Transcriptome sequencing reveals key potential long non-coding RNAs related to duration of fertility trait in the uterovaginal junction of egg-laying hens

Duration of fertility, (DF) is an important functional trait in poultry production and IncRNAs have emerged as important regulators of various process including fertility. In this study we applied a genome-guided strategy to reconstruct the uterovaginal junction (UVJ) transcriptome of 14 egg laying birds with long- and short-DF (n = 7); and sought to uncover key IncRNAs related to duration of fertility traits by RNA-sequencing technology. Examination of RNA-seq data revealed a total of 9977 IncRNAs including 2576 novel IncRNAs. Differential expression (DE) analysis of IncRNA identified 223 IncRNAs differentially expressed between the two groups. DE-IncRNA target genes prediction uncovered over 200 IncRNA target genes and functional enrichment tests predict a potential function of DE-IncRNAs. Gene ontology classification and pathway analysis revealed 8 DE-IncRNAs, with the majority of their target genes enriched in biological functions such as reproductive structure development, developmental process involved in reproduction, response to cytokine, carbohydrate binding, chromatin organization, and immune pathways. Differential expression of IncRNAs and target genes were confirmed by qPCR. Together, these results significantly expand the utility of the UVJ transcriptome and our analysis identification of key IncRNAs and their target genes regulating DF will form the baseline for understanding the molecular functions of IncRNAs regulating DF.