Origins of Host Specific Populations of Puccinia triticina Revealed by SNP Markers (Preliminary)M. Liu and J. A. Kolmer

USDA-ARS Cereal Disease Laboratory, St. Paul, MN 55108

World-wide P. triticina SSR groupsNorth AmericaSouth AmericaCentral AsiaMiddle EastEuropeNew ZealandSouth AfricaDurum isolates (EU, SA, ME, NA)Aegilops speltoides587 isolates

FST = 0.331Some geographical relationshipSA, NA vs. EU, ME, CA, NZ, SAFExcept ME1 with NA and SA

Durum groups distinct from common wheat groups

Puccinia triticina host differentiationBread wheat type highly variable for SSR genotypeDurum wheat type relatively less variable for SSR genotypeWild Emmer Wheat (AB) susceptible to bread wheat type native to Fertile Crescent

Is the common wheat type the original form of P. triticina and durum type more recently derived?

Goal: To further infer the evolutionary relationships among populations with the aid of coalescence theory and DNA single nucleotide polymorphism (SNP) markers

Why SNP?Development of SNP markersPreliminary results(poster: theme 1, #30 )

Why SNP?

Why SNP?Ubiquitous accessible, representative

Why SNP?Ubiquitous accessible, representativeVariable mutation ratesSuitable to automatic genotypingAmiable to sequence-based analytical toolsAlternative approach

Why SNP?Development of SNP markersPreliminary results(poster: theme 1, #30 )

Sampling7

Preliminary results100100Clusters of P. triticina populations based on 94 SNPs from three house keeping genes, seven SSR flanking regions and six IGV selected anonymous loci.L=134 CI=0.709 RI=0.884

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Preliminary resultsOne of 258367 most parsimonious phylograms based on SNPs from three house keeping genes and six IGV selected anonymous loci. Isolates on durum wheat formed clade.L=271 CI=0.915 RI=0.955 AegETH durumDurumNZSAFEU-7CA-3NA-4ME-1NA-1SA-51001009978

Preliminary resultsInference of haplotypes based on diploid (dikaryotic) dataPHASE 2.1 Stephens, M et al 2001. A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics 68:978989

Coalescence analysisIM, IMa, IMa2Carbone LabDepartment of Genome Science, U of Washington

ACKNOWLEDGEMENTSWe thank Drs. Les Szabo, John Fellers and Christina Cuomo for facilitating ML to access IGV and Pt whole genome database; Kun Xiao, Jerry Johnson and Kim Phuong Nguyen for technical help.

*The comparison of the whole sample seems that *It is reasonable to ask why SNPs, how to develop them, what kind of results we might end up with. I made a poster, which will be posted in BGRI, mainly presented our research on the development of SNP marker. *There are quite a few review papers out there to discuss about the merits and limitations of SNP markers. To summarize the points:*1. SNPs are ubiquitous in genome. This provided two opportunities. First opportunity is it is easy to get hold of them. 2nd, it provides the opportunity to get hold of the loci which are good representative of the whole genome. *2. Some hypovariable SNPs might have parallism or called multiple hits represnted as homoplasy, others might have evolved too slow, but because of the abundance, we will more or less hit some SNPs evolve just about the right rate. 3. people estimated that to get a good representative of the whole genome 50~500 loci are needed. Down the road, high through put automatic genotype seems the choice. SNP is suitable for that purpose. 4. More and more analytic tools need DNA sequences as input, such as the programs for coalescence analysis. That is another major reason we choose SNPs. Finally even if SNP marker does not have the above mentioned merits, after all it is totally independent of SSRs. We all agree that to verify or falsify a hypothesis with independent evidence would make stronger case. *It is reasonable to ask why SNPs, how to develop them, what kind of results we might end up with. I made a poster, which will be posted in BGRI, mainly presented our research on the development of SNP marker. *After screening, now we got total 14 loci to test. We used 16 sample. The samples were chosen based on this SSR tree. **We were also be able to sequencd 6 IGV loci and 3 house keeping genes for Puccnia persistens as outgroup, which can show us some polarity of the evolution. We can see from this tree that the Aegilop type divergent earlier than other two types. Compare the durum type with common wheat type, the clusters roughly congruent. Coalescence analysis might be able to shed more light on the evolutionary history.*Another challenge coming along with the nature of the variations among the population is that most of the variations in Pt show heterozygous pattern. The software for coalescence analysis, at least for the one I know of, does not recognize. In order to perform coalescence analysis, we have to convert the diploid data to haploid data. There are many software based on different theory to handle this problem. I used the program called PHASE, which used Baysian approach, based on genotype data from the populations, to predict the haplotypes with highest possibility.*