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Massive Project Moving Forward on Wheat Diversity

Cindy Lawley
| Jan 16, 2013

During yesterday’s Illumina technology workshop, the talk by Eduard Akhunov of Kansas State on genomic patterns of SNP variation in worldwide wheat populations did not disappoint. Despite being a very biology-heavy talk, Eduard did a great job of taking us from “How does genotyping in hexaploid wheat work”? to “What are the patterns and why should we care?” He presented information on three consortium genotyping tools— two SNP genotyping tools (Wheat 9k and Wheat 90k) and a software tool for automated calling of clusters in genotyping data.

This is the biggest diversity project in wheat to date (12,000 worldwide accessions/samples for Wheat 9k, and 48,000 accessions for Wheat 90k). The community is holding its collective breath waiting for the publication, as this stunning amount of data will be an enormous resource. Just talking to PAG folks this week, I have heard of over 12 papers that are waiting for Akhunov’s results to be published so that they can reference the paper. So, back to the two major questions addressed in the talk.

How does genotyping in hexaploid wheat work? 

Akhunov highlighted the challenges with using manual methods of genotype calling and showed screen shots of GenomeStudio’s new automated polyploidy calling software. The new software calls clusters and relies on researchers to determine the actual genotype represented by the clusters based upon biological knowledge. I was fortunate enough to get a copy of Eduard’s slide here, outlining the benefits of the new software relative to the diploid version of GenomeStudio. 

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What are the patterns and why should we care?

Eduard summarized the utility of the Wheat 90k content for the diversity of wheat accessions genotyped. The Wheat HapMap project represented here will rival the Human HapMap Project. They have the capacity to determine haplotype block structure in the accessible genome in major wheat cultivars (breeding varieties) as well as landraces (wild types). He was already able to show the rate of LD decay observed as you increase genetic distance in cultivars versus landraces (although you have to wait for the publication to see this image, as I did not ask him for it). Population structure is mostly defined by geography rather than by growth habit or improvement level, yet surprisingly he found that traits under such strong selection were not fixed or even highest in minor allele frequency among cultivars. He used Pairwise Haplotype Sharing (PHS; Toomajian et al., 2006), to show regions of homozygosity in PHS were different in genome regions under short- versus long-term selection.

Overall, it was a very informative talk, satisfying my desire for hard data. And like many other wheat researchers, I am very much looking forward to the publication!