Project Number: 5335-21000-035-00
Project Type: Appropriated

Start Date: Feb 25, 2013
End Date: Feb 24, 2018

Objective:
The long-term goal of this research is to identify and characterize genes that regulate growth and development in maize: Objective 1: Identify genes that regulate plant architecture in maize by using mutant analysis and positional cloning. Objective 2: Determine function of cloned genes with molecular, genomic and genetic techniques. Objective 3: Map and clone modifiers of plant architecture genes to understand their function. To truly understand the function of a gene, one needs a mutation. The mutation reveals how that gene functions. Mutations that result in a morphological phenotype identify genes that are critical for growth and development. Maize has a rich history of genetic analysis based on the ease of obtaining and analyzing mutants. Although many classically identified mutations have now been cloned, new ones are continually being discovered. Some of these new mutants are dominants, which are rare compared to recessives, and thereby have not been previously identified. Other mutants are background dependent and may have been overlooked because they appear different in each inbred and thus are difficult to track. We have several mutants and modifiers at different stages of analysis. In each case, we will identify the gene by recombination mapping. We will identify the lesion that causes the mutation and in the case of modifiers, we will seek to determine how the inbred allele differences affect the mutant phenotype. We will determine how the genes function in their normal context and in the mutant context by RNA, phenotypic, and genetic analysis. We will identify paralogs and determine their function when possible. The end goal is a clear understanding of each gene’s function and how it impacts growth and development.

Approach:
Objective 1: Identify genes that regulate plant architecture in maize by using mutant analysis and positional cloning. Hypothesis: Genes defined by a morphological phenotype are important for growth and development. We have identified 4 new mutants by screening in different inbred backgrounds. All four mutants affect both the leaf and inflorescence. We will clone these genes by identifying recombinants. The goal is to reduce the interval to 1-2 genes and then sequence. The mutants have been made in defined inbred backgrounds making identification of the EMS induced lesion straight-forward. Objective 2: Determine function of cloned genes with molecular, genomic and genetic techniques. Hypothesis: Knowing how a gene functions provides important information about developmental processes. For each mutant we analyze and gene we clone, a series of steps are carried out. We will determine where the gene is expressed. We will determine the putative function of the gene. We will analyze closely related paralogs and for some proteins, we will identify interacting partners. Objective 3: Map and clone modifiers of plant architecture genes to understand their function. Hypothesis: Modifiers of mutants provide information about the genetic basis of natural diversity. For Lgn, we will identify recombinants to identify the modifer. We will also use RNAseq experiments and genetic screens. For nod, we will map the modifier after developing well introgressed material. It is possible that there is not a single modifier, but multiple genes. If that is the case, the RNAseq analysis should prove helpful.