Table 2 Distribution of fiber quality, yield, seed, leaf morphology and resistance QTL across the cotton genome

c1

5

8

11

1

5

3

0

0

c2

3

0

6

5

6

0

0

0

c3

5

16

11

1

2

1

1

0

c4

2

7

7

3

1

0

0

0

c5

6

4

16

4

2

2

1

0

c6

1

6

12

3

3

8

0

0

c7

9

7

4

3

5

2

0

0

c8

2

5

3

3

1

9

0

0

c9

2

5

9

3

5

6

1

0

c10

1

4

8

2

4

1

1

1

c11

5

1

2

0

0

3

0

0

c12

7

9

11

10

7

0

1

0

c13

1

3

4

1

3

0

0

0

c14

9

8

13

5

8

4

2

1

c15

3

4

13

5

9

2

0

0

c16

10

2

10

4

2

1

1

0

c17

0

1

7

7

4

2

0

0

c18

6

6

9

4

4

4

1

0

c19

2

9

10

2

12

3

0

0

c20

2

4

5

4

6

0

0

0

c21

5

6

9

3

4

2

0

0

c22

1

0

3

4

2

2

0

0

c23

13

10

6

1

8

4

0

0

c24

26

5

17

6

9

0

1

0

c25

4

7

20

2

3

11

1

0

c26

2

14

8

5

3

1

0

0

Total

132

151

234

91

118

71

11

2

Fiber quality and yield QTL traits

Chromosome

WT

Wall thick

SLF

HI

BW

LI

LP

SCY

c1

0

0

0

0

1

0

0

1

c2

0

0

0

2

1

0

0

2

c3

0

1

0

0

0

0

1

1

c4

0

0

0

0

1

1

1

0

c5

0

1

0

0

2

1

2

0

c6

0

0

0

0

0

0

0

1

c7

0

0

0

0

0

1

3

1

c8

0

0

0

0

0

0

0

0

c9

0

1

0

0

0

1

1

3

c10

1

0

0

0

0

1

1

1

c11

0

0

0

0

1

2

3

1

c12

0

0

0

0

1

2

2

2

c13

0

0

0

0

0

0

0

1

c14

1

0

0

1

4

2

1

3

c15

0

0

0

0

1

0

1

1

c16

0

0

0

0

1

0

2

1

c17

0

0

0

0

0

0

1

0

c18

0

1

1

2

3

0

0

3

c19

0

0

0

0

0

0

0

0

c20

1

0

0

0

0

0

0

1

c21

0

0

0

0

1

0

0

0

c22

0

0

1

0

3

1

0

0

c23

0

0

0

0

1

0

3

0

c24

0

0

0

0

1

0

0

1

c25

0

0

0

0

2

1

0

2

c26

0

0

0

0

2

2

3

3

Total

3

4

2

5

26

15

25

29

Yield and seed QTL traits

Chromosome

LY

BN

LB

Gossypol

Protein

Oil

HP

EPP

LargenumFS

c1

3

0

0

0

0

1

0

0

0

c2

0

1

0

0

2

0

0

0

0

c3

1

0

0

1

3

1

1

0

0

c4

0

0

0

0

1

0

0

0

0

c5

1

0

0

0

3

1

0

0

0

c6

1

0

0

0

2

0

0

1

0

c7

2

0

0

0

0

0

0

0

0

c8

0

0

0

0

0

0

0

0

0

c9

1

0

0

0

0

0

0

0

0

c10

0

0

0

0

0

0

0

0

0

c11

0

1

0

0

0

1

0

0

0

c12

1

0

0

0

2

2

0

0

1

c13

2

0

0

1

0

0

0

0

0

c14

3

1

0

0

1

0

1

0

0

c15

1

0

0

0

2

1

0

1

0

c16

1

0

0

0

1

1

0

0

0

c17

0

0

0

0

0

0

0

0

0

c18

2

0

0

1

0

0

0

0

0

c19

0

0

0

2

3

3

0

0

0

c20

1

0

0

0

2

1

0

0

0

c21

0

