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Table 5 Summary of the combinations used for clustering by MetaQTL

From: Meta-analysis of cotton fiber quality QTLs across diverse environments in a Gossypium hirsutum x G. barbadenseRIL population

        

RIL experimental site$

BC$

 

Chr

Trait

Total QTLs

Parent

Total clusters identified*

Meta - cluster designation

Clusters coalesced into Meta - clusters

cM

Ge6

Cs7

Mp7

Br7

Ga7

Lu7

Cs8

Mp8

Lu8

Br8

Cs9

BC1

BC2

BC2S1

Confirms litera - ture

2

Fineness

18

Gua

3(+ 1)

FIN_2

1 + 2 + 3

23 + 36 - 43

   

x

x

x

 

x

  

x

 

(x)

x

yes (# loc)

 

Elongation

6

Gua

1

ELO_2

1

46

NA

NA

NA

  

NA

x

x

 

x

x

   

yes

3

Length

26

VH8

3(+ 1)

LEN_3

2 + 3

36 - 47

   

x

x

x

 

(x)

 

(x)

 

x

x

x

yes

 

Strength

9

VH8

1(+ 3)

STR_3

4

110

 

NA

 

x

 

x

 

x

 

x

x

(x)

 

(x)

yes

 

Fineness

15

VH8

3

indicative

3

(101)

 

x

 

x

 

x

     

x

(x)

(x)

yes (# loc)

4

Length

9

Gua

1

LEN_4

1

67

 

x

x

 

x

x

x

x

      

yes

5

Fineness

11

Gua

4

indicative

1 + 2 + 3

(25 - 45 - 50)

  

x

x

   

x

x

 

x

   

yes

 

Length

11

Gua

3(+ 1)

indicative

1 + 2 + 3

(22 - 32 - 49)

x

x

x

     

x

 

x

   

yes

6

Color

13

Gua

3

COL_6

3

35 - 45 - 51

 

NA

x

x

x

x

NA

 

NA

x

NA

x

 

x

yes

8

Color

34

Gua

7

COL_8A

2 + 3 + 4

46 - 51 - 54

x

NA

x

x

x

 

NA

x

NA

 

NA

    
     

COL_8B

5 + 6 + 7 + 8

84 - 88 - 109 - 121

 

NA

x

   

NA

 

NA

x

NA

x

 

x

yes

9

Fineness

25

VH8

4(+ 3)

FIN_9A

1 + 2 + 3

20 - 41 - 51

x

  

x

   

x

 

x

x

  

x

 
     

FIN_9B

6 + 7

95 - 102

    

x

x

 

x

      

yes

 

Length

8

Gua

3

LEN_9

1 + 2 + 3

18 - 36 - 39

x

    

x

x

x

      

yes (oppos)

10

Fineness

16

VH8

5(+ 1)

FIN_10

3 + 4 + 5

58 - 70 - 81

  

x

  

x

x

   

x

(x)

 

x

yes

12

Fineness

20

VH8

2(+ 4)

FIN_12

1 + 2

4 - 14

(x)

x

 

(x)

(x)

x

x

x

 

x

x

   

yes

15

Fineness

30

VH8

6

FIN_15

2 + 3 + 4 + 5

62 - 67 - 73 - 84

 

x

 

x

x

x

(x)

 

x

x

x

 

(x)

(x)

yes

 

Elongation

10

Gua

2(+ 2)

ELO_15

2 + 3

68 - 72

NA

NA

NA

x

x

NA

x

  

x

   

(x)

yes

16

Fineness

10

VH8

6

indicative

1 + 2 + 3

(41 - 50 - 64)

 

(x)

 

x

(x)

x

(x)

x

      

yes

17

Fineness

14

VH8

2

FIN_17

1 + 2

18 - 28

 

x

x

x

x

   

x

x

    

yes

18

Fineness

17

VH8

5

FIN_18

3

49

 

x

x

 

x

(x)

 

x

(x)

 

x

x

 

(x)

yes (oppos)

19

Elongation

14

Gua

5

indicative

1 + 2 + 3/4 + 5†

(83 - 148)

NA

NA

NA

x

x

NA

   

x

 

x

x

x

yes

 

Length

15

Gua

5

indicative

2 + 3 + 4

(64 - 101)

x

    

x

 

x

   

x

 

x

yes (oppos)

 

Fineness

18

Gua

7

indicative

2 + 3 + 4 + 5/6 + 7†

(51 - 200)

x

 

x

  

x

x

x

x

  

x

x

 

yes (oppos)

21

Strength

7

VH8

2(+ 2)

STR_21

2 + 3

75 - 80

(x)

NA

(x)

  

(x)

x

 

x

 

x

   

yes

 

Fineness

23

VH8

7 + 1

FIN_21A

2 + 3 + 4 + 5

65 - 73 - 81 - 93

 

x

 

x

 

x

 

x

  

x

 

x

x

yes

     

FIN_21B

6 + 7 + 8

129 - 149 - 163

   

x

 

x

x

 

x

x

  

x

x

yes

23

Length

10

VH8

2 + 1

LEN_23

2 + 3

98 - 117

    

x

   

(x)

x

 

x

x

x

yes (# loc)

 

Strength

9

VH8

2(+ 2)

indicative

3 + 4

(86 - 102)

 

NA

         

x

x

x

yes

24

Length

7

VH8

1(+ 1)

LEN_24

1 + 2

67 - 75

x

  

x

  

x

   

x

   

yes (# loc)

25

Color

25

Gua

5(+ 1)

COL_25A

1 + 2 + 3

46 - 57 - 66

 

NA

x

x

x

 

NA

 

NA

x

NA

x

x

x

yes

     

COL_25B

4 + 5

80 - 84

 

NA

x

x

x

x

NA

 

NA

 

NA

 

x

  
 

Fineness

25

VH8

5

FIN_25

2

48 - 60

 

x

  

(x)

 

x

x

 

x

x

 

x

 

yes

26

Length

16

Gua

5

indicative

1 + 2/3/4 + 5†

(8 to 94)

x

    

x

x

x

    

x

x

yes (oppos)

  1. * the 1st number represents the number of "reliable" clusters supported by QTLs from multiple experimental sites. Additional clusters represented by isolated QTLs are shown in parentheses
  2. $ x, indicates that meta-cluster was supported by QTL detected at this experimental site, (x) that isolated QTLs was observed, NA that the trait was not measured
  3. † the slash separates groups of clusters suspected to delineate different indicative meta-clusters
  4. Summary of the 30 trait x chromosome combinations used for clustering by MetaQTL software and of 25 highly supported meta-clusters. Total of QTLs (LOD>2) detected, shared direction of additivity (toward Guazuncho-2 (GUA), G. hirsutum, or VH8-4602 (VH8), G. barbadense, parent), number of clusters in best clustering model as proposed by MetaQTL (following Akaike-information criterion), names and positions of highly supported clusters and meta-clusters, and indication for an occurrence of at least one congruence (same region and same directionality Gh/Gb) with QTL reported in the literature. Meta-cluster designation (trait acronym and chromosome) is suffixed with a letter (A, B) when several meta-cluster are mapped on the same chromosome.
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BMC Plant Biology

ISSN: 1471-2229

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