Table 2 Significant QTLs associated with pod and seed number/plant and seed weight identified and mapped on eight chickpea LGs/chromosomes using an intra-specific mapping population (ICC 4958 × ICC 12968)

From: A combinatorial approach of comprehensive QTL-based comparative genome mapping and transcript profiling identified a seed weight-regulating candidate gene in chickpea

QTLs

LGs/chromosomes

Marker intervals with genetic positions (cM)

Markers associated with QTLs

2012

2013

LOD

PVE (R2%)

A

LOD

PVE (R2%)

A

Caq'PN1.1 & Caq'SN1.1

CaLG(Chr01)

Ca-IISNP18 (16.8) to Ca-IISNP20 (18.6)

Ca-IISNP18

NS

NS

NS

4.6

12.7

8.9

Caq'PN1.2 & Caq'SN1.2

CaLG(Chr01)

Ca-IISNP32 (29.5) to Ca-IISNP35 (32.1)

Ca-IISNP34

5.1

7.8

4.5

NS

NS

NS

Caq'PN1.3 & Caq'SN1.3

CaLG(Chr01)

Ca-IISNP116 (127.6) to Ca-IISNP119 (130.9)

Ca-IISNP116

8.5

12.4

6.3

7.8

14.7

5.4

Caq'PN2.1 & Caq'SN2.2

CaLG(Chr02)

Ca-IISNP330 (154.9) to Ca-IISNP332 (157.5)

Ca-IISNP331

10.5

10.8

11.4

9.8

12.4

8.9

Caq'PN3.1 & Caq'SN3.1

CaLG(Chr03)

Ca-IISNP398 (24.7) to Ca-IISNP401 (27.7)

Ca-IISNP399

6.4

9.4

10.9

NS

NS

NS

Caq'PN4.1 & Caq'SN4.1

CaLG(Chr04)

Ca-IISNP649 (12.7) to Ca-IISNP651 (123.1)

Ca-IISNP649

11.4

19.8

12.9

10.2

18.5

9.5

Caq'PN5.1 & Caq'SN5.1

CaLG(Chr05)

Ca-IISNP831 (89.1) to Ca-IISNP834 (92.5)

Ca-IISNP832

8.5

12.5

6.5

7.3

14.7

5.7

Caq'PN6.1 & Caq'SN6.1

CaLG(Chr06)

Ca-IISNP1104 (154.8) to Ca-IISNP1108 (157.6)

Ca-IISNP1106

NS

NS

NS

4.8

8.5

5.1

Caq'PN7.1 & Caq'SN7.1

CaLG(Chr07)

Ca-IISNP1332 (199.5) to Ca-IISNP1335 (202.2)

Ca-IISNP1335

5.7

6.8

10.2

NS

NS

NS

a Caq'PN8.1 & Caq'SN8.1

CaLG(Chr08)

Ca-IISNP1487 (152.9) to Ca-IISNP1489 (154.6)

Ca-IISNP1487

9.6

9.5

3.1

8.5

8.8

2.5

Caq'SW1.1

CaLG(Chr01)

Ca-IISNP151 (169.1) to Ca-IISNP154 (171.3)

Ca-IISNP152

13.8

25.8

10.7

12.6

24.5

8.9

Caq'SW1.2

CaLG(Chr01)

Ca-IISSR55 (196.5) to Ca-IISSR25 (199.5)

Ca-IISSR55

8.5

11.6

3.9

NS

NS

NS

Caq'SW1.3

CaLG(Chr01)

Ca-IISNP186 (202.6) to Ca-IISSR56 (204.9)

Ca-IISNP186

9.5

13.4

5.1

8.7

16.3

4.6

a Caq'SW2.1

CaLG(Chr02)

Ca-IISNP234 (44.2) to Ca-IISNP238 (47.6)

Ca-IISNP236

7.6

9.7

4.7

7.0

9.5

5.1

Caq'SW3.1

CaLG(Chr03)

Ca-IISNP465 (115.6) to Ca-IISNP468 (118.5)

Ca-IISNP466

NS

NS

NS

7.2

10.6

8.6

Caq'SW4.1

CaLG(Chr04)

Ca-IISNP579 (3.3) to Ca-IISNP581 (5.8)

Ca-IISNP579

8.5

10.3

4.7

7.8

11.4

3.8

a Caq'SW4.2

CaLG(Chr04)

Ca-IISNP749 (275.3) to Ca-IISNP752 (278.8)

Ca-IISNP751

6.9

9.8

7.1

6.5

8.5

6.7

Caq'SW6.1

CaLG(Chr06)

Ca-IISNP972 (13.2) to Ca-IISNP975 (16.0)

Ca-IISNP974

4.7

8.7

8.9

NS

NS

NS

  1. *Caq'PN1.1 (Cicer arietinum QTL for pod number on chromosome 1 number 1), Caq'SN1.2 (Cicer arietinum QTL for seed number on chromosome 1 number 2) and Caq'SW2.1 (Cicer arietinum QTL for 100-seed weight on chromosome 2 number 1), PVE: Percentage of phenotypic variation explained by QTLs, A: Additive effect; positive additive effect infers alleles from ICC 4958 with increasing trait values. Details regarding Ca-IISSR and Ca-IISNP markers are provided in the Supplementary Table S1.
  2. aknown QTLs from previous studies by Cobos et al. (28,44), Hossain et al. (45), Varshney et al. (22) and Gowda et al. (37). NS: non-significant QTLs.
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