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Table 3 Genome-wide significant QTSs associated with five fatty acids at -log10p > 7 (at least one kind of effect of QTS)

From: Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study

Trait

QTS

aChr.

bAllele

cEffect type

Predict value

−log10p

h2(%)

Oleic

A1_44951529

A1

A/G

a

−0.276

17.8

2.98

A1_85724143

A1

C/T

a

0.094

2.57

0.35

A3_4717931

A3

C/T

a

0.139

3.99

0.76

A3

C/T

d

−0.399

8.98

3.11

A7_2266630

A7

A/G

a

0.288

18.18

3.24

A7

A/G

d

0.357

2.27

2.48

A12_120581335

A12

G/T

a

−0.275

14.45

2.95

A12

G/T

d

0.452

9.43

3.99

D1_1087912

D1

C/T

d

0.478

7.04

4.46

D1_37367501

D1

A/G

a

0.171

7.29

1.14

D3_1889546

D3

T/C

d

1.019

8.09

20.28

D5_24437741

D5

A/G

a

0.263

15.41

2.70

D5

A/G

d

−0.42

2.58

3.45

D5_31125264

D5

G/A

a

−0.079

1.59

0.24

D5

G/A

d

−0.4

8.31

3.11

D9_148268

D9

T/C

a

−0.228

9.74

2.03

D9_45944489

D9

T/C

a

0.17

7

1.13

A1_44951529 & A1_85724143

A1 & A1

A/G & C/T

aa

−0.186

8.45

2.69

Linoleic

A6_69314946

A6

T/G

a

−0.268

8

1.10

A9_23536520

A9

G/A

a

0.325

10.5

1.62

A12_117532394

A12

G/A

a

−0.255

8.42

0.99

A13_29883619

A13

T/C

a

0.388

16.99

2.30

A13

T/C

d

−0.847

7.98

5.49

D4_21291786

D4

G/A

a

−0.359

15.41

1.97

D5_47644432

D5

G/C

d

0.47

3.67

1.69

D6_59379832

D6

A/C

a

−0.275

9.34

1.15

D6

A/C

d

0.853

3.63

5.56

D4_21291786 & D5_47644432

D4 & D5

G/A & G/C

aa

−0.16

3.21

0.79

D4 & D5

G/A & G/C

ad

0.505

3.95

3.89

D4 & D5

G/A & G/C

dd

1.618

2.53

20.00

Palmitic

A1_61493378

A1

T/G

a

0.216

8.3

1.04

A1

T/G

d

0.522

1.65

3.06

A7_642514

A7

C/T

a

−0.572

51.11

7.36

A11_600080

A11

A/G

a

0.293

12.82

1.93

A12_117532394

A12

G/A

a

0.269

12.83

1.63

A13_119809048

A13

G/A

a

0.258

11.54

1.50

A13

G/A

d

1.025

6.27

11.82

D4_10313468

D4

A/C

a

−0.254

10.73

1.45

D4

A/C

d

−0.944

11.1

10.02

D5_66975738

D5

A/G

a

−0.256

10.59

1.48

D6_10836500

D6

T/C

a

−0.292

14.63

1.91

A7_642514 & D4_10313468

A7 & D4

C/T & A/C

aa

−0.219

7.76

2.17

A7 & D4

C/T & A/C

da

0.407

2.12

3.72

A7 & D4

C/T & A/C

dd

1.809

5.89

36.79

Myristic

A1_35871478

A1

C/T

a

−0.014

10.62

2.54

A1

C/T

d

−0.029

2.33

5.30

A1_54364850

A1

T/C

a

0.017

15.02

3.52

A1_67270927

A1

T/C

a

−0.014

8.52

2.34

A1

T/C

d

−0.012

1.82

0.89

A7_642514

A7

C/T

a

−0.02

18.61

4.70

A7

C/T

d

−0.029

3.05

5.00

A8_86207865

A8

G/A

a

−0.012

7.96

1.78

A12_37853320

A12

G/A

a

0.006

2.03

0.46

A12

G/A

d

0.026

7.3

4.13

A13_19834182

A13

C/T

a

0.015

9.08

2.92

A13

C/T

d

−0.026

10.99

4.25

Stearic

A4_17627308

A4

G/A

a

0.017

3.71

0.84

A4

G/A

ae1

−0.045

8.27

6.13

A4

G/A

ae2

−0.032

4.53

3.13

A4

G/A

ae3

0.07

18.95

14.79

A11_110829220

A11

A/G

a

0.025

7.46

1.83

D1_10742184

D1

T/A

a

−0.024

7.15

1.74

D10_30598593

D10

T/G

ae1

−0.019

1.51

1.04

D10

T/G

ae2

−0.039

5.18

4.52

D10

T/G

ae3

0.055

9.84

9.15

D10

T/G

de3

0.035

1.54

1.89

  1. aChromosome. A represents A genome of cotton and D represents D genome of cotton. b(Major allele/minor allele). ca, d, aa, ad, da and dd denote the additive effect, the dominant effect, the epistasis effects of the additive × additive, the additive × dominance, the dominance × additive, the dominance × dominance respectively; ae1, ae2 and ae3 denote the interaction effects of the additive with the first, the second and the third environments respectively, de3 denotes the interaction effect of the dominance with the third environment. h2 is the heritability in percentage due to each genetic effect of significant QTSs
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BMC Genomics

ISSN: 1471-2164

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