Long noncoding RNAs and mRNAs profiling in ovary during laying and broodiness in Taihe Black-Bone Silky Fowls (Gallus gallus Domesticus Brisson)

Abstract

Background: Broodiness significantly impacts poultry egg production, particularly notable in specific breeds such as the black-boned Silky, characterized by pronounced broodiness. An understanding of the alterations in ovarian signaling is essential for elucidating the mechanisms that influence broodiness. However, comparative research on the characteristics of long non-coding RNAs (lncRNAs) in the ovaries of broody chickens (BC) and high egg-laying chickens (GC) remains scant. In this investigation, we employed RNA sequencing to assess the ovarian transcriptomes, which include both lncRNAs and mRNAs, in eight Taihe Black-Bone Silky Fowls (TBsf), categorized into broody and high egg-laying groups. This study aims to provide a clearer understanding of the genetic underpinnings associated with broodiness and egg production.

Results: We have identified a total of 16,444 mRNAs and 18,756 lncRNAs, of which 349 mRNAs and 651 lncRNAs exhibited significantly different expression (DE) between the BC and GC groups. Furthermore, we have identified the cis-regulated and trans-regulated target genes of differentially abundant lncRNA transcripts and have constructed an lncRNA-mRNA trans-regulated interaction network linked to ovarian follicle development. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analyses have revealed that DE mRNAs and the target genes of DE lncRNAs are associated with pathways including neuroactive ligand-receptor interaction, CCR6 chemokine receptor binding, G-protein coupled receptor binding, cytokine-cytokine receptor interaction, and ECM-receptor interaction.

Conclusion: Our research presents a comprehensive compilation of lncRNAs and mRNAs linked to ovarian development. Additionally, it establishes a predictive interaction network involving differentially abundant lncRNAs and differentially expressed genes (DEGs) within TBsf. This significantly contributes to our understanding of the intricate interactions between lncRNAs and genes governing brooding behavior.

Keywords: Broodiness; Egg production; Ovarian follicle development; Transcriptomes; lncRNA.

Fig. 1

LncRNA classification and genomic features in the ovaries of TBsf. A LncRNA classification. B The transcript length distribution of lncRNAs and mRNAs. C The exon number distribution of lncRNAs and mRNAs. D The ORFs length distribution of lncRNAs and mRNAs

Fig. 2

Differential expression of lncRNAs and mRNAs between the BC and GC. Up-regulated genes are shown in red, down-regulated genes are shown in green, and genes with no significant difference in expression are indicated in blue; significance was indicated by a p-value < 0.05. A Differential expression of lncRNAs. B Differential expression of mRNAs

Fig. 3

GO and KEGG analysis of differential mRNA expression. A Histogram of GO enrichment of DE mRNAs. B Scatter plot of KEGG enrichment for DE mRNAs

Fig. 4

GO and KEGG analysis of differential lncRNAs target gene. A Histogram of GO enrichment of target gene of DE lncRNAs in cis-regulatory. B Scatter plot of KEGG enrichment of target gene of DE lncRNAs in cis-regulatory. C Histogram of GO enrichment of target gene of DE lncRNAs in trans-regulatory. D Scatter plot of KEGG enrichment of target gene of DE lncRNAs in trans-regulatory

Fig. 5

Interacting network of lncRNAs and their trans-regulated target genes associated with ovarian follicle development. The blue circles and green squares represent lncRNAs and potential target genes, respectively, where orange circles and yellow squares denote central nodal lncRNAs and target genes

Fig. 6

Validation of RNA-seq by qRT-PCR