Brassica rapa is an economically important vegetable and oilseed crop, and serves as an excellent model for evolutionary research studies. Even though the whole genome sequence of B. rapa is available, only a very few genome based resources are currently available. The advent of high-throughput next generation sequencing technologies allowing whole transcriptome sequencing (RNA-Seq) along with the development of novel computational approaches provides the opportunity for efficiently addressing this problem. Here, we report the deep sequencing of B. rapa transcriptome in order to provide a more comprehensive set of genomic resources for functional studies. As a proof-of-concept, we used the developed genomic resources for a variety of applications including genome annotation, polymorphism detection, gene-based genetic markers detection, genotyping of a mapping population, genetic map construction, QTL and eQTL mapping. We hope that the large-scale RNA sequencing effort described here, along with the development and application of the resulting resources will significantly help researchers in the mapping and functional analysis of quantitative traits in Brassica rapa.
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