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ARS Home » Pacific West Area » Albany, California » Plant Gene Expression Center » Research » Research Project #434464

Research Project: Characterization of Plant Architectural Genes in Maize for Increased Productivity

Location: Plant Gene Expression Center

Project Number: 2030-21000-052-00-D
Project Type: In-House Appropriated

Start Date: Feb 25, 2018
End Date: Feb 24, 2023

The long-term goal of our research is to identify genes that regulate plant architecture in maize. We recently positionally cloned four genes that were defined by mutant phenotype. The phenotypes affect multiple aspects of architecture including leaf shape, internode length, tassel branching and sex determination. The phenotypes vary depending on inbred background. Of the four genes, one encodes a plasma membrane bound protein, one encodes a kinase, a third encodes an enzyme and the fourth is a conserved gene of unknown function. In order to connect their interesting phenotypes to mechanism we are identifying interacting partners, carrying out RNAseq and conducting metabolomic analysis. The work will increase our dataset from four genes to entire pathways. We will then combine knowledge of these pathways to transcription factor targets that are being developed in collaboration with others. This combined information will provide a network of connectivity that could be useful for breeding. For example, if we hope to change leaf angle, we can ask which genes appear to function solely in leaf angle and not also in leaf width or tassel branching. If we are selecting for improved abiotic stress, we can examine our network and see what genes are likely to have large or small effects. Objective 1: Dissect gene networks that regulate leaf architecture and internode elongation in maize to provide targets for breeding more productive maize. Subobjective 1A. Identify proteins that interact with NOD (NARROW ODD DWARF) and confirm the interaction, in vivo and in vitro. Subobjective 1B. Identify proteins that are phosphorylated by LGN and carry out transcriptome analysis. Subobjective 1C. Map modifiers of nod that are responsible for the inbred differences. Objective 2: Characterize genes that regulate tassel branching and sex determination in maize for higher yields. Subobjective 2A. Prove identity of Tasselseed5 (Ts5) gene by obtaining a revertant allele and by overexpressing the gene. Subobjective 2B. Map the modifiers that differentiate Ts5 in Mo17 compared to B73. Subobjective 2C. Obtain additional feminized upright narrow (fun) alleles and carry out RNAseq analysis. Objective 3: Determine coordinated and independent pathways that regulate leaf, inflorescence, and internode development in maize for enhanced productivity.

For Objective 1, we hypothesize that NARROW ODD DWARF (NOD), a plasma membrane localized protein known to function in calcium signaling, is an essential protein in plants with a role in development and immunity. We are using proteomics to identify interacting partners and testing these interactions with biochemical and genetic experiments. We also hypothesize that LIGULELESS NARROW (LGN) is critical, given the severe mutant phenotype when it is not able to phosphorylate other proteins. We will determine the targets of this kinase and determine how and when it interacts with NOD. We have antibodies to both of these proteins that function in westerns and in Co-immunoprecipitation. Both NOD and LGN mutants are distinct in different inbreds. We mapped a modifier to LGN and plan to identify the modifiers for NOD. We hypothesize that there are distinct loci responsible for the ligule defects and other loci responsible for the auto-immunity defects. The modifiers will be identified using genotyping by sequencing (GBS) methods. We also have the possibility of mapping the modifiers by crossing to recombinant inbred lines in the GBS method doesn’t work. For objective 2, we hypothesize that Ts5 encodes an enzyme in the jasmonic acid (JA) pathway. We will obtain a revertant of Ts5 using ethyl methyl sulfonate (EMS). If this doesn’t work, we will verify its function by following JA metabolites during wounding. We also plan to overexpress the gene in Brachypodium and determine the effect on plant development. Ts5 is completely feminized in the Mo17 inbred and it is mild in B73. We crossed Ts5 to the recombinant B73 Mo17 inbred lines (IBM) and identified 10 major quantitative trait locus (QTL). We combined this data with an RNA sequencin (RNAseq) experiment that identified the differentially expressed genes between Ts5 and normal tassels. Four genes were identified and we will obtain mutants in these genes to examine their function. The fun mutant is also feminized, but may not be in the JA pathway. From analysis of double mutants, we hypothesize it is in the brassinosteroid (BR) pathway. We are determining the BR levels and will analyze an RNAseq dataset to explore this hypothesis. Because FUN is a gene of unknown function, additional alleles will be useful for understanding the domains. These will be obtained by EMS screens. For Objective 3, we will combine our different datasets into a network analysis. We hypothesize that few genes function in only one tissue and will determine the overlap in the tassel network and leaf network. This analysis may lead to genes that are not yet identified by a mutant phenotype and would be worth study in the future.