Javed Akhatar and Surinder Singh Banga
Genome-Wide Association Mapping for yield components and root traits in Brassica juncea (L.) Czern & Coss.
Molecular Breeding
Javed Akhatar and Surinder Singh Banga
Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
Corresponding author: S.S. Banga ()
Table S1 List of the 48 genotypes included in the panel with their country of origin and description
S.N. / Genotype / Origin / Description1 / NPJ79/In_HE / India / high erucic acid line
2 / QM7-335/In_LE / India / low erucic acid line
3 / K9-108/In_LE / India / low erucic acid line
4 / NLM80/In_LE / India / low erucic acid line
5 / RLC1/In_LE / India / low erucic acid line
6 / PLM2/In_LE / India / low erucic acid line
7 / MLM19/In_LE / India / low erucic acid line
8 / VARUNA/In_HE / India / high erucic acid line
9 / QM7-196/In_LE / India / low erucic acid line
10 / NLM13/In_LE / India / low erucic acid line
11 / K109-113/In_LE / India / low erucic acid line
12 / PLM4/In_LE / India / low erucic acid line
13 / EC564646/Ch_LE / China / low erucic acid line
14 / EC564647/Ch_HE / China / high erucic acid line
15 / ELM303/In_LE / India / low erucic acid line
16 / JM06006/In_LE / Australia / low erucic acid line
17 / JJ210-5-4/In_Al / India / alloplasmic lines
18 / JM06021/In_LE / Australia / low erucic acid line
19 / ELM134/In_LE / India / low erucic acid line
20 / ELM123/In_LE / India / low erucic acid line
21 / JM06026/Aus_LE / Australia / low erucic acid line
22 / JM06010/Aus_LE / Australia / low erucic acid line
23 / JC1359-23-558/In_Al / India / alloplasmic lines
24 / JA56/Aby_Al / India / Erucastrum abyssinicum alloplasmic line
25 / ELM151/In_LE / India / low erucic acid line
26 / ELM108/In_LE / India / low erucic acid line
27 / ABBY-RLC1/Aby_Int / India / Erucastrum abyssinicum introgression line
28 / JPM2/In_HE / India / high erucic acid line
29 / RLM619/Ca_Al / India / Diplotaxis cardaminoides alloplasmic line
30 / JT152-2/Te_Int / India / Diplotaxis tenuisiliqua introgression line
31 / M633/Ca_Int / India / Diplotaxis cardaminoides introgression line
32 / M379-1/Ca_Al / India / Diplotaxis cardaminoides alloplasmic line
33 / JR049/Ca_Al / India / Diplotaxis cardaminoides alloplasmic line
34 / JT152-1/Te_Int / India / Diplotaxis tenuisiliqua introgression line
35 / CP98/Ca_Int / India / Diplotaxis cardaminoides introgression line
36 / M305/Ca_Int / India / Diplotaxis cardaminoides introgression line
37 / CP117/Ca_Int / India / Diplotaxis cardaminoides introgression line
38 / MCP632/Ca_Int / India / Diplotaxis cardaminoides introgression line
39 / EKLA/EE / East European / Brassica nigra cytoplasm
40 / NRCDR2/In_HE / India / high erucic acid line
41 / PUSA-BOLD/In_HE / India / high erucic acid line
42 / RL1359/In_HE / India / high erucic acid line
43 / NRCHB101/In_HE / India / high erucic acid line
44 / PBR357/In_HE / India / high erucic acid line
45 / PBR97/In_HE / India / high erucic acid line
46 / PBR91/In_HE / India / high erucic acid line
47 / EC564649/Ch_HE / China / high erucic acid line
48 / PBR210/In_HE / India / high erucic acid line
Table S2 Water (mm) use by B. juncea in year 201-12 and 2012-13 under control (C) and restricted moisture (RM) condition.
Water source / 2011-12 / 2012-13C / RM / C / RM
Irrigation water / 180.0 / 60.0 / 180.0 / 60.0
Rainfall water / 65.2 / 65.2 / 155.6 / 155.6
Total water (mm) / 245.2 / 125.2 / 335.6 / 215.6
Table S3 Basic descriptive statistics of yield contributing and root traits in nuclear groups (NG) defined by structure analysis, in term of their mean±SE with range (in bracket) in control and restricted moisture condition in both year (2011-12 and 2012-13).
