基于RNA-Seq测序的高、低产双黄蛋高邮鸭卵巢组织SNP筛选分析

SNP Screening and Analysis of Ovaries Between Gaoyou Ducks with High and Low Yield Double-yolk Egg Based on RNA-Seq

试验旨在进一步完善高邮鸭基因组结构信息,探索高邮鸭双黄蛋产蛋性能的调控机制。通过高通量测序技术对高邮鸭双黄蛋高、低产组卵巢组织转录组进行RNA-Seq测序,对测序数据进行质控和注释,筛选与高邮鸭双黄蛋产蛋性能相关的SNP位点。测序获得的初始数据(raw reads)进行系列质控筛选,6个高邮鸭卵巢组织分别获得84540140~87479660个有效数据(clean data),70.79%以上的测序数据被已注释的鸭基因组数据覆盖;在所覆盖的基因组数据中,检测到位于基因外显子区域的108260~116478个SNP位点(转换和颠换类型),转换类型总数极显著高于颠换类型总数(P<0.01)。利用KEGG数据库对筛选出的SNP位点所在基因进行信号通路分析,筛选出前20条信号通路,其中包括核糖体信号通路、碳代谢信号通路和氨基酸生物合成信号通路等。试验对双黄蛋高、低产组高邮鸭的卵巢进行了RNA-Seq测序分析,为发掘高邮鸭双黄蛋产蛋性能相关SNP位点提供了基础,为进一步研究高邮鸭双黄蛋产蛋性能的调控机制提供了新的数据支撑。

This study was aimed to improve the gene structure of Gaoyou duck,and explore its regulation mechanism of double-yolk egg performance.RNA-Seq technology was used to analyze the transcriptome of ovaries in high and low double-yolk egg yield Gaoyou ducks.SNP related to the double-yolk egg performance were screened by quality control and gene annotations from RNA-Seq data.Raw reads from RNA-Seq data were selected with quality control,84540140-87479660 clean reads were screened from total 6 samples,over 70.79%of the sequencing data were covered by the annotated genome data of ducks.Based on these data,108260-116478 SNP were found in the exon area of the annotched genes,and the number of transition SNP was extremely significant higher than the number of transversion(P<0.01).KEGG database was used to analyze the related pathways from these selected SNP.Top 20 pathways were screened,including Ribosome signaling pathway,Carbon metabolism signaling pathway,Biosynthesis of amino acids signaling pathway,and so on.The ovaries’transcriptome of Gaoyou ducks with high and low double-yolk performance were analyzed through RNA-Seq technology,the results provided the basis for mining and annotating new genes of Gaoyou ducks,and improved the data bases for the study of its regulation mechanism of double-yolk egg performance.