Mapping of chromosome arm1RS

The three goals of this proposal are: (1) Physically map, or bin map, ESTs (Expressed Sequence Tags) in the short arm of rye chromosome 1R (1RS), (2) develop 1RS-specific SSR markers, and (3) map these SSRs genetically and physically in 1RS. 1. An estimated total of 500 wheat unigenes, localized on the short arms of wheat chromosomes 1A, 1B, and 1D, will be mapped to bins on 1RS using disomic wheat-rye-1RS deletion lines and wheat-rye-translocation lines. These unigenes include 172 1RS-specific unigenes selected from 9000 rye ESTs on the basis of their sequence homologies to 1AS-, 1BS-, and 1DSspecific wheat ESTs. Unigenes mapped to 1RS will accelerate the identification and isolation of agronomically useful genes. 2. 1RS-specific DNA will be used in an enrichment procedure to isolate 1RSspecific SSR markers. For this purpose DNA, isolated from flow sorted 1RS chromosomes, will be amplified with Phi29 DNA polymerase. Since this amplification produces randomly occurring fragments, SSR markers along the total length of the chromosome arm are expected. We intend to isolate at least 100 multiallelic SSR markers. 3. SSR markers will be tested for polymorphism using a panel of rye inbred lines. Then they will genetically be mapped in 1RS using an F2 population of two inbred lines of large genetic distance. They will be bin-mapped as well, using the deletion- and translocation lines mentioned above. SSR markers will provide a skeletal map for 1RS. Such a map will have many applications, from mapping agronomic traits up to positional cloning of genes. Numerous known and unknown 1RS translocation wheats, distributed all over the world, allow considering 1RS to be part of the wheat germplasm. Investigating the physical organization, especially the expressed part of 1RS in comparison to the short arms of homoeologous group 1 wheat chromosomes, will significantly contribute to our understanding of cereal chromosome structure and polyploid evolution. It will yield important information on content and distribution of genes on this chromosome arm and facilitate the targeting of specific genes. This work is stimulated by the American Wheat Genome Mapping Project, which in 2004 published the bin-mapping of a large number of ESTs to all seven homoeologous group chromosomes of wheat.

The three goals of this proposal are: (1) Physically map, or bin map, ESTs (Expressed Sequence Tags) in the short arm of rye chromosome 1R (1RS), (2) develop 1RS-specific SSR markers, and (3) map these SSRs genetically and physically in 1RS. 1. An estimated total of 500 wheat unigenes, localized on the short arms of wheat chromosomes 1A, 1B, and 1D, will be mapped to bins on 1RS using disomic wheat-rye-1RS deletion lines and wheat-rye-translocation lines. These unigenes include 172 1RS-specific unigenes selected from 9000 rye ESTs on the basis of their sequence homologies to 1AS-, 1BS-, and 1DSspecific wheat ESTs. Unigenes mapped to 1RS will accelerate the identification and isolation of agronomically useful genes. 2. 1RS-specific DNA will be used in an enrichment procedure to isolate 1RSspecific SSR markers. For this purpose DNA, isolated from flow sorted 1RS chromosomes, will be amplified with Phi29 DNA polymerase. Since this amplification produces randomly occurring fragments, SSR markers along the total length of the chromosome arm are expected. We intend to isolate at least 100 multiallelic SSR markers. 3. SSR markers will be tested for polymorphism using a panel of rye inbred lines. Then they will genetically be mapped in 1RS using an F2 population of two inbred lines of large genetic distance. They will be bin- mapped as well, using the deletion- and translocation lines mentioned above. SSR markers will provide a skeletal map for 1RS. Such a map will have many applications, from mapping agronomic traits up to positional cloning of genes. Numerous known and unknown 1RS translocation wheats, distributed all over the world, allow considering 1RS to be part of the wheat germplasm. Investigating the physical organization, especially the expressed part of 1RS in comparison to the short arms of homoeologous group 1 wheat chromosomes, will significantly contribute to our understanding of cereal chromosome structure and polyploid evolution. It will yield important information on content and distribution of genes on this chromosome arm and facilitate the targeting of specific genes. This work is stimulated by the American Wheat Genome Mapping Project, which in 2004 published the bin-mapping of a large number of ESTs to all seven homoeologous group chromosomes of wheat.