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

Tiansong Wang; Yong Zhang; Yong Guo; Xiong Zhang; Hong Yang; Xingzhou Tian; Min Zhu; Zhili Guo; Shanshan Zeng; Keyin Luo; Qi He

doi:10.1016/j.psj.2021.101357

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

Poult Sci. 2021 Sep;100(9):101357. doi: 10.1016/j.psj.2021.101357. Epub 2021 Jun 26.

Authors

Tiansong Wang¹, Yong Zhang², Yong Guo¹, Xiong Zhang³, Hong Yang⁴, Xingzhou Tian¹, Min Zhu¹, Zhili Guo¹, Shanshan Zeng¹, Keyin Luo⁵, Qi He⁶

Affiliations

¹ Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, 550025, China.
² Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, 550025, China. Electronic address: gzuzy@139.com.
³ Institute of Animal Husbandry and Veterinary Science, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou Province 550005, China.
⁴ Bijie City Animal Husbandry Station, Bijie 551700, China.
⁵ Liupanshui City Agriculture and Rural Bureau, Liupanshui 553001, China.
⁶ Agriculture and Rural Bureau of Huaxi District, Guiyang City, Guizhou Province 550025, China.

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.

Keywords: RNA-Seq; Wumeng crested chicken; crested traits; differentially expressed gene; epigenetic mechanism.

MeSH terms

Animals
Chickens* / genetics
Gene Ontology
Phenotype
RNA*
Sequence Analysis, RNA / veterinary

Substances

RNA