Zhenfang Wu | PubMed Health

PubMed2026

SwinePan for pig graph-based pangenome and multiomics data mining.

Pigs are one of the most important livestock species worldwide. Although multiple high-quality reference genomes exist, reliance on a single linear reference limits the detection of structural variants (SVs) and the characterization of population-specific genetic diversity. To address this limitation, we developed SwinePan, a comprehensive and integrated multiomics database for pigs built on a graph-based pangenome framework. SwinePan incorporates a variome derived from the graph-based pangenome, covering 2,598 individuals across 35 breeds, including 185,759 SVs, 117 million SNPs, and 6.8 million indels. The database also integrates transcriptomic data from liver, loin muscle, abdominal fat, and backfat, along with over 150,000 phenotypic records. The online toolkit deployed in SwinePan enables genome-wide association studies (GWAS), expression quantitative trait locus (eQTL) mapping, and colocalization, while interactive modules visualize population structure and multiomics associations, streamlining candidate gene and variant exploration. Additionally, two proof-of-concept analyses demonstrate how SwinePan pinpoints trait-associated loci and deciphers their potential regulatory mechanisms.

Journal Article↗

PubMed2026

IL17 signaling promotes oocyte developmental competence acquisition during maturation.

BACKGROUND: Defects in the acquisition of oocyte developmental competence during the maturation process causes subfertility or infertility in animals and humans. Understanding the regulatory mechanisms of oocyte maturation is essential for reproductive biology and medicine. Follicular fluid (FF) is an important microenvironment governing oocyte maturation. METHODS: A tandem mass tags (TMT)-based comparative FF proteomic analysis was employed to identify FF proteins that are potentially crucial for oocyte maturation. A very large number of pig and mouse oocytes (approximately 20,000) and embryos (over 13,000, including somatic cell nuclear transfer, parthenogenetic activation, and in vitro fertilization embryos) were used to investigate the effects of identified FF proteins on in vitro oocyte maturation and subsequent in vitro and in vivo embryo development. RNA sequencing, quantitative PCR, enzyme-linked immunosorbent assays, and immunofluorescence were used to study the expression patterns and action mechanisms of identified FF proteins in oocytes. In addition, intra-oocyte levels of glutathione and reactive oxygen species were measured to assess redox homeostasis. RESULTS: Interleukin 17D (IL17D) was identified as an important FF protein and it is significantly upregulated in porcine FF during oocyte maturation. IL17D promotes oocyte maturation by enhancing bidirectional communication between oocytes and cumulus cells, via upregulating CX43 expression and transzonal projections, which helps to maintain oocyte redox homeostasis and nuclear-cytoplasmic synchrony. IL17D treatment of oocytes enhances subsequent in vitro and in vivo full-term embryo development by modulating lipid metabolism and histone modification reprogramming. IL17D exerts its function via activating IL17 signaling through binding to CD93. Two other IL17 family members, IL17A and IL17F, also enhance oocyte maturation quality. IL17D displays a conserved expression pattern and function in pig and mouse oocytes. CONCLUSIONS: This study reveals the critical roles of IL17D in regulating oocyte developmental competence acquisition during maturation by activating IL17 signaling. The findings provide valuable insights into the molecular mechanisms underlining oocyte developmental potential acquisition and may help to develop methods for efficient production of oocytes for assisted reproduction.

Animals↗