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Table 2 Chromosomal location, probability of association (P) and R 2 values of SNPs markers representing genomic regions significantly associated (FDR adjusted P < 0.1) with stripe rust infection type (IT) and disease severity (DS) from field experiments and seedling reactions against five races of the stripe rust pathogen in the Ethiopian bread wheat accessions

From: Characterization of molecular diversity and genome-wide mapping of loci associated with resistance to stripe rust and stem rust in Ethiopian bread wheat accessions

QTL-tagging SNP indexa

SNPb

Associated SNP indexc

Chr.

Position (cM)d

RAF (%)

P values (−log)e

R 2 (%)

Traits/Pst racesf

Previously mapped Yr genes/QTLg

Field experiments

  IWB11553

T/G

IWB63258, IWB42176

1B

64.9

8.4

2.6–6.3

3.1–9.6

PLM_IT_12, MTV_DS_13, MTV_IT_13, MTV_IT_14

Yr15, Yr24, YrAlp, Yr64, YrCH52, Yr65, QYr.caas-1BL.1RS_SHA3/CBRD

  IWB9661

A/G

IWB20091

1B

74.4

7.0

2.7–4.6

3.4–6.7

PSTv-37, PLM_IT_12

QYr.cim-1BS_Pastor

  IWB11136

T/G

IWB22615, IWB71860

2A

9.4

6.7

2.5–5.2

3.5–8.3

ETH_IT_12, ETH_IT_14, ETH_DS_14, PLM_IT_12, PLM_DS_12

Yr17, Yr56, QYr.tam-2AS_TAM111, QYr.uga-2AS_26R61, QYr.ufs-2AS_Cappelle Desprez

  IWB6584

A/G

IWB42693

2A

26.0

10.6

2.4–7.3

3.1–11.2

PSTv-41, ETH_IT_12, ETH_IT_14, PLM_IT_12, PLM_DS_12

  IWB57199

T/C

IWB63394

2A

47.2

9.5

2.6–6.8

3.4–9.5

PSTv-41, ETH_IT_12, ETH_IT_14, ETH_DS_14, PLM_IT_12, PLM_DS_12

QYrva.vt-2AS_VA00W-38, QYr.inra-2AL_CampRemy

  IWB24187

T/C

-

4A

114.5

19.0

2.3–4.3

2.8–6.1

MTV_DS_12, MTV_IT_14

Yr51, QYr-4A_Sachem, QYrst.orr-4AL_Stephens

  IWA1280

A/G

IWA7226, IWA8119, IWB11086, IWB58658

5A

15.7

17.7

2.1–4.6

2.7–6.1

PLM_DS_12, PLM_IT_14, ETH_IT_14

_

  IWB28837

T/C

IWB79251

5A

89.6

44.7

2.6–4.5

3.0–7.1

MTV_DS_12, MTV_IT_13

_

  IWB69846

A/G

_

6A

136.9

10.6

2.4–5.5

3.1–8.3

PLM_DS_12, PLM_IT_12

QYr-6A_Avocet, QYr-6A_Saar, QYr.ufs-6A_Kariega, YrLM168, QYr.cim-6AL_Francolin

  IWA3506

A/G

IWB33903, IWB39783

7B

56.9

64.8

2.6–5.2

3.1–8.1

PSTv-41, PLM_DS_14, MTV_IT_14, PLM_IT_12

_

  IWB58601

A/G

_

7B

155.4

5.0

2.3–5.3

3.1–8.4

PLM_IT_14, MTV_DS_14

Yr59, YrC591, Yr52, Yr67, YrZH84, QYr7BL_Strongfield, QYr.cim-7BL_Pastor

Seedling resistance

  IWB9661

A/G

IWB20091

1B

74.4

7.4

5.9

13.2

PSTv-37, PLM_IT_12

QYr.cim-1BS_Pastor

  IWB6584

A/G

IWB42693

2A

26.0

10.4

4.4

9.4

PSTv-41, ETH_IT_12, ETH_IT_14, ETH_DS_14, PLM_IT_12, PLM_DS_12

Yr17, Yr56, QYr.tam-2AS_TAM111, QYr.uga-2AS_26R61, QYr.ufs-2AS_Cappelle Desprez

  IWB57199

T/C

IWB57200

2A

47.2

11.0

4.9

10.6

PSTv-41, ETH_IT_12, ETH_IT_14, ETH_DS_14, PLM_IT_12, PLM_DS_12

QYrva.vt-2AS_VA00W-38, QYr.inra-2AL_CampRemy

  IWB43797

T/C

IWB29589, IWB81562, IWB32481

2B

134.5

33.5

6.0

13.7

PSTv-41, PSTv-106

Yr43

  IWB10441

T/G

–

2D

82.8

12.5

6.6

11.9

PSTv-106

QPst.jic-2D_Guardian

  IWB14332

T/C

–

5B

29.1

45.4

4.6

9.7

PSTv-40

Yr47, QYr.uga-5B_AGS2000

  IWB48375

T/C

IWB81061, IWB78446

5B

71.9

38.4

6.2

11.7

PSTv-14

YrEXP2, QYr.caas-5BL.1_Libellula, QYr-5B_Oligoculm

  IWA3506

A/G

IWB33903, IWB39783

7B

56.9

64.8

2.6–5.2

3.1–8.1

PSTv-41, PLM_DS_14, MTV_IT_14, PLM_IT_12

_

  1. aSNP index from the wheat 90 K iSelect assay. Within the confidence interval of the QTL, marker with the most significant associations were used as the QTL-tagging marker
  2. bUnderline indicates favorable allele
  3. cOther significant SNPs identified within the confidence interval of the QTL other than the QTL-tagging marker
  4. dScaled position from hexaploid wheat consensus map (Wang et al. 2014)
  5. eMarker-wise P value ranges - all of the 11 QTL were significant at FDR P value <0.1 in at least one environment
  6. fStripe rust IT and severity from the field experiments and response to Pst races to which the marker showed significant association at FDR-adjusted probabilities
  7. gReferences given in the text, RAF = Resistance allele frequency, Chr. = chromosome
  8. PLM_IT_12 = Pullman, infection types, 2012
  9. PLM_IT_14 = Pullman, infection types, 2014
  10. PLM_DS_12 = Pullman, disease severity, 2012
  11. PLM_DS_14 = Pullman, disease severity, 2014
  12. MTV_IT_12 = Mount Vernon, infection types, 2012
  13. MTV_IT_13 = Mount Vernon, infection types, 2013
  14. MTV_IT_14 = Mount Vernon, infection types, 2014
  15. MTV_DS_12 = Mount Vernon, disease severity, 2012
  16. MTV_DS_13 = Mount Vernon, disease severity, 2013
  17. MTV_DS_14 = Mount Vernon, disease severity, 2014
  18. ETH_IT_12 = Ethiopia, infection types, 2012
  19. ETH_IT_14 = Ethiopia, infection types, 2014
  20. ETH_DS_14 = Ethiopia, disease severity, 2014
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BMC Plant Biology

ISSN: 1471-2229

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