Table 3 Genotype-phenotype association analysis results including markers that showed significant associations with berry fresh weight (BFW) (A), bunch weight (BWe) (B), berry length (BL) (C), berry width (BWi) (D) and berry volume (BV) (E), as determined in a set 13 RxS segregants with contrasting phenotypes for berry size. P-values of associations and variance explained by each SNP/InDel marker (R²) are indicated for the GLM models obtained for seasons 2010, 2011 and 2012. Statistically significant associations are highlighted with an asterisk (p < 0.05)

Marker

Chr

p-value

R²(%)

p-value

R²(%)

p-value

R²(%)

TSRNAINDELS120073669

6

0.0173*

41.6

0.1572

18.9

0.0365*

34

TSRNAINDELS120073728

6

0.0419*

32.5

0.3932

7.4

0.0925

23.6

TSRNAINDELS120073761

6

0.0419*

32.5

0.3932

7.4

0.0925

23.6

TSRNAINDELS120073788

6

0.0419*

32.5

0.3932

7.4

0.0925

23.6

TSRNASNP120668018

8

0.2449

12.1

0.0073*

12.1

0.1162

12.1

TSRNASNP120671217

8

0.2449

12.1

0.0073*

12.1

0.1162

12.1

TSRNASNP120671218

8

0.2449

12.1

0,0073*

12.1

0.1162

12.1

TSRNASNP120671409

8

0.2449

12.1

0,0073*

12.1

0.1162

12.1

TSRNASNP120206984

15

0.0339*

49.2

0.2812

49.2

0.1126

49.2

TSRNASNP120273500

17

0.0019*

59.9

0.0191*

59.9

0.0005*

59.9

TSRNASNP120275823

17

0.0019*

59.9

0.0191*

59.9

0.0005*

59.9

TSRNASNP120277213

17

0.0019*

59.9

0.0191*

59.9

0.0005*

59.9

TSRNASNP120278360

17

0.0019*

59.9

0.0191*

59.9

0.0005*

59.9

TSRNASNP120279487

17

0.0019*

59.9

0.0191*

59.9

0.0005*

59.9

TSRNASNP120280865

17

0.0019*

59.9

0.0191*

59.9

0.0005*

59.9

TSRNASNP120275548

17

0.0134*

44.0

0.1049

44.0

0.0108*

44.0

BWe 2010

Marker

Chr

p-value

R²(%)

p-value

R²(%)

p-value

R²(%)

TSRNASNP120273500

17

0.0430*

32.2

0.2441

13.3

0.0010*

67.8

TSRNASNP120275823

17

0.0430*

32.2

0.2441

13.3

0.0010*

67.8

TSRNASNP120277213

17

0.0430*

32.2

0.2441

13.3

0.0010*

67.8

TSRNASNP120278360

17

0,0430*

32.2

0.2441

13.3

0.0010*

67.8

TSRNASNP120279487

17

0.0430*

32.2

0.2441

13.3

0.0010*

67.8

TSRNASNP120280865

17

0.0430*

32.2

0.2441

13.3

0.0010*

67.8

TSRNASNP120275548

17

0.09226

23.6

0.1669

18.2

0.0025*

61.7

BL 2010

BL 2011

BL 2012

Marker

Chr

p-value

R²(%)

p-value

R²(%)

p-value

R²(%)

