Rye

GABI RYE-EXPRESS: Establishing a high-density transcript map in rye based on stress-induced genes

Persons in charge: Grit Haseneyer, Eva Bauer
Project duration: 01.01.2008-31.12.2010
Project partners: Nils Stein, IPK Gatersleben; Klaus Mayer, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH)
Project management agency: Project Management Jülich (PTJ)
Funding: Federal Ministry of Education and Research (BMBF)

Project description:

Rye exhibits a high tolerance to abiotic stresses (drought, frost, low soil fertility) but missing sequence information of the rye genome hampers the exploration of the genetic potential that might be useful for breeding progress and cultivar improvement. The main emphasis of the project is to unlock this genetic potential of rye by establishing a functional genomics resource for the EXPRESSed portion of the rye genome. Five highly diverse rye inbred lines will be used for cDNA sequencing. To capture a comprehensive part of the rye transcriptome, RNA of each genotype will be obtained from a set of plant tissues and developmental stages. cDNAs will be pooled per genotype, normalized and sent for sequencing (Roche/454 GS-FLX). EST sequence data will become available via databases to the scientific community as a resource for research on abiotic stresses. EST assemblies will be performed and are expected to deliver a robust set of unigenes shared among all genotype-specific sequence datasets for in silico SNP mining. The goal is to develop a High-Throughput genotyping platform for SNPs present primarily in stress-related rye genes. This will likely be designed as Oligo Pool Assay (OPA) for the Illumina GoldenGate® genotyping service. Within the scope of this project three rye mapping populations (set A), a diversity panel of inbred lines representing the available rye genepools and parents of additional mapping populations and the material used in GABI RYE-FROST (set B) will be genotyped. Data obtained from set A will be used to generate a high-density rye transcript map. The map will be instrumental to assess colinearity of the rye genome to other grass genome resources. Genotyping data from set B will be used for estimating intra- and inter-chromosomal linkage disequilibrium within GABI RYE-FROST and for the assessment of genetic diversity parameters.