Application Of Bioinformatics In Basic Physiology Research Of Model Plant Arabidopsis And Corp Maize

Bioinformatics plays an important role in life science research.Among the methods of bioinformatics,RNA-seq is widely used in various fields of scientific research.RNAP II(RNA POL II)stalling prepares genes for rapid response to developmental signals,it represent a key regulatory step for gene transcription in development.In this paper,based on our previous research about card1-1,we try to discover whether stalled RNAP II existing in plants.If “yes”,we also try to find the motif that associated with RNAP II while stalling at promoter.The main results are as follows:(1)Compared with Col-0,the level of Ser5 P of CTD in card1-1 is lower.Based on the analysis of RNA-seq of card1-1,we find the number of up-regulated genes is much more than down-regulated genes.It suggests that the level of Ser5 P of CTD affects genes expression level.(2)We cut the sequence of 400 bp up-stream and 100 bp down-stream of TSS of all up-regulated genes for enriching functional element of them.We discover that a part of genes could enrich a core element “PPRE” motif(GGCCCA).However,enrichment of PPRE motif in housekeeping genes and down-regulated genes is not obvious.(3)HSP70-2 and HSP20 are selected for molecular experiment.After site-directed mutagenesis or deletion of PPRE motif,we find that the expression level of HSP70-2 is enhanced as well as HSP20.It suggests that PPRE motif may have a negative regulation of the member of HSP gene family.We deem that RNAP II stalling at transcription process likely exist in plants.Also,PPRE motif is a potential acting promoter element for RNAP II stalling.In addition,in order to explore the ability of resistance lodging with high-density planting,we set a series of quantitative analysis about morphogenesis of different maize lines include inbred lines and hybrid lines.We also do RNA-seq analysis about primary root of Chang7-2 and Qi319.The main results are as follows:(1)Through phenotype observations of seedlings of different maize lines under high and low density planting,we discover that high-density planting will increase the length of primary root while decline the lateral root density.The phenotypic characters is obvious in Chang7-2.(2)Using Qi319 as comparison sample,RNA-seq of primary root of Chang7-2 both under high-density planting and low-density planting are analyzed.We find that genes related with light and hormones signals are down-regulated expression with high-density planting.It suggests that light signal may affect the root development of maize while planting under high density.We deem that reduced lamina area of receiving light signal with high-density planting leads to primary root length increased and lateral root density decreased.