Comparative Transcriptomic Profiling In Ovarian Tissues Of Lohmann Hens And Chengkou Mountain Chicken During Peak Laying Period

Egg production performance is an important economic trait in the poultry industry,and egg production is a key index to evaluate egg production performance.The growth and development level of ovaries and follicles directly affect egg production in poultry.The local domestic chicken has been selected by natural selection over a long period of time and has obvious advantages over commercial breeds in terms of adaptability,disease resistance and product quality,but it is significantly less efficient in terms of egg production and efficiency than commercial breeds due to the lack of intensive artificial selection.By exploring the differences in the regulation of gene expression between local and commercial breeds during peak laying period,it provides a relevant theoretical basis for the subsequent breeding of high-yielding local chickens breeds.In this study,transcriptomic sequencing of ovarian tissues from Lohmann commercial generation hens and Chengkou Mountain chicken during peak laying period was performed to reveal the differences in gene expression regulation of ovarian tissues under different laying levels,screen candidate genes related to ovulation advantage,and analyze their regulatory networks.The main findings are enumerated as follows.(1)A total of 70.01 GB clean reads was retained after being filtered from mRNA and lncRNA libraries downstream sequencing data of six samples.By comparing with the chicken reference genome,93.68% of the clean reads could be mapped to the reference genome.The small RNA library resulted in 80,034,358 high-quality clean reads,and over 72% of mapped reads were consistent with the reference genome after screening.(2)The analysis of transcriptome data showed that a total of 303 differentially expressed mRNAs,68 differentially expressed lncRNAs,79 differentially expressed miRNAs,and 533 differentially expressed circRNAs were screened in the ovarian tissues of Chengkou Mountain chicken and Lohmann commercial hens during peak laying period.(3)Functional annotation results of candidate genes showed that a total of 284 candidate genes with significant differences were annotated to 1,019 GO entries.They were mainly related to glutamate synapse,calcium ion binding,neuropeptide signaling pathway,and dopamine secretion regulation.KEGG enrichment analysis revealed that a total of 73 candidate genes with significant differences were enriched in 57 KEGG pathways.They were mainly significantly involved in neuroactive ligand-receptor interactions,phagosomal,and steroid hormone biosynthesis pathways related to ovarian development.(4)Functional prediction results of lncRNA target genes revealed that a total of328 lncRNA target genes were annotated to 820 GO terms.They were mainly enriched in integral membrane components and nucleus and involved in positive regulation of transcription by RNA polymerase II.KEGG enrichment analysis revealed that differentially expressed lncRNA target genes were mainly involved in metabolic pathways,cell adhesion molecules(CAMs),Purine metabolism,cytokine–cytokine receptor interaction,and other pathways.(5)Functional and pathway enrichment analysis of differential miRNA target genes between groups revealed that the differential miRNA target genes were annotated to2,190 GO terms.They were mainly associated with cytosol and nucleus.A total of 246 differentially miRNA target genes were mainly enriched to 131 KEGG pathways,and significant enrichment was observed for 22 pathways,such as metabolic pathways,endocytosis,cell cycle,etc.(6)Functional annotation of the source genes of differential circRNAs between groups showed that 255 differential circRNA source genes were enriched to 43 GO terms,including cytosol,cytoplasm,ATP binding,and cell migration.KEGG enrichment analysis revealed that a total of 123 differential circRNA source genes were enriched to 84 KEGG pathways,such as endocytosis,CAMs,and focal adhesion.(7)Association analysis of the differentially expressed RNAs between groups showed that a total of 18 lncRNA–miRNA–mRNA pairs(consisting of 13 lncRNAs,13 miRNAs,and 17 mRNAs)and 54 circRNA–miRNA–mRNA pairs(consisting of 36 circRNAs,17 miRNAs,and 23 mRNAs)were screened.Among them,two ceRNA regulatory networks associated with ovarian development were screened,namely,novel＿circ＿000985-mi R-449b-5p-LCK and novel＿circ＿002475-mi R-460b-3p-FST.(8)The RT-qPCR validation results of 52 candidate RNAs with differences between groups revealed that the differential expression rules of all RNAs were basically consistent with the transcriptome sequencing results,indicating that the transcriptome sequencing related data analysis was highly accurate.In summary,this study carried out a comparative study on the differences in the expression profiles of ovarian tissues from Chengkou mountain hens and Lohmann hens during peak laying period by transcriptome resequencing technology.A series of candidate genes related to ovarian development,ovulation and egg production were screened.In particular,a large number of genes were enriched in neuroactive ligand-receptor interactions,Wnt signaling pathways,cell adhesion molecules,and steroid hormone biosynthesis.Meanwhile,an interaction regulatory network of lncRNA/ circRNA–miRNA–mRNA was constructed and further clarified the regulatory mechanism of ovaria-related transcription factors in the ovaries of laying hens during peak laying period,laying a foundation for revealing the genetic regulatory mechanism of laying hens’ high egg performance and resource utilization and development of local chickens.