Transcriptome Profiling During The Early Development Of The Maize Brace Root And Functional Analysis Of Candidate Genes

Maize has a complex root system composed of different root types formed during different stages of development. The shoot borne roots, which represent the major portion of the postembryonic roots, include crown roots formed underground and brace roots born on the stem nodes of successive basal phytomers. So far, research on the maize brace roots has been focused mainly at the morphological and physiological levels, the molecular regulation mechanisms involved in the early development of the maize brace root are poorly known. To gain insight into the transcriptome dynamics that are associated with its development, genome-wide gene expression profiling was conducted by Solexa sequencing. More than 5 million tags were generated from the stem node tissues without and with just-emerged brace roots, including 149524 and 178131 clean tags in the two libraries, respectively. Of these, 82864 (55.4%) and 91678 (51.5%) tags were matched to the reference genes. The tags with log2 ratio >2 or <-2 (P<0.001) were characterized as the most differentially expressed tags and further analyzed, representing 143 up-regulated and 152 down-regulated tags except function unkown tags, which were classified into 11 functional categories. The most enriched categories were those of metabolism, signal transduction and cellular transport. Gene categories showed obvious increase in transcript abundance involved in protein binding and cell wall metabolism. On the contrary, transcriptional abundance for genes participating in transcript regulation, cell cycle and DNA replication pathways were reduced. These obvious up-regulated or down-regulated genes might be involved in the regulation of maize brace root early development. Then, the expression patterns of 23 genes were assessed by qRT-PCR, and the results showed general agreement with the Solexa analysis.Compared with previous lateral and adventitious root transcriptome profile, we found that many genes or biological pathways were commonly shared between the brace root and lateral or adventitious root development, such as genes participating in cell wall degradation and synthesis, auxin transport and signaling, stress resistance signaling etc. Furthermore, comparing the brace root transcriptome with that of maize primary root indicated substantial differences in categories and abundances of expressed transcripts, indicating the function and the regulation mechanism of the brace root is obviously different from the mechanism of the primary root.Then, 15 candidate genes were selected to be heterologously overexpressed in Arabidopsis. We mainly observe the root system phenotypes of transgene lines for preliminary function research. So far, of all the Arabidopsis overexpression lines obtained, overexpression of ZmCCD (Zea mays cortical cell-delineating protein) lines were observed with the suppressed primary root elongation. Furthermore, the pheynotype of shorter primary root of 35S::CCD can be recovered under high concentration of auxin, indicating that ZmCCD may play a role in the regulation of maize root or brace root early development by auxin.In conclusion, we firstly reveals the complex changes in the transcriptome during the early development of maize brace root and provides a comprehensive set of data essential for understanding its molecular regulations. What's more, we have characterized some candidate genes which take part in the regulation of brace roots initiation.