Xu Hai-Ming, Kong Xiang-Dong, Chen Fei, Huang Ji-Xiang, Lou Xiang-Yang, Zhao Jian-Yi
Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Road, Hangzhou, 310021, China.
BMC Genomics. 2015 Oct 24;16:858. doi: 10.1186/s12864-015-2062-7.
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.
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.
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.
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.
This study provided a comprehensive overview on the pod transcriptomes of two varieties with different oil-contents at the three developmental stages.
甘蓝型油菜是一种重要的油料作物。剖析与油脂相关生物学过程的遗传结构将极大地促进油菜籽的遗传改良。豆荚发育过程中的差异基因表达提供了一个关于负责油脂积累的基因的快照。为了在先前报道的连锁峰中鉴定候选基因，我们使用RNA测序（RNA-Seq）技术分析了德国品种Sollux和中国自交系高邮的豆荚转录组。
在开花后5-7、15-17和25-27天（DAF）收集RNA样本用于RNA-Seq。进行生物信息学分析以研究差异表达基因（DEG）。将基因注释分析与QTL定位和甘蓝型油菜豆荚转录组分析相结合，以检测油料作物中的潜在候选基因。
在同一阶段的两个品种之间以及每个品种的不同时期分别鉴定出465个和2114个候选DEG。然后，通过将这些DEG与数量性状位点（QTL）定位结果相结合，在Sollux和高邮之间鉴定出33个DEG作为影响种子油含量的候选基因，其中一个被发现与拟南芥脂质相关基因同源。
QTL区域中脂质途径的品种间DEG代表了与油脂相关性状的重要候选基因。转录组分析、QTL定位和与其他相关物种的比较基因组学的综合分析导致有效鉴定出与油含量相关性状的最合理功能基因，为改善甘蓝型油菜的育种计划提供了有价值的资源。
本研究全面概述了两个不同油含量品种在三个发育阶段的豆荚转录组。
