福清山羊与努比亚黑山羊发情期卵巢组织RNA-Seq分析

Transcriptome Analysis of Differentially Gene Expression Associated with Ovary Tissue During the Follicular Stage in Fuqing Goat and Nubian Black Goat

【目的】研究福清山羊与努比亚黑山羊发情期卵巢组织转录组差异表达水平,一方面为山羊繁殖性状形成的分子机制提供理论依据,另一方面为利用努比亚黑山羊杂交改良福清山羊提供可加快遗传进展的分子标记。【方法】利用转录组测序方法对福清山羊和努比亚黑山羊发情期卵巢组织进行研究,筛选品种间的差异表达基因(differentially expressed genes,DEGs),并对DEGs功能进行注释和若干基因荧光定量PCR(quantitative real-timePCR,qRT-PCR)验证;同时通过与参考基因组比对,分析和筛选测序样品中存在的SNP/InDel。【结果】6个样品共得到46.68Gb Clean Data,DESeq分析发现了福清山羊和努比亚黑山羊发情期卵巢组织的DEGs149个(包含25个新转录本),其中表达上调53个,表达下调96个;初步认为输卵管素基因(oviductin,OVN)、类固醇合成快速调节蛋白基因(steroidogenic acute regulatory protein,STAR)、早期生长应答1基因(early growth response 1,EGR1)可作为福清山羊繁殖性能的候选基因。149个DEGs中的108个基因能被GO(gene ontology)数据库注释,30个DEGs能够被COG(Cluster of Orthologous Groups of proteins)数据库注释,91个DEGs能够被KEGG(kyoto encyclopediaof genes and genomes)数据库注释。KEGG通路分析表明DEGs共富集到21条信号通路中,6条通路显著富集。经过进一步的与参考基因组序列比对分析,共发掘1506个新转录本。经qRT-PCR验证,所选基因(转录本)表达变化模式与转录组测序结果一致,表明测序结果可靠。【结论】在转录组水平上筛选出了福清山羊和努比亚黑山羊发情期卵巢组织的149个DEGs,发掘了1506个新转录本,初步揭示了OVN、STAR和EGR1在山羊繁殖过程中可能发挥重要作用,为进一步探索山羊繁殖性状相关机理提供参考依据。

【Objective】The aim of this study was to analyze the differentially expressed genes of ovary tissue during follicular stage in Fuqing goat and Nubian black goat.【Method】Transcriptome sequencing of ovary tissue during the follicular stage in Fuqing goat and Nubian black goat were performed by using the Illumina HiSeq^TM 2500 platform with 3 biological replicates per goat breed, and verified by quantitative real-time PCR (qRT-PCR). Differentially expressed genes (DEGs) were selected and enriched based on GO, COG and KEGG database.【Result】A total of 46.68 Gb clean data were obtained in six samples. 149 DEGs were found between Fuqing goat and Nubian black goat, including 53 DEGs up-regulated genes and 96 DEGs down-regulated genes. According to published papers, the genes, including OVN, STAR and EGR1, were considered as candidate genes of fecundity in goats. 108, 30 and 91 DEGs were enriched by GO, COG and KEGG database, respectively. KEGG pathway analysis showed that DEGs annotated to 21 metabolic pathways, and 6 pathways were enriched significantly, such as autoimmune thyroid disease, and allograft rejection, and phagosome and viral myocarditis associated with reproduction traits in goat. 1506 new genes or transcripts were found by BLAST, including 25 DEGs between two breeds. Verified by qRT-PCR, the pattern of selected genes was consistent with the results of transcriptome sequencing, which showed the sequencing results were reliable.【Conclusion】149 DEGs and 1506 new genes of ovary tissue during follicular stage in Fuqing goat and Nubian black goat were screened by transcriptonal analysis. DEGs between Fuqing goat and Nubian black goat, including OVN, STAR and EGR1, maybe play an important role in goat reproduction traits.