Unraveling porcine juvenile striping: insights from the integration of genomics, transcriptomics and ATAC-seq

Juvenile stripe (JU) is an inborn camouflage color of the wild boar piglet, and it gradually disappears as the piglet grows up. It also appears in the hybrid population of wild boar, as well as in the intercross population of white Duroc with Erhualian pig. At present, few studies have investigated the formation and maintenance mechanisms of JU. To decode the genetic basis of JU, chip-based and imputation-based genome-wide association analyses (GWAS) were performed on 932 F 2 offspring of crosses between white Duroc boars and Erhualian sows. Two suggestive association signals were detected on chromosomes (SSC) 6 and 8, and MC1R and KIT were the underlying positional candidate genes, respectively. JU pigs did not have MC1R c.67_68insCC and KIT duplication, but some individuals without these mutations did not exhibit JU. A conditional GWAS identified another genomic locus on SSC8, and CORIN was the gene near the conditional association signal. To preliminarily explore the molecular basis for spatial patterning in JU, skin samples from the light and dark stripes were collected from three 2-day-old JU piglets. Comparative transcriptome sequencing (RNA-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) were conducted in parallel. An accessible chromatin region was identified 1.8 kb downstream of the TYRP1 gene, and this gene was significantly upregulated in dark-stripe skin. The c.67_68insCC mutation in MC1R and the duplication of KIT may disrupt the formation of JU. TYRP1 showed spatially restricted differential expression between dark and light dorsal skin regions; a putative SOX10-binding accessible chromatin region may contribute to this pattern.