1

0

0

2

3

0

0

0

c22

1

0

0

1

1

0

0

0

0

c23

0

0

1

0

0

0

0

0

0

c24

1

0

0

0

2

1

0

0

0

c25

0

0

1

0

2

0

0

0

0

c26

1

0

0

0

0

0

0

0

0

Total

23

4

2

6

29

16

2

2

1

Seed quality QTL traits

Chromosome

NOFuzFib

SW

SI

SM

c1

0

0

0

0

c2

0

0

0

1

c3

0

0

1

0

c4

0

0

0

0

c5

0

0

0

0

c6

0

0

0

0

c7

0

1

1

0

c8

0

0

0

0

c9

0

2

0

0

c10

0

0

0

0

c11

0

1

0

0

c12

2

0

0

0

c13

0

0

0

0

c14

0

0

3

0

c15

0

0

0

0

c16

0

1

0

0

c17

0

0

1

0

c18

0

0

0

0

c19

0

0

0

0

c20

0

0

0

0

c21

0

0

0

0

c22

0

0

1

0

c23

0

0

1

0

c24

0

0

1

0

c25

0

0

0

0

c26

0

0

1

0

Total

2

5

10

1

Morphological QTL traits

Chromosome

FB num

FB node

Pubescence

NFFB

HNFFB

Leaf morph

c1

0

0

1

1

0

2

c2

0

0

0

0

0

1

c3

0

0

0

0

0

1

c4

0

0

0

0

0

1

c5

1

0

0

1

0

0

c6

0

0

2

1

0

3

c7

0

0

0

0

0

0

c8

0

0

0

0

0

0

c9

0

0

0

0

0

2

c10

0

0

0

0

0

1

c11

1

0

0

1

0

0

c12

0

0

0

0

0

1

c13

0

0

0

0

0

0

c14

1

0

0

0

0

0

c15

0

1

0

0

0

6

c16

1

2

0

0

0

0

c17

0

0

0

2

1

4

c18

0

0

0

0

0

1

c19

0

0

0

0

0

0

c20

0

0

0

0

0

0

c21

0

1

0

0

0

0

c22

0

0

0

0

0

1

c23

0

0

1

0

0

0

c24

0

0

0

0

0

0

c25

0

1

2

0

0

1

c26

0

0

0

0

0

0

Total

4

5

6

6

1

25

Abiotic and biotic resistance QTL traits

Chromosome

OP

Nematode related

VW

Fusarium

Xcm

c1

2

1

0

0

0

c2

1

0

0

1

0

c3

0

2

0

0

0

c4

0

2

0

0

0

c5

0

7

6

0

1

c6

1

0

0

0

0

c7

0

13

2

0

0

c8

0

0

2

0

0

c9

0

4

1

0

0

c10

0

0

0

0

0

c11

0

17

0

0

0

c12

0

0

0

0

0

c13

0

0

0

0

0

c14

0

8

0

0

1

c15

0

4

0

1

0

c16

0

0

16

0

0

c17

0

0

0

0

0

c18

0

1

0

0

0

c19

0

6

3

0

0

c20

0

3

0

0

0

c21

0

3

2

0

0

c22

0

1

2

0

0

c23

0

2

26

0

0

c24

0

0

1

0

0

c25

1

0

0

0

0

c26

0

0

2

0

0

Total

5

74

63

2

2

Physiological and drought tolerance QTL traits

Chromosome

Chlorophyll

CIR

CT

c1

0

0

0

c2

2

0

0

c3

0

0

0

c4

0

0

0

c5

0

0

0

c6

0

0

1

c7

0

0

0

c8

0

0

0

c9

0

0

0

c10

0

0

0

c11

0

0

0

c12

0

0

0

c13

0

0

0

c14

1

1

0

c15

0

1

0

c16

0

0

0

c17

0

1

0

c18

0

0

0

c19

0

0

0

c20

0

0

0

c21

0

0

0

c22

0

0

0

c23

0

0

0

c24

0

0

0

c25

0

1

0

c26

0

0

0

Total

3

4

1