Transcriptome profiling reveals differential gene expression in the rumen of Hu lambs at different developmental stages

Abstract

The development of the rumen is a critical physiological challenge in newborn ruminants. However, the molecular mechanism underlying different stages of rumen development in sheep remains poorly understood. Here, RNA sequencing and bioinformatics analysis were performed to compare the transcription profiles of rumen development at 7, 28 and 56 days of birth (D7, D28 and D56). We identified 1246, 2257 and 627 differentially expressed genes (DEGs) between D7 and D28, between D7 and D56, between D28 and D56, respectively. Also, 70 DGEs were co-expressed at these three time points. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated most DEGs mainly related to transporter activity, channel activity and metabolism pathways. Noteworthy, the expression levels of most genes (CA4, CA9, CA12 and CA14) in nitrogen metabolic pathways were negatively correlated with the papilla length and width, but the papilla length and width were positively correlated with the expression of genes (PLA2G3, SLC26A9, SLC34A3) in ion transport pathway, suggesting that these genes may be involved in nitrogen metabolic and ion transport pathway and thus affect rumen development. These results provide new insight into the changes in RNA expression at different time points of rumen development in Hu sheep.

Keywords:

• Hu lambs
• rumen
• RNA-seq
• different stages
• co-expressed genes

Authors’ contributions

X. J. Wang and X. X. Zhang: conceived and designed the study. D. Y. Zhang, X. J. Wang, W. M. Wang, F. Lv, X. Pang, G. H. Liu and F. D. Li: contributed to the biological sample collection and prepared. D. Y. Zhang, X. J. Wang, F. Lv, X. Pang and G. H. Liu: participated in RNA extraction, X. J. Wang: wrote the manuscript. X. J. Wang and X. X. Zhang: revised the paper. All authors read and approved the final manuscript.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

All the sequences involved in the present study are deposited in the NCBI Bioproject with the accession codes PRJNA738639.

Additional information

Funding

This work was supported by the National Natural Science Foundation of China [31760682].