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Table 2 Single nucleotide polymorphism (SNP) markers significantly (P < 0.001) associated with stem rust resistance at two growth phases (HA and SM) using general linear model (GLM

From: Genome-wide association study on stem rust resistance in Kazakh spring barley lines

Marker

Phase

Chr.

cM

P

R2

Allele

MAF, %

Effect

SCRI_RS_216088

HA

1H

122,2

1.0365E-5

0.19524

T/C

C(0.12)

T(−0.95)

BOPA1_4235-1617

HA

2H

132,6

4.7965E-4

0.1287

G/A

G(0.23)

G(0.60)

SCRI_RS_96016

HA

4H

59,5

7.6236E-4

0.11891

A/C

C(0.14)

A(−0.69)

BOPA2_12_10844

HA

5H

93,9

8.9373E-5

0.15758

A/C

A(0.23)

A(0.66)

SCRI_RS_189878

HA

6H

28,5

1.2523E-4

0.15157

T/C

C(0.14)

T(−0.78)

BOPA1_5448-298

HA

6H

44,1

6.4042E-4

0.12209

A/G

G(0.18)

A(−0.63)

BOPA1_8005-914

HA

6H

63,5

1.8827E-5

0.18494

A/G

G(0.16)

A(−0.81)

BOPA2_12_30637

HA

6H

63,5

1.8827E-5

0.18494

A/G

G(0.16)

A(−0.81)

BOPA1_7370-818

HA

6H

63,5

1.4199E-6*

0.22878

G/A

A(0.14)

G(−0.96)

SCRI_RS_152841

HA

6H

63,5

1.4199E-6*

0.22878

A/C

C(0.14)

A(−0.96)

BOPA1_6205-683

HA

6H

63,9

1.4318E-4

0.15073

A/G

G(0.18)

A(−0.70)

BOPA1_2026-302

HA

U

0

5.9975E-5

0.16635

A/G

G(0.17)

A(−0.76)

BOPA1_5611-811

HA

U

0

9.0519E-4

0.11825

G/A

G(0.16)

G(0.65)

BOPA2_12_30158

HA

U

0

3.0675E-4

0.13688

A/G

A(0.20)

A(0.65)

BOPA1_5554-1971

HA

U

0

1.4318E-4

0.15073

A/G

G(0.18)

A(−0.70)

BOPA2_12_21386

SM

3H

131,3

7.9601E-4

0.11937

C/A

A(0.39)

C(−1.05)

SCRI_RS_189710

SM

3H

135,6

9.1218E-4

0.11685

A/G

G(0.32)

A(1.09)

  1. P values indicated by star are significant after Bonferroni correction