IDC tolerance-related traits such as VCR and SCMR across the stages (30, 60 and 90 DAS) showed normal distribution (Fig. 2) in the rainy seasons of 2019 and 2020. ANOVA showed significant differences for VCR and SCMR among the RILs (Supplemental Tables 3 and 4). Across the years, TMV 2 showed susceptible response to IDC over all the three stages with VCR ranging from 3.0 to 4.0 and SCMR ranging from 17.1 to 29.9, while TMV 2-NLM was found to be tolerant to IDC with VCR ranging from 1.0 to 2.0 and SCMR ranging from 28.3 to 40.2 (Table 1). Wide variation was observed among the RILs for VCR, which ranged from 1.0 to 5.0 over the three stages across the years, while SCMR ranged from 2.8-52.9 (Fig. 1b and 1c; Table 1). The average VCR score increased from VCR30 to VCR60, but it decreased in VCR90 with the recovery of some of the RILs. The average SCMR reduced from SCMR30 to SCMR60, but increased in SCMR90 again with some RILs showing recovery (Fig. 2).
Table 1
Estimates of genetic variability for tolerance to iron deficiency chlorosis among the RILs of TMV 2 and TMV 2- NLM of peanut
Traits
|
Parents
|
RILs
|
PCV
(%)
|
GCV
(%)
|
h2BS
(%)
|
GA
|
GAM
(%)
|
TMV 2
|
TMV 2-NLM
|
Mean
|
Range
|
VCR30
|
3.0
|
1.0
|
1.5
|
1.0-4.0
|
10.8
|
9.0
|
68.7
|
0.2
|
15.3
|
VCR60
|
4.0
|
2.0
|
2.0
|
1.0-5.0
|
16.7
|
16.0
|
91.5
|
0.6
|
31.5
|
VCR90
|
4.0
|
2.0
|
1.9
|
1.0-5.0
|
31.1
|
30.8
|
98.0
|
1.2
|
62.8
|
SCMR30
|
29.9
|
40.2
|
30.5
|
4.0-47.4
|
11.2
|
8.2
|
52.9
|
3.7
|
12.2
|
SCMR60
|
17.1
|
28.3
|
21.2
|
2.8-48.8
|
17.6
|
12.7
|
51.9
|
4.0
|
18.8
|
SCMR90
|
20.1
|
32.3
|
28.4
|
2.8-52.9
|
18.2
|
16.3
|
80.2
|
8.5
|
30.0
|
NPPP
|
7.8
|
3.1
|
6.1
|
1.3-17.4
|
29.7
|
26.6
|
80.4
|
3.0
|
49.2
|
PYPP
|
5.6
|
2.4
|
4.0
|
0.4-15.1
|
28.1
|
23.4
|
69.2
|
1.6
|
40.0
|
PCV: Phenotypic coefficient of variation (%); GCV: Genotypic coefficient of variation (%); h2BS: Heritability in broad sense (%); GAM: Genetic advance as percent of mean (%); VCR30: Visual chlorosis rating at 30 days after sowing (DAS); VCR60: Visual chlorosis rating at 60 DAS; VCR90: Visual chlorosis rating at 90 DAS; SCMR30: SPAD chlorophyll meter reading at 30 DAS; SCMR60: SPAD chlorophyll meter reading at 60 DAS; SCMR90: SPAD chlorophyll meter reading at 90 DAS; NPPP: Number of pod per plant and PYPP: Pod yield per plant |
Phenotypic coefficient of variation (PCV) and genotypic coefficient of variation (GCV) for VCR and SCMR increased over the stages. Highest PCV and GCV observed for VCR were 31.1% and 30.8%, respectively. SCMR showed the highest PCV and GCV of 18.2% and 16.3%, respectively. Heritability and genetic advance over mean (GAM) also increased over the stages for VCR and SCMR. The highest heritability and GAM recorded for VCR were 98.0% and 62.8%, respectively, while SCMR showed the highest heritability and GAM of 80.2% and 30.0%, respectively.
VCR across the stages showed positively significant correlations (0.3-0.7). SCMR also showed positively significant correlations (0.3-0.5). However, VCR and SCMR were significantly negatively correlated across all the three stages (-0.2 to -0.8) (Table 2). VCR across the stages showed a significantly negative correlation with the number of pods per plant (NPPP) and pod yield per plant (PYPP), while SCMR showed significantly positive correlations with productivity traits. Multiple regression analysis showed the significant coefficients for VCR60 and SCMR30 with the model showing a multiple R2 of 16.2% (F of 10.1 with p value < 0.05).
