Detecting Biomarkers Of A Critical Transition State Of Plant Growth And Development By Dynamic Network Analysis

The higher plants undergo a succession of developmental phases during their life cycle including embryonic pattern formation,seed germination,seedling formation,vegetative growth,flowering,fruiting,senescence and death.There are several important transitional stages in the series of developmental stages,and the phase transitions related to plant development include the seed-to-seedling transition,the vegetative-to-reproductive transition,the initiation-to-maturation floral transition,and so on.The flowering transition which is controlled by a complex and intricate gene regulatory network plays an important role in the reproduction for offspring of plants.It is a challenge to identify the critical transition state as well as the genes that control the transition of flower development.In this work,to reveal a critical transition state and identify the transition-specific genes of flower development,we implemented a genome-wide dynamic network analysis on temporal gene expression data in Arabidopsis by dynamic network biomarker(DNB)method to detect the flowering developmental transition.To construct the gene regulatory network controlling the flowering transition,we applied NARROMI algorithm based on mutual information(MI)and recursive optimization(RO)to reducing the noisy,redundant and indirect regulations on the expression data of the transition-specific genes.In the results,the critical transition state detected during the formation of flowers corresponded to the development of flowering on the 7th to 9th day in Arabidopsis.Among of 233 genes identified to be highly fluctuated at the transition state,a high percentage of genes with maximum expression in pollen was detected,and 24 genes were validated to participate in stress reaction process,as well as other floral-related pathways.Composed of three major subnetworks,a gene regulatory network with 150 nodes and 225 edges was found to be highly correlated with flowering transition.The gene ontology(GO)annotation of pathway enrichment analysis revealed that the identified genes are enriched in the catalytic activity,metabolic process and cellular process.To verify the effectiveness of dynamic network analysis methods,a similar analysis was performed on the flowering development data in rice.Ultimately,we detected a critical transition state of flower development in rice.This critical transition state detected during the formation of flowers corresponded to the development of specific floral organs(anther and pistil)in rice.Not only that,we also detected the DNB members composed by 206 genes that may herald the imminent critical transition during the formation of flowers.This study provides a novel insight to identify the real causality of the phase transition with genome-wide dynamic network analysis.