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Transcriptome analysis of Brassica napus pod using RNA-Seq and identification of lipid-related candidate genes

文献类型： 外文期刊

作者： Xu, Hai-Ming 1 ; Kong, Xiang-Dong 1 ; Chen, Fei 2 ; Huang, Ji-Xiang 2 ; Lou, Xiang-Yang 3 ; Zhao, Jian-Yi 2 ;

作者机构： 1.Zhejiang Univ, Coll Agr & Biotechnol, Inst Bioinformat, Hangzhou 310003, Zhejiang, Peoples R China

2.Zhejiang Acad Agr Sci, State Key Lab Breeding Base Zhejiang Sustainable, Inst Crop & Nucl Technol Utilizat, Hangzhou 310021, Zhejiang, Peoples R China

3.Tulane Univ, Dept Biostat & Bioinformat, New Orleans, LA 70112 USA

关键词： Transcriptome;RNA-Seq;QTL regions;Comparative genomics;Lipid-related candidate genes;Brassica napus

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2015 年 16 卷

页码：

收录情况： SCI

摘要： Background: Brassica napus is an important oilseed crop. Dissection of the genetic architecture underlying oil-related biological processes will greatly facilitates the genetic improvement of rapeseed. The differential gene expression during pod development offers a snapshot on the genes responsible for oil accumulation in. To identify candidate genes in the linkage peaks reported previously, we used RNA sequencing (RNA-Seq) technology to analyze the pod transcriptomes of German cultivar Sollux and Chinese inbred line Gaoyou. Methods: The RNA samples were collected for RNA-Seq at 5-7, 15-17 and 25-27 days after flowering (DAF). Bioinformatics analysis was performed to investigate differentially expressed genes (DEGs). Gene annotation analysis was integrated with QTL mapping and Brassica napus pod transcriptome profiling to detect potential candidate genes in oilseed. Results: Four hundred sixty five and two thousand, one hundred fourteen candidate DEGs were identified, respectively, between two varieties at the same stages and across different periods of each variety. Then, 33 DEGs between Sollux and Gaoyou were identified as the candidate genes affecting seed oil content by combining those DEGs with the quantitative trait locus (QTL) mapping results, of which, one was found to be homologous to Arabidopsis thaliana lipid-related genes. Discussion: Intervarietal DEGs of lipid pathways in QTL regions represent important candidate genes for oil-related traits. Integrated analysis of transcriptome profiling, QTL mapping and comparative genomics with other relative species leads to efficient identification of most plausible functional genes underlying oil-content related characters, offering valuable resources for bettering breeding program of Brassica napus. Conclusions: This study provided a comprehensive overview on the pod transcriptomes of two varieties with different oil-contents at the three developmental stages.

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