Comparative profiling of genome-wide small RNAs in non-heading Chinese cabbage [Brassica rapa subsp. chinensis (L.) Hanelt]

Non-heading Chinese cabbage is characterized with diversity of leaf shape and of leaf architecture. Small RNAs are broadly involved in leaf development. To understand how small RNAs regulated leaf shape and leaf architecture, we choose two representative genotypes of non-heading Chinese cabbage (Brassica. rapa ssp. chinensis cv Wut) with distinct leaf shapes, and performed small RNA deep sequencing. Huaq, a genotype with long blades and wide petioles, generated 13.30 million small RNA reads while Wut, a genotype with round blades and long petioles, produced 14.69 million. After normalizing to RP10M, they share 0.5 million small RNAs with about 4 million reads which are mapping to the genome. Four types of small RNAs were selected from the libraries: miRNAs, ta-siRNAs, mRNA-derived siRNAs and rasiRNAs. 45 miRNA members among 75 display different expressional level such as miR166 and miR319, which play important role in leaf development. It indicated the different leaf phenotype between Huaq and Wut that possibly regulated by miRNA dosage. One of the small RNAs originated from TAS3 is Huaq dominant. About 2 thousand small RNAs derived from genes were expressionally different between genotypes, and some of them derived from antisense chains of genes. Chloroplast derived small RNAs were found that Wut were more than Huaq, which is consistent with its greener leaves. Comparative analysis of small RNAs on genome-wide level will broaden our view of molecular events underling diversity of leaf shape and architecture.