Regulatory pathway analysis of coat color genes in Mongolian horses

An analysis of skin thickness in the Dezhou donkey population and identification of candidate genes by RNA-seq

The aim of the present study was to analyze the main factors that have a significant impact on skin thickness, and to further identify the genes and signaling pathways regulating skin growth by RNA-seq in Dezhou donkeys. Skin samples from different body regions of 15 slaughtered donkeys were obtained to study variations in skin thickness over the bodies. Skin thickness data for another 514 donkeys was obtained by minimally invasive skin sampling from the back, and measurements of the donkeys' body size traits and pedigree data were also collected. These data were used to analyze changes in skin thickness and estimate genetic parameters. In addition, transcriptomic analysis was conducted on the skin tissues of individuals from two groups with significant differences in skin thickness. Our results showed that skin thickness over the bodies ranged from 1.08 to 4.36 mm. The skin from the back was the thickest and had the highest correlation with that of other regions of the body. The skin thickness decreased from the back to the side of the ventral abdomen, and the skin thickness on the limbs increased from the proximal end to the distal end. The results also showed that the skin from the same body regions of jacks was thicker than that of jennies in the same age group. The skin thickness of jennies increased from birth to the age of 2 and then clearly decreased after 2 years of age. The estimated heritability of skin thickness was 0.15, and the genetic correlations between skin thickness and body size traits were negligible. Transcriptome analysis showed that the thick-skin group had 65 up-regulated genes and 38 down-regulated genes compared with the thin-skin group. The differentially expressed genes were highly enriched in epidermal development and cell adhesion molecule signaling pathways. We identified the candidate genes responsible for variations in skin thickness in the Dezhou donkey, including KRT10, KRT1, CLDN9, MHCII and MMP28. These results contribute to a better understanding of the growth and development of donkey skin, reveal the molecular mechanism responsible for donkey skin thickness and suggest directions for genetic selection in the Dezhou donkey population.

The role of KLF4 in melanogenesis and homeostasis in sheep melanocytes

KLF4 expression has been associated with hair color in mammals and has also been found to regulate melanoma cell growth. Here, we assessed the influence of KLF4 on coat color formation and melanocytes. We found that KLF4 was highly expressed in the black skin of sheep both at the mRNA and protein levels compared with white skin. KLF4 immunostaining further showed that KLF4 protein was mainly expressed in epidermal, outer root, and hair bulb regions. In sheep melanocytes, the proliferation of melanocytes was inhibited by KLF4 overexpression and this decrease in cell proliferation was coupled with induction of the S phase, cell cycle arrest, and apoptosis. In vitro cell migration assays showed that KLF4 suppressed cell migration. In addition, KLF4 overexpression significantly increased melanin production and pigment-related gene expression. Collectively, our findings show that KLF4 is important for coat color formation and melanocyte homeostasis.

Transcriptomic Analysis of Coding Genes and Non-Coding RNAs Reveals Complex Regulatory Networks Underlying the Black Back and White Belly Coat Phenotype in Chinese Wuzhishan Pigs

Coat color is one of the most important characteristics for distinguishing Chinese indigenous pig breeds. In Wuzhishan pigs, the animals have black on the back and white on the abdomen. However, the molecular genetic basis of this phenotype is unclear. In this study, we used high-throughput RNA sequencing to compare expression profiles of coding and non-coding RNAs from white and black skin samples obtained from individual Wuzhishan pigs. The expression profiling revealed that 194 lncRNAs (long non-coding RNAs), 189 mRNAs (messenger RNAs), and 162 miRNAs (microRNAs) had significantly different levels of expression (|log₂ fold change| > 1, p-value < 0.05) in white and black skin. Compared to RNA levels in black skin, white skin had higher levels of expression of 185 lncRNAs, 181 mRNAs, and 23 miRNAs and lower levels of expression of 9 lncRNAs, 8 mRNAs, and 139 miRNAs. Functional analysis suggested that the differentially expressed transcripts are involved in biological processes such as melanin biosynthesis, pigmentation and tyrosine metabolism. Several key genes involved in melanogenesis, including MLANA, PMEL, TYR, TYRP1, DTC, TRPM1 and CAMK2A, had significantly different levels of expression in the two skin tissues. Potential lncRNA–miRNA–gene interactions were also examined. A total of 15 lncRNAs, 11 miRNAs and 7 genes formed 23 lncRNA–miRNA–gene pairs, suggesting that complex regulatory networks of coding and non-coding genes underlie the coat color trait in Wuzhishan pigs. Our study provides a foundation for understanding how lncRNA, miRNA and genes interact to regulate coat color in black-back/white-belly pigs. We also constructed lncRNA–miRNA–gene interaction networks to elucidate the complex molecular mechanisms underlying skin physiology and melanogenesis. The results extend our knowledge about the diversity of coat color among different domestic animals and provide a foundation for studying novel mechanisms that control coat color in Chinese indigenous pigs.