Until this study, the genetic machinery of the porcine carpal gland was essentially terra incognita. The researchers note that only a single genome-wide association study had previously touched on the organ, and no transcriptomic investigation had ever been carried out. That gap is striking given the gland’s ecological and practical importance. Beyond its role in pig behavior, the gland’s secretions have even found value in wild boar population management, where chemical signaling can be exploited to monitor or influence free-ranging populations. Understanding which genes build and operate the gland could therefore matter not just for fundamental biology, but for livestock breeding and wildlife management alike.

To lay the groundwork, the team began with classical histology. Carpal glands were dissected from the forelegs of pigs and immediately fixed in 10 percent paraformaldehyde for two to three days, a step that preserves cellular architecture in lifelike detail. The fixed tissues were then embedded in paraffin, sliced into sections just five micrometers thick, and stained with hematoxylin and eosin, the workhorse dye pair that has served histologists for more than a century. Under the light microscope, the stained sections revealed the gland’s secretory architecture in fine detail, allowing the researchers to count secretory portions and secretory cells and to compare structures across animals.

The histological comparisons produced a clear and intriguing pattern. Both the visible phenotypes and the underlying tissue structures of the carpal glands differed significantly among the four populations studied: wild boars, Min pigs, Duroc pigs, and HS pigs. Wild boars and Min pigs, the more extensively characterized of the groups, possessed more carpal gland secretory portions and more secretory cells than their Duroc and HS counterparts. This gradient, running from wild and indigenous Chinese breeds toward commercially selected Western breeds, hints that intensive domestication and selection for production traits may have reshaped an organ whose primary business is chemical communication rather than meat yield.

With the anatomical baseline established, the researchers turned to the transcriptome. They sequenced the RNA of 32 carpal glands using RNA-seq, a technique that captures a snapshot of every gene being actively transcribed in the tissue at the moment of sampling. The sequencing data revealed a total of 5,205 differentially expressed genes, or DEGs, when the team compared populations with one another and males with females. That such a large fraction of the transcriptome varies across breeds and sexes underscores how dynamic the gland’s molecular program is, and it provided a rich dataset for the next stage of analysis.

Raw lists of differentially expressed genes can be overwhelming, so the team applied weighted gene co-expression network analysis, or WGCNA, a statistical framework that groups thousands of genes into modules based on the correlated patterns of their expression across samples. Genes that rise and fall together often participate in the same biological processes, so modules can act as functional units rather than isolated data points. The analysis identified two modules whose expression profiles showed the highest correlation coefficients with carpal gland-related traits, effectively narrowing thousands of genes down to a handful of coordinated gene networks most likely to be shaping the organ’s structure and output.

To interrogate those modules further, the researchers layered on additional computational tools. Gene set enrichment against Gene Ontology and KEGG databases flagged seven pathways associated with the carpal gland, including ‘gland development’ (GO:0048732) and ‘tube development’ (GO:0035295), terms that fit neatly with the organ’s role as a secretory skin structure whose ducts and acini must be built during development. The team also constructed protein-protein interaction networks, which map the physical and functional relationships among the proteins encoded by the module genes, and predicted transcription factors, the regulatory proteins that switch genes on and off, acting on the hub genes within the WGCNA modules.

The convergence of these analyses distilled the dataset to a remarkably compact candidate list. Ten hub genes emerged as plausible candidates for the porcine carpal gland: CCL2, GJA1, S100A4, PLAUR, LUM, ANXA1, BGN, BMP1, GPNMB, and SERPINE1. Several of these are familiar faces in secretory and structural biology. LUM and BGN encode small leucine-rich proteoglycans that scaffold the extracellular matrix, while BMP1 is a procollagen-processing enzyme central to tissue remodeling. GJA1 encodes connexin 43, a gap junction protein that allows secretory cells to communicate directly, and CCL2 and ANXA1 participate in signaling and inflammatory pathways that often intersect with glandular secretion. Alongside the ten hub genes, the team pinpointed two transcription factors, SNAI1 and SNAI2, as important candidate regulators of the gland.

Critical to the credibility of any genomics study is validation, and the researchers did not stop at computational prediction. They confirmed their key findings using quantitative real-time PCR, or qRT-PCR, an independent laboratory technique that measures the expression of specific genes with high sensitivity. They also performed quantitative trait-transcript analysis, known as QTT analysis, which links transcript abundance directly to measured quantitative traits across individuals, providing a statistical bridge between gene expression and the physical characteristics of the gland. This two-pronged validation strategy strengthens the case that the identified hub genes and transcription factors are genuinely tied to carpal gland biology rather than artifacts of a single analytical pipeline.

The study’s authors, led by Dengshuai Cui and corresponding author Yuanmei Guo at Jiangxi Agricultural University’s National Key Laboratory for Pig Genetic Improvement and Germplasm Innovation, describe their work as outlining the transcriptome profiling of the carpal gland across four populations and providing new insights into the genetic mechanism of the organ. The identification of two highly correlated co-expression modules, ten hub genes, and the SNAI1 and SNAI2 transcription factors gives researchers concrete molecular entry points for future experiments, whether those involve functional studies of individual genes, breeding programs that account for chemical signaling traits, or comparative work on scent glands in other mammals. For an organ that has spent centuries quietly shaping pig societies while escaping molecular scrutiny, the carpal gland has finally begun to reveal its genetic secrets, and the implications may ripple from the pigsty to wildlife management well beyond it.

Subject of Research: Transcriptomic analysis of the porcine carpal gland to identify genes and regulatory modules underlying its structure and pheromone secretion

Article Title: Identification of crucial modules and genes associated with carpal gland using RNA-seq and WGCNA in four pig (Sus scrofa) populations

Article References: Identification of crucial modules and genes associated with carpal gland using RNA-seq and WGCNA in four pig (Sus scrofa) populations. (n.d.). https://doi.org/10.1186/s12864-026-13445-9

Image Credits: AI Generated

DOI: 10.1186/s12864-026-13445-9

Keywords: pig, carpal gland, RNA-seq, WGCNA, transcriptomics, hub genes, transcription factors, pheromones, Sus scrofa, differentially expressed genes, histology, BMC Genomics