Transcriptomics Analysis Of Ovaries Of High And Low Egg Production Jinghai Yellow Chicken

Jinghai yellow chicken, a new yellow broiler breed, is cultivated by conventional breeding and molecular marker assisted selection methods in 10 years. In the present study,8 female Jinghai yellow chickens (300-day-old), including 4 high egg production chickens and 4 low egg production chickens, were selected. Total RNA was extracted to construct cDNA library. The RNA sequencing was performed using Illumina HiSeq2500. Sequencing results were conducted to bioinformatics analysis. New genes were mined and performed to function annotation and pathway analysis and gene structure was improved subsequently.12 DEGs were verified using fluorescent quantitative real-time PCR. The DEGs associated with egg production were screened and performed to function annotation and pathway analysis. The main results are:(1) Sequencing was carried out using HiSeq2500 with a PE125 sequencing read.61.09GB Clean Data, including 484,992,074 reads, were generated after quality control.1 445 264 SNPs were screened in Jinghai yellow chicken. The average number of alternative splicing of 8 samples was 12 883. Gene structures of 7481 gene were optimized.4431 new genes were mined by mapping clean data to reference genome.1809 new genes were annotated by comparing to different databases.1795 (99.2%) genes shared significant similarity with mapped sequences from different databases. GO analysis showed that 89 new genes were involved in reproduction, which accounted for 2% out of 1890 new genes. KEGG analysis showed that the top five KEGG pathways were MAPK signaling pathway, endocytosis, ubiquitin mediated proteolysis, RNA transport and Regulation of actin cytoskeleton.(2) In the present study,86 DEGs were identified between the high egg production and low egg production group.48 genes were up-regulated and 38 genes were down-regulated. GO analysis of 86 DEGs showed that in biological category,18 genes involved in reproduction term, including 5 known genes (Zona pellucida glycoprotein 2 (ZP2), Dopamine beta-hydroxylase (DBH), Cystic fibrosis transmembrane conductance regulator (CFTR), Centrosomal protein 57kDa-like 1 (CEP57L1) and Chromosome alignment maintaining phosphoprotein 1 (CHAMP 1)), were annotated. KEGG analysis of DEGs suggested that the Cytokine-cytokine receptor interaction pathway was the most significant pathway. Three DEGs IL22RA2, IL8 and AMH were involved in this pathway.(3) qRT-PCR was used to detected the expression level of DEGs. The results showed that all the expression trends of DEGs detected by qRT-PCR corresponded with the results of RNA-seq. It suggests that the DEGs identified by RNA-seq are reliable in our study.