Advancements in next-generation sequencing technology have enabled whole genome re-sequencing in many species providing unprecedented discovery and characterization of molecular polymorphisms. There are limitations, however, to next-generation sequencing approaches for species with large complex genomes such as barley and wheat. Genotyping-by-sequencing (GBS) has been developed as a tool for association studies and genomics-assisted breeding in a range of species including those with complex genomes. GBS uses restriction enzymes for targeted complexity reduction followed by multiplex sequencing to produce high-quality polymorphism data at a relatively low per sample cost. Here we present a GBS approach for species that currently lack a reference genome sequence. We developed a novel two-enzyme GBS protocol and genotyped bi-parental barley and wheat populations to develop a genetically anchored reference map of identified SNPs and tags. We were able to map over 34,000 SNPs and 240,000 tags onto the Oregon Wolfe Barley reference map, and 20,000 SNPs and 367,000 tags on the Synthetic W9784 × Opata85 (SynOpDH) wheat reference map. To further evaluate GBS in wheat, we also constructed a de novo genetic map using only SNP markers from the GBS data. The GBS approach presented here provides a powerful method of developing high-density markers in species without a sequenced genome while providing valuable tools for anchoring and ordering physical maps and whole-genome shotgun sequence. Development of the sequenced reference genome(s) will in turn increase the utility of GBS data enabling physical mapping of genes and haplotype imputation of missing data. Finally, as a result of low per-sample costs, GBS will have broad application in genomics-assisted plant breeding programs.

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Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach

An ordered draft sequence of the 17-gigabase hexaploid bread wheat (Triticum aestivum) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the divergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

1: Wheat Rusts and the Genetic Bases on Disease Resistance. Introduction. Biology of Pathogen and Host. Host:Pathogen Genetics. Methodologies in Wheat Rust Disease. A Coordinated Strategy for Rust Control. Conclusion. Guide to Gene Descriptions and Illustrations. 2: The Genes for Resistance to Leaf Rust in Wheat and Triticale. Catalogued Leaf Rust Resistance Genes. Temporarily Designated and Miscellaneous Leaf Rust Resistance Genes. 3: The Genes for Resistance to Stem Rust in Wheat and Triticale. Catalogued Leaf Rust Resistance Genes. Temporarily Designated and Miscellaneous Stem Rust Resistance Genes. 4: The Genes for Resistance to Stripe Rust in Wheat and Triticale. Catalogued Stripe Rust Resistance Genes. Temporarily Designated and Miscellaneous Stripe Rust Resistance Genes. References. Appendix I: Species Names Used in the Text, Genomic Formulae and Synonyms. Appendix II: Pathotypes and Accessions (Cultures) Used in Photography.

Wheat Rusts: An Atlas of Resistance Genes

Wild relatives of common wheat, Triticum aestivum, and related species are an important source of disease and pest resistance and several useful traits have been transferred from these species to wheat. C-banding and in situ hybridization analyses are powerful cytological techniques allowing the detection of alien chromatin in wheat. C-banding permits identification of the wheat and alien chromosomes involved in wheat-alien translocations, whereas genomic in situ hybridization analysis allows determination of their size and breakpoint positions. The present review summarizes the available data on wheat-alien transfers conferring resistance to diseases and pests. Ten of the 57 spontaneous and induced wheat-alien translocations were identified as whole arm translocations with the breakpoints within the centromeric regions. The majority of transfers (45) were identified as terminal translocations with distal alien segments translocated to wheat chromosome arms. Only two intercalary wheat-alien transloctions were identified, one induced by radiation treatment with a small segment of rye chromosome 6RL (H25) inserted into the long arm of wheat chromosome 4A, and the other probably induced by homoeologous recombination with a segment derived from the long arm of a group 7 Agropyron elongatum chromosome with Lr19 inserted into the long arm of 7D. The presented information should be useful for further directed chromosome engineering aimed at producing superior germplasm.

Characterization of wheat-alien translocations conferring resistance to diseases and pests: current status

The Deletion Stocks of Common Wheat

A standard karyotype based on N-banding, C-banding, and modified C-banding has been constructed for Triticum aestivum L. 'Chinese Spring'. An idiogram and a nomenclature system have been developed ...

T. R. Endo

Papers

Standard karyotype and nomenclature system for description of chromosome bands and structural aberrations in wheat (Triticum aestivum)