RNA-sequence reveals differentially expressed genes affecting the crested trait of Wumeng crested chicken

Abstract

Wumeng crested chicken has a cluster of slender feathers on its head, and the underlying skull region exhibits an obvious tumor-like protrusion. This is the typical skull structure of crested chickens. The associated regulatory genes are located on autosomes and are incompletely dominant. This trait is related to brain herniation, but the genetic mechanisms of its formation and development are unclear. In this study, RNA sequencing ( RNA-Seq ) analysis was conducted on 6 skull tissue samples from 3 Wumeng crested chickens with prominent skull protrusions and 3 without a prominent skull protrusion phenotype. A total of 46,376,934 to 43,729,046 clean reads were obtained, the percentage of uniquely mapped reads compared with the reference genome was between 89.73%–91.00%, and 39,795,458–41,836,502 unique reads were obtained. Among different genomic regions, the highest frequency of sequencing reads occurred in exon regions (85.44–88.28%). Additionally, a total of 423 new transcripts and 26,999 alternative splicings ( AS ) events were discovered in this sequencing analysis. This study identified 1,089 differentially expressed genes ( DEGs ), among which 485 were upregulated and 604 were downregulated. Gene Ontology ( GO ) and Kyoto Encyclopedia of Genes and Genomes ( KEGG ) pathway analyses indicated that the DEGs were enriched in terms related to signal transduction, cell development, cell differentiation, the lysosome, serine, and threonine metabolism, and the interaction of cytokines with cytokine receptors. Based on the comprehensive analysis of DEGs combined with reported quantitative trait loci ( QTLs ), the expression of BMP2, EPHA3, EPHB1, HOXC6, SCN2B, BMP7 , and HOXC10 was verified by real-time quantitative polymerase chain reaction ( qRT-PCR ). The qRT-PCR results were consistent with the RNA-Seq results, indicating that these 7 genes may be candidates genes regulating the crested trait.

Chicken HOXC8 and HOXC10 genes may play a role in the altered skull morphology associated with the Crest phenotype

“…Silkie and Beijing You chickens are classified as “small crest” breeds as opposed to chicken breeds such as Polish and Houdan, which display a relatively large crest (Li et al, 2021). Another recent study using RNA sequencing of skull tissue samples of Wumeng chickens with and without a skull protrusion phenotype identified several genes, BMP2 , EPHA3 , EPHB1 , HOXC6 , SCN2B , BMP7 , that were considered as candidates affected by the mutation of HOX genes (T. Wang et al, 2021). Among them, BMP2 and BMP7 were mentioned in the study of Y. Wang et al (2012), who compared the expression levels of several HOXC8 downstream targets between Silkie and noncrested chickens.…”

Comprehensive analysis of the differential expression of mRNAs, lncRNAs, and miRNAs in Zi goose testis with high and low sperm mobility

“…Experiment III: Following the protocols outlined by Liu et al (2017) and Wang et al (2021) , the testes of the six ganders from experiment II were collected for histological observation and whole-transcriptome sequencing analysis.…”

Gene Expression Profile Analysis of Human Epidermal Keratinocytes Expressing Human Papillomavirus Type 8 E7

“…The Database for Annotation, Visualization, and Integrated Discovery (DAVID) database was used for KEGG pathway and GO analyses of DEGs, as described previously [ 15 , 17 ]. In brief, a false discovery rate with a threshold ≤0.05 was used to determine the p -value in multiple tests and ClusterProfiler R (3.4.4) software was used to visualize the KEGG pathway enrichment ( http://www.genome.jp/kegg/ ) and GO terms ( http://www.geneontology.org/ ).…”