Abstract
The species Brassica rapa includes many important vegetable crops. For a genome-wide survey of small RNAs in B. rapa, we performed massively parallel small RNA deep sequencing by using two representative varieties of non-heading Chinese cabbage (B. rapa ssp. chinensis) that are distinct in leaf shape, size, color and curvature. In total, 13.30 million small RNA reads were generated from Huaq, a variety with up-curved blades and wide petioles, and 14.69 million for Wut, a variety with down-curved blades and narrow petioles. After normalization, about half of small RNA reads in each variety were mapped to the published reference genome of B. rapa. In Huaq seedlings, unique small RNAs were much more than in Wut seedlings. Among them, 45 miRNAs were up-regulated or down-regulated in one variety, compared with those in another variety. Numbers of ta-siRNAs (trans-acting siRNAs) and ra-siRNAs (repeat-associated siRNAs) in Huaq seedlings were more than those detected in Wut seedlings, while gene-derived siRNAs (siRNAs derived from the sense and antisense strands of annotated genes regeion) in Huaq seedlings were less than in Wut seedlings. Especially, bra-miR156, bra-miR166 and bra-miR319 and one of ta-siRNAs that play important role in leaf shape, leaf size, leaf curvature and phase transition were differentially expressed between two varieties. In addition, total number of small RNAs derived from chloroplast genome of Wut was more than that of Huaq. The differentially-expressed small RNAs on genome-wide level provides the clue for the study of small-RNA-mediated morphology of leaves and is useful for developing of small RNA markers for leaf traits desirable for high yield and quality.
Comparative Profiling of Small RNAs Originated From Two Varieties of Chinese Cabbage (Brassica Rapa) With Distinct Leaf Traits
