8th INTERNATIONAL WHEAT CONFERENCE

The development of genome-wide set of SNPs for wheat is challenged by the large size
of its genome, polyploidy and low level of polymorphism in breeding populations, especially
in the wheat D genome. To overcome these limitations we adopted next-generation
sequencing technologies for large scale SNP discovery in the genic regions of the wheat
genome. The syntenic relationships between homologous chromosomes of related species
will allow using the gene-associated SNPs to gain access to genomic and genetic resources
developed for other crop species. The SNP discovery was performed by 454 sequencing
of wheat transcriptome and targeted re-sequencing of genic regions of the wheat genome
using sequence capture approach combined with Illumina short-read sequencing technology.
Discovery of SNPs in transcript assemblies was shown to be challenging due to
the presence homoeologous transcripts but was facilitated by the availability of long 454
sequence reads. Nearly 50,000 high-quality SNPs have been identified in coding and untranslated
regions of the wheat transcript assemblies providing an excellent resource for
the design of genome-wide genotyping assays. The sequencing of captured DNA fragments
was used as alternative approach for targeted analysis of sequence variation in 3.5
Mb of low copy genic regions from the wheat genome. Both approaches were shown to be
efficient for the discovery of a genic SNPs distributed across the wheat genome. The utility
of SNPs for high-throughput wheat genotyping was tested in a large panel of spring and
winter US wheat cultivars using 1536-plex Illumina OPA. The SNP genotyping data was
used to infer the population structure and genome-wide patterns of genetic diversity and
linkage disequilibrium in a collection of wheat cultivars. The utility of an assembled hexaploid
wheat panel for LD mapping using SNPs was assessed. The results of our research
will be used as an example to discuss the future challenges in application of genome level
data and genomic technologies to wheat breeding and studying wheat genetics.
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Barbazuk et al., (2007) Plant J 51:910-918.
Hyten et al., (2008) Theor Appl Genet 116:945–952
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