Using Deep RNA Sequencing for Polymorphism Detection, Genome Annotation Improvement and Transcript Profiling in Two Brassica rapa Genotypes with Divergent Shade Avoidance Responses

In response to overcrowding, plants exhibit increased elongation, hyponasty, reduced leaf size, and reduced seed set, collectively known as shade avoidance response (SAR). For many plants SAR is a beneficial response, however it reduces crop plant yield.  Understanding the genetic mechanism of SAR will allow development of crops with reduced SAR, increasing yield at high densities. To elucidate SAR networks, we performed RNA-sequencing of five tissues from two Brassica rapa genotypes - R500 and IMB211 with divergent SAR. Because functional gene analysis and mapping of SAR traits in Brassica rapa can be greatly improved with physically positioned genetic markers and complete genome annotation, we first defined DNA sequence polymorphisms in the two varieties, constructed a near-comprehensive Brassica rapa transcriptome, and improved the current genome annotation.  Nearly 200,000 SNPs were identified in transcribed regions with an average frequency of one SNP per 500bp. The reassembled Brassica rapa transcriptome has 48,513 protein-coding genes including 7,494 novel transcripts and 2,586 models with structural modifications. A total of 4,555 genes significantly changed their expression level in response to shade in internode, leaf, root, silique and seedlings. There are no common shade-responsive genes among all tissues indicating the complex nature of SAR network.  Internode tissue was found to have the largest transcriptional shade response, correlating with its strong elongation response. Functional analysis, SNP and genome annotation and expression studies in the different tissues and different conditions will help explain the role of SAS genes in the plant growth and development in the future