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Sequence Assembly and Analysis of Chromosome 5Mg of Aegilops geniculata

IWGSC Coordinating Committee members Vijay Tiwari and Bikram Gill (Kansas State University, USA), in collaboration with IWGSC members at the Institute of Experimental Botany (Czeck Republic), published an article in Plant Journal describing sequence assembly and analysis of chromosome 5Mg of Aegilops geniculata, and comparison with wheat chromosome 5D.

Another example of the use of IWGSC Chromosome Survey Sequence data for wheat improvement

Link to the article: " Exploring the Tertiary Gene Pool of Bread Wheat: Sequence Assembly and Analysis of Chromosome 5Mg of Aegilops geniculata "

Summary

Next Generation Sequencing (NGS) provides a powerful tool for the discovery of important genes and alleles in crop plants and their wild relatives. Despite great advances in NGS technologies, whole-genome shotgun sequencing is cost-prohibitive for species with complex genomes. An attractive option is to reduce genome complexity to a single chromosome prior to sequencing.

This work describes a strategy for studying the genomes of distant wild relatives of wheat by isolating single chromosomes from addition or substitution lines followed by chromosome sorting using flow cytometry and sequencing of chromosomal DNA by NGS technology. We flow-sorted chromosome 5Mg from a wheat-Aegilops geniculata disomic substitution line (DS5Mg (5D)) and sequenced it using Illumina HiSeq2000 at ~50x coverage. Paired-end sequences were assembled and used for structural and functional annotation. A total of 4,236 genes were annotated on 5Mg, in close agreement with the predicted number of 4,286 genes on wheat chromosome 5D. Single-gene FISH indicated no major chromosomal rearrangements between chromosomes 5Mg and 5D. Comparing chromosome 5Mg with model grass genomes identified synteny blocks in Brachypodium, rice, sorghum and barley. Chromosome 5Mg-specific SNPs and cytogenetic probe-based resources were developed and validated. Deletion bin mapped and ordered 5Mg SNP markers will be useful to track 5M-specific introgressions and translocations.

This study provides a detailed sequence-based analysis about the composition of a chromosome from a distant wild relative of bread wheat and opens up opportunities to develop genomic resources for wild germplasm to facilitate crop improvement.