig

“…Our transcriptome analysis indicated that the genes, such as IRS2, FOXO1, and GLUT4, involved in the insulin signaling response were also more highly expressed in the longissimus dorsi muscle of Xiang pigs than in Large White pigs, which is consistent with previous studies that up regulated genes involved in insulin signaling pathway and insulin resistance in local pig breeds compared to western commercial pigs 14,34 . Interestingly, we observed that some genes harboring SV were enriched in the insulin signaling pathway 29 ) appeared more frequently in Xiang pigs than in Large White pigs, suggesting that variation in these genes may leads to high expression of related genes in the insulin signaling related pathway in Xiang pigs. In addition, the PFKFB3 gene regulates the synthesis and degradation of fructose-2, 6-bisphosphate and fructose-6-phosphate during glucose metabolism.…”

“…We further collected genetic variation between Xiang pigs and Western commercial pigs previously reported by our group 29 , and we found 75 DEGs covering 152 loci of structural variation (SV), which deletion accounted for the major type of variation and most of the variations were located in introns (Table S11, Fig. 5A,B).…”

Effect and Mechanism Analysis of Pig FUT8 Gene on Resistance to Escherichia coli F18 Infection

“…These genes are involved in cell lamin filament, intermediate filament cytoskeletons, supramolecular complexes, cell differentiation, regulation of macromolecule metabolic processes, etc. [ 16 ]. However, the roles of FUT8 regulating E. coli F18 susceptibility in IPEC-J2 cells remains unclear.…”