Table 4 Single-population GWAS candidate QTLs.

From: Multi-population GWAS detects robust marker associations in a newly established six-rowed winter barley breeding program

Trait

Pop

Regiona

Lead SNP

MACb

p

Gene/protein functionc

PVE(%)d

6RW

2RW

6RS

2RS

Heading date

2RW

2H:25,680,956-26,781,024 bp

Marker6863

1101

4.57E-12

Ppd-H1 /Pseudo-response regulator 7

4.6

16.6

6.9

<0.1

2RW

2H:138,380,194-460,538,308 bp

Marker5780

68

7.32E-13

Histidinol dehydrogenase, chloroplastic

0.2

7.0

1.1

<0.1

6RS

2H:634,395,585-639,427,862 bp

Marker3101

81

3.21E-07

NA

<0.1

<0.1

9.7

<0.1

2RS

3H:558,347,932-562,968,862 bp

Marker11212

31

5.14E-15

NA

<0.1

<0.1

1.3

3.5

2RW

4H:589,422,386-595,541,830 bp

Marker4161

225

1.68E-12

NA

NA

7.0

<0.1

<0.1

6RW

4H:609,359,514 bp

Marker1077

393

1.54E-06

NA

6.9

1.4

0.1

NA

2RS

7H:41,824,853 bp

Marker33

34

9.86E-09

VRN3

0.2

<0.1

2.1

1.0

Lodging

2RS

1H:501,998,439-502,124,385 bp

Marker11732

60

1.68E-06

NAD-dependent epimerase/dehydratase domain-containing protein

0.8

<0.1

0.5

1.8

6RS

2H:616,147,288-644,960,866 bp

Marker7239

59

1.47E-08

HvCP3-31/Cysteine protease

1.9

3.0

19.5

0.3

2RS

3H:558,347,932-562,272,693 bp

Marker11289

30

2.13E-15

Oxidoreductase

0.3

1.3

1.8

8.8

2RS

4H:19,092,878 bp

Marker8874

365

1.43E-12

NA

3.1

NA

0.2

4.7

2RW

5H:1,331,317 bp

Marker2721

609

7.34E-10

NA

0.4

9.5

0.2

0.6

6RS

7H:611,450,495 bp

Marker4844

32

6.85E-08

NA

3.3

<0.1

12.0

<0.1

  1. NA results from the SNP marker being monomorphic in the population.
  2. Pop populations, NA not applicable.
  3. aThe associated region is defined as the interval covered by the GWAS peak, i.e. the start position corresponding to the associated SNP closest to the 5’ end of the chromosome and the end position corresponding to the associated SNP closest to the 3’ end of chromosome.
  4. bMinor allele count in the analysed population.
  5. cFor intergenic SNP markers, the closest gene is reported.
  6. dPopulation-wise percentage of additive genetic variance explained by the lead SNP marker when using the estimated SNP regressions from single-population GWAS model on 6RW, 2RW, 6RS or 2RS.
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