Abstract
BackgroundBrassica 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.MethodsThe 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.ResultsFour 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.DiscussionIntervarietal 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.ConclusionsThis study provided a comprehensive overview on the pod transcriptomes of two varieties with different oil-contents at the three developmental stages.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2062-7) contains supplementary material, which is available to authorized users.
Highlights
Brassica napus is an important oilseed crop
This study provided a comprehensive overview on the pod transcriptomes of two varieties with different oil-contents at the three developmental stages
As rapeseed oil is accumulated during the development of pod and the differential expression in the parents offers a snapshot on that of the mapping population, in this study, we focused our research on the German variety Sollux and Chinese variety Gaoyou, which have been used as the parents to develop the quantitative trait locus (QTL) mapping population for oil content [3, 13]
Summary
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. Rapeseed (Brassica napus L.) is one of the primary sources of vegetable oil for human nutrition; it occupies a pivotal position on oil supply in China. The seed oil content is a very important economic character in rapeseed production. Its genetic architecture has been investigated by quantitative trait locus (QTL) mapping based on appropriate mapping populations. Several QTLs controlling seed oil content have been identified [1]. Qiu et al [2] analyzed the QTLs of seed oil and erucic acid content using a comparative linkage map of oilseed rape. Zhao et al [3] detected eight QTLs with additive
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