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

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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 ... – PowerPoint PPT presentation

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


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. L134 CI0.709 RI0.884
100
79
100
lt50
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. L271 CI0.915 RI0.955
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 68978989
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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