Table 2
Pearson correlation coefficients for iron deficiency chlorosis related traits among the RILs of TMV 2 and TMV 2-NLM of peanut
Traits
|
VCR30
|
VCR60
|
VCR90
|
SCMR30
|
SCMR60
|
SCMR90
|
VCR30
|
1.0
|
|
|
|
|
|
VCR60
|
0.3**
|
1.0
|
|
|
|
|
VCR90
|
0.3**
|
0.7**
|
1.0
|
|
|
|
SCMR30
|
-0.5**
|
-0.3**
|
-0.2**
|
1.0
|
|
|
SCMR60
|
-0.3**
|
-0.8**
|
-0.6**
|
0.3**
|
1.0
|
|
SCMR90
|
-0.3**
|
-0.6**
|
-0.8**
|
0.3**
|
0.5**
|
1.0
|
NPPP
|
-0.1
|
-0.3**
|
-0.2**
|
0.2**
|
0.2**
|
0.1**
|
PYPP
|
-0.0
|
-0.3**
|
-0.2**
|
0.2**
|
0.2**
|
0.2**
|
**. Correlation is significant at the 0.01 level (2-tailed); |
VCR30: Visual chlorosis rating at 30 days after sowing (DAS); VCR60: Visual chlorosis rating at 60 DAS; VCR90: Visual chlorosis rating at 90 DAS; SCMR30: SPAD chlorophyll meter reading at 30 DAS; SCMR60: SPAD chlorophyll meter reading at 60 DAS; SCMR90: SPAD chlorophyll meter reading at 90 DAS; NPPP: Number of pod per plant and PYPP: Pod yield per plant |
QTL analysis using the BLUPs over two seasons identified a total of 11 and 12 QTLs for VCR and SCMR, respectively (Fig. 3; Table 3). Among the 11 QTLs for VCR, two, four and five QTLs were detected for VCR30, VCR60 and VCR90, respectively. Among them qVCR30_Ah04-1 on chromosome Ah04 was a major QTL for VCR30 with a PVE of 20.0% and LOD value of 4.4. TMV 2-NLM contributed the favourable allele at this QTL for VCR. Two major QTLs (qVCR90_Ah13-1 and qVCR90_Ah12-1) on chromosome Ah13 and Ah12 were detected for VCR90 with a PVE of 34.4% and 10.3% and LOD values of 4.3 and 4.3 respectively.
Table 3
Identification of main effect QTLs for iron deficiency chlorosis related traits among the RILs of TMV 2 and TMV 2-NLM of peanut
Trait
|
Chr
|
Position (cM)
|
Flanking distance
|
Left marker
|
Right marker
|
LOD
|
PVE
|
Additive effect
|
VCR30
|
|
|
|
|
|
|
|
|
qVCR30_Ah04-1
|
Ah04
|
9.2
|
0.0-15.4
|
AhTE0087
|
TC11H06
|
4.4
|
20.0
|
-0.007
|
qVCR30_Ah16-1
|
Ah16
|
2.0
|
0.0-7.1
|
AhTE0242
|
AhTE0060
|
5.7
|
6.9
|
0.013
|
VCR60
|
|
|
|
|
|
|
|
|
qVCR60_Ah03-1
|
Ah03
|
130.2
|
123.2-133.8
|
AhTE1158
|
AhTE0249
|
3.1
|
6.5
|
0.042
|
qVCR60_Ah03-2
|
Ah03
|
135.8
|
133.8-141.4
|
AhTE0249
|
AhTE0164
|
4.3
|
5.7
|
0.039
|
qVCR60_Ah09-1
|
Ah09
|
111.1
|
111.1-112.7
|
AhTE0303
|
Ah09_117710533
|
3.6
|
3.4
|
-0.030
|
qVCR60_Ah14-1
|
Ah14
|
153.8
|
151.8-154.9
|
Ah14_54578739
|
Ah14_32873753
|
4.5
|
5.6
|
-0.043
|
VCR90
|
|
|
|
|
|
|
|
|
qVCR90_Ah03-1
|
Ah03
|
136.8
|
133.8-141.4
|
AhTE0249
|
AhTE0164
|
5.0
|
8.4
|
0.120
|
qVCR90_Ah12-1
|
Ah12
|
19.7
|
5.7-30.2
|
Ah02_100365825
|
Ah12_108904988
|
4.1
|
10.3
|
0.003
|
qVCR90_Ah13-1
|
Ah13
|
163.3
|
159.3-178.3
|
Ah13_80163117
|
Ah13_50074616
|
4.3
|
34.4
|
0.005
|
qVCR90_Ah18-1
|
Ah18
|
27.4
|
27.4-30.8
|
AhTE0556
|
Ah18_3399929
|
4.0
|
3.8
|
0.082
|
qVCR90_Ah18-2
|
Ah18
|
50.8
|
49.8-53.9
|
AhTE0517
|
AhTE0143
|
4.4
|
7.5
|
0.117
|
SCMR30
|
|
|
|
|
|
|
|
|
qSCMR30_Ah09-1
|
Ah09
|
111.1
|
111.1-112.7
|
AhTE0303
|
Ah09_117710533
|
4.4
|
4.1
|
0.314
|
qSCMR30_Ah11-1
|
Ah11
|
67.3
|
67.3-69.8
|
AhTE0212
|
AhTE0129
|
4.8
|
4.6
|
-0.328
|
qSCMR30_Ah13-1
|
Ah13
|
161.3
|
159.3-178.3
|
Ah13_80163117
|
Ah13_50074616
|
5.1
|
11.5
|
-0.461
|
qSCMR30_Ah14-1
|
Ah14
|
24.1
|
17.1-24.2
|
AhTE0050
|
