Progress 10/01/09 to 09/30/10
Outputs
Progress Report Objectives (from AD-416) The objectives of this cooperative research project are to increase our understanding of genome organization of cereals and the QTLs associated with crop enhancement including response to the environment and nutritional improvement. Approach (from AD-416) 1) Development of genetic and physical markers for maize. Annotation of maize sequences will be used to identify SSR sequences to be used as genetic markers. In addition we will use the regions of synteny established between the rice genome sequence and maize genetic and physical map markers to identify rice gene models for genetic marker development. These resources will be used to enhance the emerging integrated maize genetic and physical map. 2) Molecular and quantitative trait loci (QTL) mapping of traits associated with improved crop performance and nutritional content in maize and other model species (i.e. Arabidopsis) will be carried out to isolate and characterize genes associated with these traits. We will leverage the near complete rice genome sequence and annotations and the known synteny among the grasses to identify candidate genes associated with QTLs and sequence these regions. This project is awaiting administrative close-out. There is no progress to report. Research was concluded on 9/14/2009.
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Progress 10/01/08 to 09/30/09
Outputs
Progress Report Objectives (from AD-416) The objectives of this cooperative research project are to increase our understanding of genome organization of cereals and the QTLs associated with crop enhancement including response to the environment and nutritional improvement. Approach (from AD-416) 1) Development of genetic and physical markers for maize. Annotation of maize sequences will be used to identify SSR sequences to be used as genetic markers. In addition we will use the regions of synteny established between the rice genome sequence and maize genetic and physical map markers to identify rice gene models for genetic marker development. These resources will be used to enhance the emerging integrated maize genetic and physical map. 2) Molecular and quantitative trait loci (QTL) mapping of traits associated with improved crop performance and nutritional content in maize and other model species (i.e. Arabidopsis) will be carried out to isolate and characterize genes associated with these traits. We will leverage the near complete rice genome sequence and annotations and the known synteny among the grasses to identify candidate genes associated with QTLs and sequence these regions. Significant Activities that Support Special Target Populations In FY 2009, research has focused on understanding the relationship between microRNA genes and bract root development. For this work, the support has been provided for a graduate student to study the available maize mutants as well as the maize NAM diversity panel for Bract root phenotypes with the longer term objective that this information will be used for Genome Wide Association Analysis. In addition, the student has also focused on developing additional germplasm resources to facilitate genetic dissection of the bract root phenotype. The group has provided mutant seed and protocols for harvesting the tissue at the appropriate developmental stage. Discussion and review of the objectives are reviewed at least twice a year in conference calls or in-person meetings.
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Progress 10/01/07 to 09/30/08
Outputs
Progress Report Objectives (from AD-416) The objectives of this cooperative research project are to increase our understanding of genome organization of cereals and the QTLs associated with crop enhancement including response to the environment and nutritional improvement. Approach (from AD-416) 1) Development of genetic and physical markers for maize. Annotation of maize sequences will be used to identify SSR sequences to be used as genetic markers. In addition we will use the regions of synteny established between the rice genome sequence and maize genetic and physical map markers to identify rice gene models for genetic marker development. These resources will be used to enhance the emerging integrated maize genetic and physical map. 2) Molecular and quantitative trait loci (QTL) mapping of traits associated with improved crop performance and nutritional content in maize and other model species (i.e. Arabidopsis) will be carried out to isolate and characterize genes associated with these traits. We will leverage the near complete rice genome sequence and annotations and the known synteny among the grasses to identify candidate genes associated with QTLs and sequence these regions. Significant Activities that Support Special Target Populations This work focuses on understanding the maize genome, through identification and anchoring of functional units and phenotypes to the maize genetic, physical and sequenced based maps. In the past year the Davis group has focused their work on providing resources for microRNA identification under varying stress conditions and understanding the regulatory networks leading to shoot borne root development and patterning in maize root. The Davis group has provided tissue from stress and genetic mutants to the Ware group for analysis of microRNA target analysis. The Davis group has performed QTL mapping studies on the B73 X Mo17 mapping population for shoot borne root development and identified 33 QTL. In addition they began a preliminary association analysis on 164 microRNA genes or their targets against the shoot borne root phenotype. Preliminary analysis identified 35 genes with preliminary associations to several phenotypes. Currently in development, the group is exploring the opportunity to visualize microRNA and gene targets during shoot borne development using a confocal microscope. Management and Communication: Discussion and review of the objectives occur at least twice a year with conference calls or in person meetings. NP 301 Component 2 and Component 3.