TSRNAINDELS120073669

6

0.0463*

31.4

0.0334*

34.9

0.0589

28.8

TSRNASNP120668018

8

0.0952

23.2

0.0273*

37.1

0.3045

9.5

TSRNASNP120671217

8

0.0952

23.2

0.0273*

37.1

0,3045

9.5

TSRNASNP120671218

8

0.0952

23.2

0.0273*

37.1

0.3045

9.5

TSRNASNP120671409

8

0.0952

23.2

0.0273*

37.1

0.3045

9.5

TSRNAINDELS120025818

15

0.2293

25.5

0.3628

0.18

0.0312*

50.0

TSRNASNP120206984

15

02293

25.5

0.3628

0.18

0.0312*

50.0

TSRNASNP120273500

17

0.0083*

48.3

0.0140*

43.6

0.0059*

51.2

TSRNASNP120275823

17

0.0083*

48.3

0.0140*

43.6

0.0059*

51.2

TSRNASNP120277213

17

0.0083*

48.3

0.0140*

43.6

0.0059*

51.2

TSRNASNP120278360

17

0.0083*

48.3

0.0140*

43.6

0.0059*

51.2

TSRNASNP120279487

17

0.0083*

48.3

0.0140*

43.6

0.0059*

51.2

TSRNASNP120280865

17

0.0083*

48.3

0.0140*

43.6

0.0059*

51.2

TSRNASNP120275548

17

0.0738

26.2

0.0471*

31.2

0.0153*

42.8

BWi 2010

BWi 2012

Marker

Chr

p-value

R²(%)

p-value

R²(%)

p-value

R²(%)

TSRNAINDELS120073669

6

0.0223*

39.1

0.0104*

46.4

0.0214*

39.5

TSRNASNP120728591

9

0.0383*

33,5

0.0434*

32.1

0.0652

27.7

TSRNAINDELS120095050

9

0.0383*

33,5

0.0434*

32.1

0.0652

27.7

TSRNASNP120729221

9

0.0383*

33,5

0.0434*

32.1

0.0652

27.7

TSRNASNP120729235

9

0.0383*

33,5

0.0434*

32.1

0.0652

27.7

TSRNASNP120730012

9

0.0383*

33,5

0.0434*

32.1

0.0652

27.7

TSRNASNP120731088

9

0.0383*

33,5

0.0434*

32.1

0.0652

27.7

TSRNASNP120731107

9

0.0383*

33,5

0.0434*

32.1

0.0652

27.7

TSRNAINDELS120095636

9

0.0383*

33,5

0.0434*

32.1

0.0652

27.7

TSRNASNP120734745

9

0.0383*

33,5

0.0434*

32.1

0.0652

27.7

TSRNAINDELS120095711

9

0.0383*

33,5

0.0434*

32.1

0.0652

27.7

TSRNASNP120735535

9

0.0383*

33.5

0.0434*

32.1

0.0652

27.7

TSRNAINDELS120025818

15

0.1045

36.3

0.4111

16.3

0.0486*

45.4

TSRNASNP120206984

15

0.1045

36.3

0.4111

16.3

0.0486*

45.4

TSRNASNP120273500

17

0.0142*

43.5

0.0053*

52.2

0.0012*

62.8

TSRNASNP120275823

17

0.0142*

43.5

0.0053*

52.2

0.0012*

62.8

TSRNASNP120277213

17

0.0142*

43.5

0.0053*

52.2

0.0012*

62.8

TSRNASNP120278360

17

0.0142*

43.5

0.0053*

52.2

0.0012*

62.8

TSRNASNP120279487

17

0.0142*

43.5

0.0053*

52.2

0.0012*

62.8

TSRNASNP120280865

17

0.0142*

43.5

0.0053*

52.2

0.0012*

62.8

TSRNASNP120275548

17

0.0461*

31.5

0.0379*

33.6

0.0067*

50.2

Marker

Chr

p-value

R²(%)

p-value

R²(%)

p-value

R²(%)

TSRNAINDELS120073669

6

0.0480*

31.0

0.0244*

38.2

0.08

25.3

TSRNASNP120185697

14

0.2961

9.9

0.0452*

31.7

0.7015

1.4

TSRNASNP120273500

17

0.0017*

60.8

0.0123*

44.8

0.011*

45.9

TSRNASNP120275823

17

0.0017*

60.8

0.0123*

44.8

0.011*

45.9

TSRNASNP120277213

17

0.0017*

60.8

0.0123*

44.8

0.011*

45.9

TSRNASNP120278360

17

0.0017*

60.8

0.0123*

44.8

0.011*

45.9

TSRNASNP120279487

17

0.0017*

60.8

0.0123*

44.8

0.011*

45.9

TSRNASNP120280865

17

0.0017*

60.8

0.0123*

44.8

0.011*

45.9

TSRNASNP120275548

17

0.0274*

37.0

0.0450*

31.7

0.0430*

32.2