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Table 2 The list of significant QTNs identified through ML-GWAS models for various agronomic and yield-related traits

From: Multi-locus genome-wide association mapping for major agronomic and yield-related traits in sorghum (Sorghum bicolor (L.) moench) landraces

Trait

QTN

Chr.

Alleles

Position (bp)

LOD

r2

Method

No of genes ± LD

DF

S1_73955151

SBI-01

T/C

73,955,151

4.09–4.59

13.22–19.38

1,5

2

 

S2_6784036

SBI-02

T/G

6,784,036

4.16–8.22

2.68–5.62

1,2,4,6

5

 

S3_68605546

SBI-03

A/C

68,605,546

4.06–5.22

4.63–9.30

1,4,5,6

1

 

S4_56965234

SBI-04

T/C

56,965,234

4.38–5.85

3.10–7.08

1,2,4,5

3

 

S6_49875883

SBI-06

G/C

49,875,883

6.60–6.66

3.39–7.53

5,6

2

 

S7_57255603

SBI-07

A/T

57,255,603

4.35–6.21

4.15–4.78

1,2

2

 

S8_53108778

SBI-08

C/T

53,108,778

4.88

6.07

1

1

 

S9_1229695

SBI-09

G/A

1,229,695

5.03–8.05

3.38–4.54

2,4

3

 

S10_7288565

SBI-10

C/G

7,288,565

4.49

7.01

4

1

DM

S1_76529338

SBI-01

A/G

76,529,338

4.45–9.13

5.14–19.59

1,2,3,4,5,6

5

 

S2_54254801

SBI-02

G/A

54,254,801

5.41–4.88

3.72–3.96

2,6

2

 

S4_7763150

SBI-04

C/T

7,763,150

4.11–5.01

3.17–4.64

2,6

2

 

S5_623466

SBI-05

A/C

623,466

4.49–5.61

3.92–8.36

3,5

1

 

S6_347535

SBI-06

G/T

347,535

4.04–7.52

2.03–5.55

1,2,4

3

 

S8_979311

SBI-08

G/C

979,311

5.29–4.55

3.07–6.60

1,3

1

 

S9_48811733

SBI-09

A/G

48,811,733

4.01–5.40

2.86–7.03

1,3,5

1

 

S10_6360162

SBI-10

T/A

6,360,162

4.16–7.60

1.60-12.75

2,5,6

4

PH

S1_67415907

SBI-01

G/T

67,415,907

10.14

7.63

6

1

 

S2_1166841

SBI-02

C/A

1,166,841

1.16–8.38

1.53–10.63

1,2,3,4,6

5

 

S3_73241417

SBI-03

T/C

73,241,417

4.22–6.40

5.14–5.22

1,4

1

 

S4_3891165

SBI-04

G/C

3,891,165

4.49–6.51

3.37–5.41

1,5,6

3

 

S5_42621428

SBI-05

G/A

42,621,428

4.05–4.50

1.28–2.75

1,4

2

 

S8_14284190

SBI-08

T/G

14,284,190

4.41–5.52

1.03–2.52

1,4

2

 

S9_15670986

SBI-09

T/A

15,670,986

5.24

5.95

4

1

 

S10_16170344

SBI-10

G/T

16,170,344

4.62–5.03

3.88–11.93

5,6

2

SNPP

S1_1359747

SBI-01

T/C

1,359,747

7.17–10.38

15.84–17.02

1

2

 

S2_59151152

SBI-02

G/A

59,151,152

4.08

7.65

5

1

 

S3_62232216

SBI-03

C/T

62,232,216

4.44–8.42

2.72–8.44

1,4,6

4

 

S8_54218786

SBI-08

A/T

54,218,786

4.37–6.10

6.85–9.50

1,4

2

 

S9_50050063

SBI-09

C/G

50,050,063

4.13–8.76

3.03-18.00

1,2,3,4,5,6

5

 

S10_46922530

SBI-10

G/A

46,922,530

4.08–5.47

4.84–8.46

2,5

2

GY

S1_7317188

SBI-01

G/T

7,317,188

4.73–17.01

1.82–12.64

2,3,4

4

 

S2_3431029

SBI-02

C/G

3,431,029

4.03–10.85

1.23–10.46

1,4,5

4

 

S3_2016729

SBI-03

C/G

2,016,729

4.20–8.23

1.57–11.11

1,3,4,5,6

8

 

S4_11012794

SBI-04

C/G

11,012,794

5.48–15.77

0.63–8.79

2,4,6

3

 

S5_70402345

SBI-05

T/A

70,402,345

5.42–6.82

0.94–5.41

2,3,4,6

2

 

S6_32754749

SBI-06

C/G

32,754,749

4.45–17.01

0.75–23.93

1,2,3,4,5,6

5

 

S7_55750504

SBI-07

T/G

55,750,504

4.39–15.43

4.89–12.56

1,3,5,6

6

 

S8_61278748

SBI-08

A/G

61,278,748

4.61–15.73

1.08

2,4,5

1

 

S9_4793890

SBI-09

C/A

4,793,890

5.58–10.82

2.56–9.01

1,2,6

3

 

S10_60795709

SBI-10

C/T

60,795,709

5.27–36.13

4.07–33.58

1,2,3,4,5,6

4

TSW

S1_25033782

SBI-01

C/T

25,033,782

4.58–4.72

12.57–16.85

1,5

1

 

S2_69362046

SBI-02

G/A

69,362,046

4.71

4.88

2

1

 

S3_64354506

SBI-03

C/T

64,354,506

4.05–5.03

4.30-14.02

1,2,4,5,6

5

 

S4_51654024

SBI-04

G/C

51,654,024

4.10–4.77

4.65–8.88

2,4

1

 

S5_14397024

SBI-05

C/A

14,397,024

6.98

16.51

2

1

 

S9_52837786

SBI-09

T/C

52,837,786

4.53–4.77

3.64–3.82

2,6

2

  1. Note: Methods 1–6 are as follows: (1) mrMLM = multi-locus random-SNP-effect mixed linear model MLM., (2) FASTmrMLM = factored spectrally transformed multi-locus random-SNP-effect mixed linear model MLM; (3) FASTmrEMMA = factored spectrally transformed multi-locus random-SNP-effect efficient mixed-model association; (4) pLARmEB = polygenic-background-control-based least angle regression plus empirical Bayes; (5) pKWmEB = polygenic-background-control-based Kruskal–Wallis test plus empirical Bayes, and (6) ISIS EM-BLASSO = iterative sure independence screening EM-Bayesian LASSO. Each row corresponds to a specific QTN associated with a trait, detailing its chromosome location, position, LOD score, R² value, the method used, and the number of associated genes
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BMC Genomics

ISSN: 1471-2164

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