Identification and characterization of differentially expressed miRNAs between bamboo shoot and rhizome shoot

As one of the largest members of Poaceae family, bamboo is a very important agricultural plant in the world. The development of bamboo shoot is very special and particularly significant to bamboo production. Understanding the developmental differences between bamboo shoot and rhizome shoot is extremely valuable for us to further elucidate the mechanism of bamboo shoot formation since both bamboo shoot and rhizome shoot develop directly from rhizome bud underground. In this paper, miRNA chips with 413 miRNA probes were used to compare miRNA expressions between bamboo shoot and rhizome shoot. The experiment revealed 64 bamboo shoot upregulated and 56 rhizome shoot up-regulated miRNAs which were classified into four major categories according to deep sequencing based target prediction. Meristem and morphological development related miRNAs were most important in bamboo shoot, especially miR171 and miR156 members. While in rhizome shoot the mainstream of miRNA expressions was metabolism and nutrition related ones, especially miR395 members. The meristem and morphological development related miRNAs in bamboo shoot showed some embryonic characteristics and suggested the participation of several phytohormones like gibberellin, cytokinin and auxin, which were absent in those miRNAs of rhizome shoot. Further qRT-PCR detections of 21 up-regulated miRNAs in bamboo seedlings indicated that 12 ones were regulated to varying degrees by some environmental factors. Among them, rhizome shoot upregulated osa-miR395b was the most environment-sensitive miRNA, particularly to dehydration. And the bamboo shoot up-regulated osa-miR399j proved uniquely and strongly induced by phosphor. The existence of multiple regulation sites from same miRNA suggested the probability of crosstalks among meristem development, metabolism and stress response during bamboo shoot and rhizome shoot development.