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Progress 10/01/06 to 09/30/07
Outputs
Progress Report Objectives (from AD-416) The objectives of this cooperative research project are to increase our understanding of genome organization of cereals and the QTLs associated with crop enhancement including response to the environment and nutritional improvement. Approach (from AD-416) 1) Development of genetic and physical markers for maize. Annotation of maize sequences will be used to identify SSR sequences to be used as genetic markers. In addition we will use the regions of synteny established between the rice genome sequence and maize genetic and physical map markers to identify rice gene models for genetic marker development. These resources will be used to enhance the emerging integrated maize genetic and physical map. 2) Molecular and quantitative trait loci (QTL) mapping of traits associated with improved crop performance and nutritional content in maize and other model species (i.e. Arabidopsis) will be carried out to isolate and characterize genes associated with these traits. We will leverage the near complete rice genome sequence and annotations and the known synteny among the grasses to identify candidate genes associated with QTLs and sequence these regions. Significant Activities that Support Special Target Populations This report serves to document research conducted under a Specific Cooperative Agreement between ARS and the University of Missouri-Columbia. Funds were used to support tissue generation in maize mutants and drought stressed plants for expression profiling in maize and served as template for small RNA libraries. In addition to the isolation of tissue for expression profile, Dr. Davis� group is following up on phenotyping several maize mutants to identify whether candidate maize microRNA genes are responsible for phenotypes. Management and Communication: Discussion and review of the objectives are done at least twice a year in conference calls or in personal meetings as well as email exchanges and conference calls.
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Progress 10/01/05 to 09/30/06
Outputs
Progress Report 4d Progress report. This report serves to document research conducted under a Specific Cooperative Agreement between ARS and the University of Missouri-Columbia. Additional details of this research can be found in the report of the parent project 1907-21000-023-00D "Comparative Genomic Analyses, Bioinformatics and Resource Development for Cereal Genomes." This agreement, initiated on September 15, 2004, focuses on increasing our understanding of the maize genome organization, anchor functional elements to the genetic and physical map of maize, and identify QTL associated with crop enhancement including response to the environment and nutritional improvement. In the past year, the Davis lab continued work of anchoring predicted miRNA and their gene targets to the maize physical map using a BAC pooling strategy. This work was further extended to include additional maize expressed ESTs.
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Progress 10/01/04 to 09/30/05
Outputs
4d Progress report. This report serves to document research conducted under a Specific Cooperative Agreement between ARS and the University of Missouri-Columbia. Additional details of this research can be found in the report of the parent project 1907-21000-014-00D Comparative Plant Genomics. Through this agreement, initiated on September 15, 2004, we focus on increasing our understanding of the maize genome organization, anchor functional elements to the genetic and physical map of maize, and identify QTL associated with crop enhancement including response to the environment and nutritional improvement. Over the past year, we have progressed toward identifying genetic markers and anchoring miRNAs to the maize physical maps. To further enhance the maize physical map, we identified unanchored contigs as well as potential simple sequence repeats (SSRs) from BAC end sequences associated with the unanchored contigs. We tested 242 SSRs for polymorphism on the parents of
the IBM mapping population; 70 were found to be polymorphic and 19 failed to amplify. The features that were not polymorphic were tested on parents of six other available maize mapping populations, resulting in 66 SSRs being polymorphic. Across the parents of the seven populations tested, 56% of the markers were found to be polymorphic. In the past year, the Davis lab has been anchoring predicted miRNA and their gene targets to the maize physical map using a BAC pooling strategy, resulting thus far in the successful positioning of 33 of 37 miRNA genes. The data generated from this project will improve the quality of the maize physical map, develop criteria for selection of potential genetic markers for fine mapping based on available sequence from the maize physical map, and anchor genes known to be involved in important developmental processes to the genetic and physical maps of maize.
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