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Origins of Host Specific Populations of Puccinia triticina Revealed by SNP Markers (Preliminary)

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 groups. North America South America Central Asia Middle East Europe New Zealand

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Origins of Host Specific Populations of Puccinia triticina Revealed by SNP Markers (Preliminary)

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  1. 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

  2. World-wide P. triticina SSR groups North America South America Central Asia Middle East Europe New Zealand South Africa Durum isolates (EU, SA, ME, NA) Aegilops speltoides 587 isolates FST = 0.331 Some geographical relationship SA, NA vs. EU, ME, CA, NZ, SAF Except ME1 with NA and SA Durum groups distinct from common wheat groups

  3. Puccinia triticina host differentiation • Bread wheat type – highly variable for SSR genotype • Durum wheat type – relatively less variable for SSR genotype • Wild 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?

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

  5. Why SNP? • Development of SNP markers (poster: theme 1, #30 ) • Preliminary results

  6. Why SNP?

  7. Why SNP? • Ubiquitous — accessible, representative

  8. Why SNP? • Ubiquitous — accessible, representative • Variable mutation rates • Suitable to automatic genotyping • Amiable to sequence-based analytical tools • Alternative approach

  9. Why SNP? • Development of SNP markers (poster: theme 1, #30 ) • Preliminary results

  10. Sampling 7

  11. Preliminary results Clusters 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=0.884 100 79 100 <50 7

  12. Preliminary results One 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 Aeg ETH durum 100 78 Durum 99 SA-5 NZ SAF EU-7 100 CA-3 NA-4 ME-1 NA-1

  13. Preliminary results Inference of haplotypes based on diploid (dikaryotic) data PHASE 2.1 Stephens, M et al 2001. A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics 68:978—989

  14. Coalescence analysis Carbone Lab IM, IMa, IMa2 Department of Genome Science, U of Washington

  15. ACKNOWLEDGEMENTS We 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.

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