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A whole-genome approach to marker discovery in lettuce PI Name: Allen Van Deynze Grant Number: bio-itl04-10470 E-mail: avandeynze@ucdavis.edu Campus: UCD Award Total: $879,741 Project Period: 8/16/2005 - 8/15/2008 Non-technical Abstract: A whole genome approach to marker discovery in lettuce. Molecular markers are becoming increasingly important in breeding to manipulate and protect germplasm and to discover and manipulate in germplasm. We will build on the current genomic resources in lettuce developed at UC Davis that currently includes the sequences of over 19,000 unique genes. We will design an Affymetrix high density DNA array specifically to detect differences in at least 25,000 lettuce genes. The experimental and computional aspects will be refined using the analysis of two reference genotypes and previously characterized genetic differences. Genetic diversity will be measured by screening50 breeding lines and mapping parents. Many of the 25,000 genes represented on the chip will be placed on the genetic map by analyzing their segregation in three established lettuce populations. This will identify linkages between DNA markers in genes and disease and agronomic traits important to California. Information will be displayed in an interactive database and linked these to our current genetic maps. This resource will be invaluable for lettuce germplasm manipulation by creating both the tools and bioinformatics resources to manipulate genomic data for gene discovery, gene functional analysis and breeding. This high density chip will enable several subsequent studies including studies of gene expression and function in other Compositae species as well such as sunflower. This project is unique as no other project has developed an array specifically for polymorphism discovery within genes that can used for research into gene function as well. This project will be a model for crop species with partially developed genomics resources. A whole-genome approach to marker discovery in lettuce PI Name: Allen Van Deynze Grant Number: bio-itl04-10470 E-mail: avandeynze@ucdavis.edu Campus: UCD Award Total: $879,741 Project Period: 8/16/2005 - 8/15/2008 Non-technical Abstract: A whole genome approach to marker discovery in lettuce. Molecular markers are becoming increasingly important in breeding to manipulate and protect germplasm and to discover and manipulate in germplasm. We will build on the current genomic resources in lettuce developed at UC Davis that currently includes the sequences of over 19,000 unique genes. We will design an Affymetrix high density DNA array specifically to detect differences in at least 25,000 lettuce genes. The experimental and computional aspects will be refined using the analysis of two reference genotypes and previously characterized genetic differences. Genetic diversity will be measured by screening50 breeding lines and mapping parents. Many of the 25,000 genes represented on the chip will be placed on the genetic map by analyzing their segregation in three established lettuce populations. This will identify linkages between DNA markers in genes and disease and agronomic traits important to California. Information will be displayed in an interactive database and linked these to our current genetic maps. This resource will be invaluable for lettuce germplasm manipulation by creating both the tools and bioinformatics resources to manipulate genomic data for gene discovery, gene functional analysis and breeding. This high density chip will enable several subsequent studies including studies of gene expression and function in other Compositae species as well such as sunflower. This project is unique as no other project has developed an array specifically for polymorphism discovery within genes that can used for research into gene function as well. This project will be a model for crop species with partially developed genomics resources. |