Table 3 Significant marker-trait associations identified at least in two of three data set in the proso millet for agronomic and grain nutrients traits.

From: Genome-wide assessment of population structure and association mapping for agronomic and grain nutritional traits in proso millet (Panicum miliaceum L.)

Trait#

SNP

Chromosome

Position

2015

2016

Combined

Gene annotation

Gene ___location

effect

p-value

effect

p-value

effect

p-value

  

BT

Proso.2_14901071

2

14,901,071

0.29

3.10E-06

  

0.22

4.10E-05

PM02G15460

PmChr02 14,899,246–14,907,188 (1)

BT

Proso.12_28525796

12

28,525,796

0.26

6.80E-06

  

0.21

4.90E-05

PM12G15280

PmChr12 28,524,818–28,527,467 (1)

DF

Proso.1_11746355

1

11,746,355

  

-4.27

1.70E-08

-4.3

2.10E-10

not on gene

 

DF

Proso.14_29825523

14

29,825,523

  

1.45

1.00E-07

1.14

9.50E-06

not on gene

 

PLHT

Proso.7_1535098

7

1,535,098

-17.02

3.60E-11

-18.05

9.00E-17

-14.79

5.50E-12

TE347748

PmChr07 1,535,090–1,535,203 (-1)

PLHT

Proso.9_39130372

9

39,130,372

  

-6.63

5.20E-07

-12

6.20E-13

not on gene

 

FLBL

Proso.17_2816771

17

2,816,771

16.48

8.80E-05

  

18.74

5.50E-06

not on gene

 

FLBL

Proso.18_4062363

18

4,062,363

-12.39

7.10E-05

-14.69

6.50E-06

  

not on gene

 

FLBL

Proso.8_9836654

8

9,836,654

25.35

1.70E-08

20.62

2.50E-06

  

PM08G11490

PmChr08 9,836,493–9,842,614 (-1)

FLBL

Proso.10_24191113

10

24,191,113

14.03

3.60E-05

  

13.93

5.10E-05

Denovo_TE096034

PmChr10 24,179,287–24,191,529 (1)

FLBL

Proso.11_27996505

11

27,996,505

-14.74

2.50E-06

  

-21.27

4.80E-08

TE013419

PmChr11 27,996,274–27,996,617 (1)

FLBL

Proso.12_41890075

12

41,890,075

35.9

1.20E-08

  

37.77

1.90E-09

not on gene

 

FLSL

Proso.7_1535098

7

1,535,098

-9.06

1.10E-09

  

-12.05

1.50E-16

TE347748

PmChr07 1,535,090–1,535,203 (-1)

FLSL

Proso.12_34047515

12

34,047,515

  

-2.28

2.90E-05

-5.45

2.70E-13

PM12G21200

PmChr12 34,040,158–34,055,027 (-1)

Nnode

Proso.16_108570

16

108,570

  

-0.39

2.10E-07

-0.38

1.20E-07

Denovo_TE035623

PmChr16 106,056–109,244 (-1)

Nnode

Proso.17_2540828

17

2,540,828

-0.33

2.10E-08

  

-0.35

3.70E-13

not on gene

 

Nnode

Proso.5_6473183

5

6,473,183

0.32

3.20E-07

  

0.24

1.20E-05

PM05G07220

PmChr05 6,472,971–6,476,956 (-1)

PANEx

Proso.11_24126769

11

24,126,769

17.56

5.40E-08

13.34

2.00E-05

  

PM11G11600

PmChr11 24,125,717–24,127,809 (-1)

PEDL

Proso.5_9265830

5

9,265,830

23.72

4.30E-05

  

24.79

1.10E-05

not on gene

 

INF.PBN

Proso.7_1535098

7

1,535,098

-1.92

5.10E-20

  

-1.97

1.60E-19

TE347748

PmChr07 1,535,090–1,535,203 (-1)

INF.PBN

Proso.16_1877646

16

1,877,646

-0.45

3.50E-05

  

-0.84

1.60E-10

not on gene

 

INF.PBN

Proso.5_15388933

5

15,388,933

-0.65

4.90E-08

  

-0.48

2.40E-05

Denovo_TE004252

PmChr05 15,388,724–15,389,433 (1)

INF.PBN

Proso.9_39804416

9

39,804,416

  

0.93

9.40E-07

0.93

1.60E-06

Denovo_TE154845

Chr PmChr09 39,802,033–39,806,828 (-1)

INFL

Proso.2_2092993

2

2,092,993

-22.21

1.90E-07

  

-17.46

1.20E-06

not on gene

 

INFL

Proso.17_3253916

17

3,253,916

15.1

4.90E-06

11.29

8.30E-05

  

PM17G03120

PmChr17 3,252,571–3,255,649 (-1)

INFL

Proso.1_8346815

1

8,346,815

54.57

4.40E-08

32.76

1.50E-05

50.59

5.10E-07

PM01G10560

PmChr01 8,343,429–8,346,938 (1)

INFL

Proso.14_27820106

14

27,820,106

18.33

2.70E-05

20.37

4.40E-07

17.72

4.90E-05

PM14G15020

PmChr14 27,818,540–27,821,281 (-1)

INFL

Proso.12_34047515

12

34,047,515

-20.85

2.20E-09

-19.12

1.10E-09

-27.48

2.00E-14

PM12G21200

PmChr12 34,040,158–34,055,027 (-1)

INFL

Proso.9_39130372

9

39,130,372

-32.21

5.20E-10

  

-28.84

3.00E-09

not on gene

 

INFL

Proso.12_41890075

12

41,890,075

31.95

2.90E-07

38.06

2.70E-10

43.61

4.50E-11

not on gene

 

DM

Proso.14_29825523

14

29,825,523

  

1.26

3.30E-05

1.42

1.80E-06

not on gene

 

GYKH

Proso.9_23681963

9

23,681,963

-305.78

2.40E-08

  

-316.15

3.40E-11

not on gene

 

HSW

Proso.12_304735

12

304,735

  

0.03

2.90E-05

0.04

2.80E-07

not on gene

 

HSW

Proso.9_22773800

9

22,773,800

  

-0.01

3.10E-05

-0.03

8.70E-10

not on gene

 

Protein

Proso.10_21439333

10

21,439,333

  

-0.62

1.90E-05

-0.53

5.80E-06

not on gene

 

Protein

Proso.14_26492521

14

26,492,521

-0.4

2.00E-05

  

-0.49

8.00E-06

not on gene

 

Protein

Proso.1_61603598

1

61,603,598

  

0.42

9.60E-06

0.41

1.30E-06

not on gene

 

Zn

Proso.17_30948407

17

30,948,407

1.01

7.10E-05

  

1.3

2.00E-06

PM17G09880

PmChr17 30,907,001–30,949,614 (-1)

Fe

Proso.17_5885921

17

5,885,921

  

2.49

1.90E-08

1.6

4.80E-05

TE311547

PmChr17 5,885,645–5,886,169 (1)

Fe

Proso.9_17145336

9

17,145,336

2.7

3.10E-07

  

2.02

1.20E-06

not on gene

 
  1. # BT = Basal tillers number; DF = Days to 50% flowering; PLHT – Plant height (cm), FLBL = Flag leaf blade length (mm); Nnode = Number of nodes on main tiller; PANEx = Panicle exsertion (mm); INF- PBN = Inflorescene primary branch number; INFL = Inflorescene length (mm); DM = Days to maturity; GYKH = Grain yield (kg/ha); HSW = 100 seed weight (g).
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