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

The carpal gland is a specialized skin organ and locates at insides of pig forelegs, and it releases pheromone-laden odorants to mediate intraspecific chemical communication. Its secretions regulate mating behavior, territorial marking, social hierarchy formation and risk warning, and even have practical value for wild boar population management. The genetic mechanism of carpal gland remains limited, and only one genome-wide association study was reported, and no transcriptomic study was carried out. The aim of this study is characterizing the histological features and transcriptional profiles of porcine carpal glands in four populations. To investigate its histological characteristics, carpal glands were dissected from the forelegs and immediately immersed in 10% paraformaldehyde to fix for 2–3 days, and then they were embedded in paraffin and sectioned into 5 µ m slices. The sections were stained with hematoxylin and eosin and observed under a light microscope. The transcriptomes of 32 carpal glands were obtained using RNA-seq, and differentially expressed genes (DEGs) were identified among populations and between sexes. Then, weighted gene co-expression networks (WGCNA) and PPI-interaction networks were built, and transcription factors (TFs) of the hub genes in WGCNA were predicted. Finally, the key findings were validated with qRT-PCR and quantitative trait-transcript (QTT) analysis. Both phenotypes and histological structures of the carpal glands showed significant difference among the 4 populations. Wild boars and Min pigs had more carpal gland secretory portions and secretory cells than Duroc and HS pigs did. A total of 5,205 DEGs were identified among the 4 populations and between sexes, and 2 modules had the highest correlation coefficient with carpal gland-related traits. Seven pathways, such as ‘gland development’ (GO:0048732) and ‘tube development’ (GO:0035295), were associated with carpal gland. Moreover, ten hub genes ( CCL2 , GJA1 , S100A4 , PLAUR , LUM , ANXA1 , BGN , BMP1 , GPNMB and SERPINE1 ) and two important TFs ( SNAI1 and SNAI2 ) were identified as plausible candidate genes to the porcine carpal gland. This study outlined the transcriptome profiling of the carpal gland in 4 populations. WGCNA identified two modules that were in high correlation with carpal gland-related traits. Ten hub genes and two TFs ( SNAI1 and SNAI2 ) were picked out as plausible candidate genes for the porcine carpal gland. These findings provided new insights into the genetic mechanism of the porcine carpal gland.