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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, MN 55108. World-wide P. triticina SSR groups. North America South America Central Asia Middle East Europe New Zealand

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slide1

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
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

puccinia triticina host differentiation
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?

slide4

Goal:

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

slide5

Why SNP?

  • Development of SNP markers

(poster: theme 1, #30 )

  • Preliminary results
slide7

Why SNP?

  • Ubiquitous — accessible, representative
slide8

Why SNP?

  • Ubiquitous — accessible, representative
  • Variable mutation rates
  • Suitable to automatic genotyping
  • Amiable to sequence-based analytical tools
  • Alternative approach
slide9

Why SNP?

  • Development of SNP markers

(poster: theme 1, #30 )

  • Preliminary results
slide11

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

slide12

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

slide13

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

slide14

Coalescence analysis

Carbone Lab

IM, IMa, IMa2

Department of Genome Science, U of Washington

slide15

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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