The Molecular Basis Of Rice Lamina Joint Development And Leaf Angle Regulation Sdudied By Multi-omics

Dense planting of crops is a way to make full use of the limited land area and improve the comprehensive agricultural production capacity,but there are many problems in the practical process of rice breeding for compact plant architecture.Since the leaf angle phenotype is one of the components of ideal plant type and a key factor of dense planting,it is expected to improve the yield of green revolution varieties.Therefore,relevant research is of great importance for future agricultural development,as well as sustainability and food security.The lamina joint(LJ)is the key organ that determine leaf angle,which is the junction between leaf and sheath.The opening of the leaf angle is determined by the cytological structure of the lamina joint,and the regulatory factors at each developmental stage are different.It has been reported that some genes can regulate the cytological structure and development at different stages,but there are still many to be explored,including hormones,transcription factors and post-transcriptional regulatory factors(such as micro RNAs(mi RNAs)in small RNAs(s RNAs)).In this study,rice blade and lamina joint transcriptome data(m RNA-seq and s RNA-seq)from five typical development stages were used to mine the genetic and regulatory factors that regulate lamina joint development and leaf angle in rice,and to fully explain the regulation of leaf angle formation by specific factors in each development stage.We also fully analyzed various organ-specific factors that regulate the formation of leaf angle,and the genetic and molecular basis of s RNAs specific for each stage of development,such as mi RNAs,which regulate the lamina joint development and leaf angle formation.In addition,the dynamic expression module of m RNA fully reflected the various cytological characteristics of lamina joint from infancy to maturity,and suggested that multiple signals were involved in the formation of the cytological structure of the lamina joint at the later stage of development.These factors all provided an explanation for the good plasticity of the leaf angle.Time specific mi RNAs and their target units have been reported to be involved in the regulation of leaf and lamina joint development,and we also predicted several mi RNA and target gene pairings.Although these predicted pairings need to be further confirmed,they also provide clues to the post-transcriptional regulation of lamina joint and angle formation.Studies on post-transcriptional regulation of lamina joint and angle formation requires further experiments to prove whether it regulates the development of plant organs,whether it can carry out effective photosynthesize and improve yield.In this study,we systematically analyzed the distribution of transcription elements near the rice gene and the MIRNA site,and identified a series of transcription factors that may regulate the characteristics of lamina joint development through predicting promotor cis-regulatory elements,and established the transcriptional regulatory network of lamina joint development,and selected some representative candidates transcription factors for experimental verification.Some of these transcription factors regulate cell proliferation in early stage,some regulate cellular lignin synthesis,luminal tissue synthesis and vascular tissue formation in middle stage,and some regulate the formation of sclerenchyma and expansion of parenchyma in the proximal plane in late stage,to form the leaf angle.The phenotypic changes of CRISPR knockout lines demonstrated the effectiveness of the prediction method.The yield test results of different densities showed that the erect leaf lines can increase yield by controlling tiller number under dense planting conditions.In addition,we also performed multi-organ co-expression network analysis combined with public data and cross-analysis and forward genetic data to obtain many gene modules that regulate specific lamina joint development,as well as genes and cis-regulatory elements distributed in linkage regions.These results provide a data and resource basis for further research on reshaping rice plant type structure to obtain high yield by controlling leaf angle.