AhTE0107
|
5.0
|
5.1
|
0.357
|
qSCMR30_Ah14-2
|
Ah14
|
32.5
|
31.4-36.2
|
Ah14_138037990
|
AhTE0001
|
4.1
|
7.3
|
0.415
|
qSCMR30_Ah15-1
|
Ah15
|
32.3
|
32.3-32.4
|
PM36
|
Ah15_142386409
|
3.6
|
3.8
|
-0.330
|
SCMR60
|
|
|
|
|
|
|
|
|
qSCMR60_Ah12-1
|
Ah12
|
129.5
|
129.5-140.9
|
Ah12_1893158
|
Ah12_12348612
|
4.0
|
3.7
|
0.526
|
qSCMR60_Ah18-1
|
Ah18
|
27.4
|
27.4-30.8
|
AhTE0556
|
Ah18_3399929
|
3.6
|
3.3
|
0.252
|
SCMR90
|
|
|
|
|
|
|
|
|
qSCMR90_Ah12-1
|
Ah12
|
21.2
|
5.7-30.2
|
Ah02_100365825
|
Ah12_108904988
|
3.8
|
11.7
|
-0.251
|
qSCMR90_Ah12-2
|
Ah12
|
27.7
|
5.7-30.2
|
Ah02_100365825
|
Ah12_108904988
|
4.2
|
5.6
|
-0.834
|
qSCMR90_Ah18-1
|
Ah18
|
49.8
|
49.8-53.9
|
AhTE0517
|
AhTE0143
|
3.6
|
3.3
|
0.582
|
qSCMR90_Ah19-1
|
Ah19
|
65.2
|
65.2-67.1
|
Ah19_155127338
|
Ah19_155127364
|
3.8
|
3.5
|
0.659
|
Chr: Chromosome; LOD: Logarithm of odds; PVE: Phenotypic variance explained; |
VCR30: Visual chlorosis rating at 30 days after sowing (DAS); VCR60: Visual chlorosis rating at 60 DAS; VCR90: Visual chlorosis rating at 90 DAS; SCMR30: SPAD chlorophyll meter reading at 30 DAS; SCMR60: SPAD chlorophyll meter reading at 60 DAS and SCMR90: SPAD chlorophyll meter reading at 90 DAS |
Among the 12 QTLs for SCMR, six, two and four QTLs were detected for SCMR30, SCMR60 and SCMR90, respectively (Fig. 3; Table 3). Among them, qSCMR30_Ah13-1 on chromosome Ah13 was a major QTL for SCMR30 with a PVE of 11.5%. Likewise, qSCMR90_Ah12-1 on chromosome Ah12 was a major QTL for SCMR90 with a PVE of 11.7%. Of the two QTLs detected for SCMR60, the highest PVE of 3.7% was observed for qSCMR60_Ah12-1.
In total, two QTL clusters were identified for VCR and SCMR. Cluster 1 of 24.5 cM (5.7-30.2 cM) flanked by Ah02_100365825 and Ah12_108904988 on Ah12 chromosome was common for VCR90 and SCMR90. It showed the maximum PVE of 10.3% and 11.7% for VCR90 and SCMR90, respectively. Cluster 2 of 19 cM (159.3-178.3 cM) region flanked by Ah13_80163117 and Ah13_50074616 on chromosome Ah13 controlled VCR90 and SCMR30 with the PVE of 34.4% and 11.5%, respectively (Table 3).
Single marker analysis showed the significant association (LOD more than the threshold calculated using 1,000 permutations) of four markers (AhTE1144, AhTE0087, AhTE0120 and AhTE0242) for VCR30. The marker AhTE1144 showed the highest PVE of 7.7% followed by AhTE0242 (7.4%). AhTE0087 with a PVE of 6.3% was found in the vicinity of the major QTLs qVCR30_Ah04-1 (Supplemental Table S5). An attempt was made to find epistatic QTLs for VCR and SCMR. However, genomic regions with epistatic interactions were not identified. Multiple QTL mapping could identify the same major QTLs for all the traits.
Candidate gene discovery resulted in the identification of 300 genes in cluster 1 flanked by Ah02_100365825 and Ah12_108904988 and 259 genes in cluster 2 flanked by Ah13_80163117 and Ah13_50074616 (Supplemental Tables S6 and S7). All the markers showing significant association with VCR30 through single marker analysis were non-genic. However, an SNP marker Ah14_138037990, which showed a PVE of 4.3% with a LOD score of 3.0 for VCR30 was located in the intronic region of Arahy.QA0C1 (on chromosome Ah14) which is known to have protein binding function.