Genome-wide Analysis of mRNA Expression Profile of OvariesbetweenHigh and Low Egg Production Chicken

【作者】 张涛； Xiangqian Zhang； Kunpeng Han； Genxi Zhang； 王金玉； Kaizhou Xie； Guojun Dai； Qian Xue；

【Author】 Tao Zhang;Xiangqian Zhang;Kunpeng Han;Genxi Zhang;Jinyu Wang;Kaizhou Xie;Guojun Dai;Qian Xue;College of Animal Science and Technology,Yangzhou University;Key Laboratory for Animal Genetics,Breeding,Reproduction and Molecular Design of Jiangsu Province;

【机构】 College of Animal Science and Technology,Yangzhou University； Key Laboratory for Animal Genetics,Breeding,Reproduction and Molecular Design of Jiangsu Province；

【摘要】 egg production is an important trait of chicken(Gallus gallus).It is determined by ovary function and regulated by the hypothalamic-pituitary-ovary axis.In the present study,8 female Jinghai yellow chickens,including 4 high egg production chickens and 4 low egg production chickens,were selected.The total RNA of 8 ovaries was extracted by Trizol.In order to screen differential expressed genes between transcriptome of high and low egg production chicken ovaries,RNA sequencing was carried out.Gene Ontology(GO),Kyoto Encyclopedia of Genes and Genomes(KEGG) and Clusters of Orthologous Groups of proteins(COG) were performed on new genes and DEGs.10 DEGs were randomly selected to conduct RT-PCR to verify the RNA-seq results.Eight cDNA libraries of ovaries of Jinghai yellow chickens were constructed.61.09 GB Clean Data,including 484,992,074 reads,were generated after quality control.A total of 580,959 SNPs were screened from 8 samples,among which 362,457 SNPs and 218,502 SNPs were genic SNPs and intergenic SNPs,respectively.In order to scan unannotated transcripts,mine new transcripts and new genes and thereby enrich and improve the annotation information of genome,Cufflinks program was used to mining new genes and transcripts.4431 new genes and transcripts were mined.GO analysis showed that 2820,1139 and 3781 genes were assigned to cellular component,molecular and biological process GO categories,respectively.572 genes were mapped to KEGG pathways and 305 genes were annotated to 23 categories in COG analysis.305 DEGs were identified between the high egg production and low egg production group according to Fold Change≥2 and FDR<0.05.Compared with the low egg production group,145 genes were up-regulated and 160 genes were down-regulated in high egg production group,respectively.GO and KEGG analysis of differentially expressed genes showed that IL9 R,IGF1,PARVA,MYLK,GABRA1,CHRM3,LTB4 R,NTSR1,CCR5,IL15,VIPR2 and EDAR genes and Neuroactive ligand-receptor interaction pathway might play important roles in regulation of egg production.In order to explore the difference in the function of up-regulated and down-regulated genes,145 up-regulated genes and 160 down-regulated genes were performed to Biological process and pathway analysis.The results showed that in biological process the up-regulated genes were mainly involved in G-protein coupled receptor protein signaling pathway and cell surface receptor linked signal transduction,while the down-regulated genes were mainly involved in Wnt receptor signaling pathway and calcium modulating pathway.Pathway analysis revealed that the down-regulated genes were significantly enriched in three pathways of Hedgehog signaling pathway,Melanogenesis and Wnt signaling pathway,while no significant pathway was enriched for up-regulated genes.Ten important genes were selected and performed to RT-PCR to validate the RNA sequencing results.The results were in excellent agreement with RNA-seq results,which indicated that the RNA-seq results were reliable.This is the first avarian transcriptome analysis between high egg production and low egg production chickens.Many important candidate functional genes are identified,including IL9 R,IGF1,PARVA,MYLK,GABRA1,CHRM3,LTB4 R,NTSR1,CCR5,IL15,VIPR2 and EDAR genes.A large number of SNPs are detected.The results above will provide theoretical basis for improving of egg production and candidate markers for breeding in Jinghai yellow chicken.更多还原

【Abstract】 egg production is an important trait of chicken(Gallus gallus).It is determined by ovary function and regulated by the hypothalamic-pituitary-ovary axis.In the present study,8 female Jinghai yellow chickens,including 4 high egg production chickens and 4 low egg production chickens,were selected.The total RNA of 8 ovaries was extracted by Trizol.In order to screen differential expressed genes between transcriptome of high and low egg production chicken ovaries,RNA sequencing was carried out.Gene Ontology(GO),Kyoto Encyclopedia of Genes and Genomes(KEGG) and Clusters of Orthologous Groups of proteins(COG) were performed on new genes and DEGs.10 DEGs were randomly selected to conduct RT-PCR to verify the RNA-seq results.Eight cDNA libraries of ovaries of Jinghai yellow chickens were constructed.61.09 GB Clean Data,including 484,992,074 reads,were generated after quality control.A total of 580,959 SNPs were screened from 8 samples,among which 362,457 SNPs and 218,502 SNPs were genic SNPs and intergenic SNPs,respectively.In order to scan unannotated transcripts,mine new transcripts and new genes and thereby enrich and improve the annotation information of genome,Cufflinks program was used to mining new genes and transcripts.4431 new genes and transcripts were mined.GO analysis showed that 2820,1139 and 3781 genes were assigned to cellular component,molecular and biological process GO categories,respectively.572 genes were mapped to KEGG pathways and 305 genes were annotated to 23 categories in COG analysis.305 DEGs were identified between the high egg production and low egg production group according to Fold Change≥2 and FDR<0.05.Compared with the low egg production group,145 genes were up-regulated and 160 genes were down-regulated in high egg production group,respectively.GO and KEGG analysis of differentially expressed genes showed that IL9 R,IGF1,PARVA,MYLK,GABRA1,CHRM3,LTB4 R,NTSR1,CCR5,IL15,VIPR2 and EDAR genes and Neuroactive ligand-receptor interaction pathway might play important roles in regulation of egg production.In order to explore the difference in the function of up-regulated and down-regulated genes,145 up-regulated genes and 160 down-regulated genes were performed to Biological process and pathway analysis.The results showed that in biological process the up-regulated genes were mainly involved in G-protein coupled receptor protein signaling pathway and cell surface receptor linked signal transduction,while the down-regulated genes were mainly involved in Wnt receptor signaling pathway and calcium modulating pathway.Pathway analysis revealed that the down-regulated genes were significantly enriched in three pathways of Hedgehog signaling pathway,Melanogenesis and Wnt signaling pathway,while no significant pathway was enriched for up-regulated genes.Ten important genes were selected and performed to RT-PCR to validate the RNA sequencing results.The results were in excellent agreement with RNA-seq results,which indicated that the RNA-seq results were reliable.This is the first avarian transcriptome analysis between high egg production and low egg production chickens.Many important candidate functional genes are identified,including IL9 R,IGF1,PARVA,MYLK,GABRA1,CHRM3,LTB4 R,NTSR1,CCR5,IL15,VIPR2 and EDAR genes.A large number of SNPs are detected.The results above will provide theoretical basis for improving of egg production and candidate markers for breeding in Jinghai yellow chicken.更多还原