Analysis of Genome DNA Methylation at Inherited Coat Color Dilutions of Rex Rabbits

Background: The dilution of color in rabbits is associated with many different genetic mechanisms that form different color groups. A number of previous studies have revealed potential regulatory mechanisms by which epigenetics regulate pigmentation. However, the genome-wide DNA methylation involved in animal coat color dilution remains unknown. Results: We compared genome-wide DNA methylation profiles in Rex rabbit hair follicles in a Chinchilla group (Ch) and a diluted Chinchilla group (DCh) through whole-genome bisulfite sequencing (WGBS). Approximately 3.5% of the cytosine sites were methylated in both groups, of which the CG methylation type was in greatest abundance. In total, we identified 126,405 differentially methylated regions (DMRs) between the two groups, corresponding to 11,459 DMR-associated genes (DMGs). Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that these DMGs were principally involved in developmental pigmentation and Wnt signaling pathways. In addition, two DMRs were randomly selected to verify that the WGBS data were reliable using bisulfite sequencing PCR, and seven DMGs were analyzed to establish the relationship between the level of DNA methylation and mRNA expression using qRT-PCR. Due to the limitation of small sample size, replication of the results with a larger sample size would be important in future studies. Conclusion: These findings provide evidence that there is an association between inherited color dilution and DNA methylation alterations in hair follicles, greatly contributing to our understanding of the epigenetic regulation of rabbit pigmentation.

Insights Into the Albinism Mechanism for Two Distinct Color Morphs of Northern Snakehead, Channa argus Through Histological and Transcriptome Analyses

The great northern snakehead (Channa argus) is one of the most important economic and conservational fish in China. In this study, the melanocytes in the skin of two distinct color morphs C. argus were investigated and compared through employment of the microscopic analysis, hematoxylin and eosin (H&E) and Masson Fontana staining. Our results demonstrated the uneven distribution of melanocytes with extremely low density and most of them were in the state of aging or death. Meanwhile, there was no obvious pigment layer and melanocytes distribution pattern found in the albino-type (AT), while the melanocytes were evenly distributed with abundance in the bicolor-type (BT). The transcriptome analysis through Illumina HiSeq sequencing showed that a total of 34.93 Gb Clean Data was obtained, and Q30 base percentage reached 92.66%. The BT and AT northern snakeheads transcriptome data included a total of 56,039,701 and 60,410,063 clean reads (n = 3), respectively. In gene expression analyses, the sample correlation coefficients (r) were ranged between 0.92 and 1.00; the contribution of PC1 and PC2 were 50.25 and 13.73% by using PCA cluster analysis, the total number of DEGs were 1024 (559 up-regulated and 465 down-regulated), and the number of annotated DEGs was 767 (COG 172, KEGG 262, GO 288, SwissProt 548, Pfam 579 and NR 765). Additionally, 46,363 ± 873 and 44,947 ± 392 single nucleotide polymorphisms (SNPs) were compiled via genetic structure analysis, respectively. Ten key pigment-related genes were screened using qRT-PCR. And all of them revealed extremely higher expression levels in the skin of BT than those of AT. This is the first study to analyze the mechanism of albino characteristics of Channa via histology and transcriptomics, and also provide the oretical and practical support for the protection and development of germplasm resources for C. argus.