Analysis Of The Dynamic Co-expression Pattern Of Maize Kernel Gene Pairs

The content of carotene and fatty acid are two important quantitative traits,which are regulated by many genes.These genes could also involve in complex regulatory networks to rule various biological reactions in cells,so it will be of great value to understand the regulation mechanism of nutrition compounds biosynthesis and accumulation,and will contribute to improve maize quality.The development of high-throughput sequencing technologies enables us to access the mass of omics data,which makes it possible to construct the regulatory networks of key genes.Previously,we reported RNA sequencing of developing maize kernels from 368 inbred lines producing 28679 gene expression data.Gene co-expression dynamics study is a novel bio-computational approach to identify new candidate genes for genetic and functional studies of complex traits and explore the regulation of gene transcription in metabolic pathway in yeast and human.By taking the LA analysis of the gene expression data and the phenotype data of oil concentration,we try to dissect dynamics co-expression of genes on the whole genome scale,and to explore the transcriptional regulations in metabolic pathway,then further to identify the genes involved in carotenoid metabolic pathway on the whole genome scale and the lipid metabolism networks.These results will help us to understand the regulatory and molecular mechanism in maize nutrients synthesis and accumulation.The main results are as follows:1.A total of 1.10E12 triplets were analyzed by LA on the whole genome scale.After the analysis of the top 1000 LA pairs(LAP)with largest LA scores,the correlations of expression about 686 LAPs were found to be regulated by the LA-scouting gene.830 hotspots from positive LA results and 215 hotspots from negative LA results were identified after ranking the LA-scouting gene by frequency.Gene Ontology analysis showed that most of the positive LA-scouting genes were significantly enriched in the same metabolic processes.2.Results of LA analysis to the upstream and downstream genes involved in carotenoids metabolic pathway demonstrated that crtRBl,lcyE,lcyB,ZEPl and VDE genes play important roles in regulating the gene expression pattern of ? and ? two branches in carotene biosynthetic pathway.3.By exploring the genes regulated the dynamics co-expression pattern between oil associated genes and oil concentration on the whole genome scale,among the 26 genes known to be related with oil concentration,there were 23 genes were modulated by the 580 LA-scouting genes.The functional annotation of 580 LA-scouting genes showed that 5%genes are involved in lipid metabolic pathways,35%genes in non-lipid metabolic pathway,5%genes in stress response,10%genes playing a role of transcription factor in transcriptional regulation,8%genes acting as signals,5%genes encoding structure protein,and about 32%genes with unknown function.By focusing on the carotenoid and oil biosynthetic pathways in maize,we showed that a genome-wide LA analysis provides a novel and effective way to detect transcriptional regulatory relationships.This method will help us understand the biological role of maize kernel genes and will benefit maize breeding programs.