Traits / 2011-12 / 2012-13Control / Restricted Moisture / Control / Restricted Moisture
NG-1 / NG-2 / NG-3 / Mean / NG-1 / NG-2 / NG-3 / Mean / NG-1 / NG-2 / NG-3 / Mean / NG-1 / NG-2 / NG-3 / Mean
Plant Height (cm) / 182.1±2.16
(163.4-199.8) / 182.9±6.28
(154.6-205.3) / 179.1±3.94
(157.1-205.4) / 181.3 / 175.6±2.84
(151.3-197) / 171.4±5.92
(140.7-192.7) / 174.3±2.97
(153.9-194.7) / 173.8 / 157.6±2.8
(125.7-180.6) / 161.3±4.4
(146.1-178.8) / 163.8±3.52
(139-187.1) / 160.9 / 165.4±1.97
(140.8-184.8) / 162.6±4.43
(147.8-178.4) / 164±3.29
(143.5-193.8) / 164.0
Primary Branches / 6±0.14
(4.9-7.5) / 6.1±0.36
(4.7-7.8) / 6.1±0.19
(4.8-7.1) / 6.1 / 5.6±0.08
(4.9-6.4) / 5.3±0.14
(4.8-5.9) / 5.7±0.14
(5.1-6.7) / 5.5 / 6.4±0.09
(5.4-7.3) / 6.5±0.11
(5.9-6.9) / 6.5±0.14
(5.6-7.6) / 6.5 / 5.5±0.12
(4.6-7.1) / 5.6±0.2
(4.5-6.3) / 5.6±0.15
(4.6-6.9) / 5.6
Secondary Branches / 15.9±0.4
(11.1-19.7) / 15.9±0.67
(11.9-18) / 16.1±0.6
(12.8-21) / 16.0 / 14.2±0.25
(12-16.4) / 12.8±0.53
(11.1-15.3) / 13.9±0.74
(9.9-21.3) / 13.6 / 16.4±0.6
(12.3-22.3) / 16.5±0.94
(14.1-21.6) / 18.1±0.62
(14.8-23.2) / 17.0 / 18.6±0.52
(14.8-24.3) / 18.4±0.44
(16.7-20.4) / 18.1±0.72
(11.8-24.7) / 18.4
Pods on Main Shoot / 46.2±0.82
(35-53.7) / 44.1±1.76
(37.4-52.6) / 44±1.14
(37.1-49.4) / 44.8 / 40.5±0.89
(30.1-48) / 39±1.23
(33.4-43.1) / 39.8±0.74
(35-45.2) / 39.7 / 37.9±1.14
(24.6-46.2) / 39.6±1.01
(34.2-42.2) / 41±0.76
(36.9-45.3) / 39.5 / 42.7±0.83
(35.3-52.4) / 40.6±2.21
(29.2-48.2) / 42.3±1.11
(35.7-54) / 41.9
Seeds per Pod / 158.3±4.98
(122-207.9) / 158.9±5.88
(131.9-180.8) / 154.3±6.03
(111-199.8) / 157.2 / 141.3±4.92
(91.6-186.6) / 138.7±10.1
(96.4-183.7) / 141.7±4.86
(103.5-179.5) / 140.6 / 163.1±4.04
(114.6-197.9) / 156.4±6.24
(130.7-182.3) / 151.1±5.44
(110.3-188.6) / 156.9 / 147.9±4.06
(110.6-184.1) / 161.2±10.9
(125.3-213.4) / 142.1±5.96
(113.1-191.6) / 150.4
Thousand Seed Weight (gm) / 3.12±0.09
(2.41-3.88) / 3.14±0.2
(2.52-4.03) / 2.89±0.13
(1.47-3.59) / 3.05 / 3.31±0.12
(2.2-4.5) / 3.04±0.18
(2.43-4.03) / 3.05±0.16
(1.84-4.02) / 3.13 / 3.51±0.18
(2.08-5.77) / 3.73±0.26
(2.64-4.69) / 3.26±0.2
(1.58-4.74) / 3.50 / 3.81±0.23
(2.47-6.69) / 3.85±0.32
(2.4-5.07) / 3.42±0.25
(1.09-4.84) / 3.7
Grain Yield (kg/ha) / 2048±105
(973-3134) / 2002±129
(1635-2586) / 1796±134
(424-2588) / 1948.7 / 1940±102
(743-3010) / 1877±194
(1305-2775) / 2090±184
(360-3189) / 1969 / 1516.8±92.9
(634.4-2149) / 1575±196
(495-2303) / 1509±122
(539-2246) / 1533.6 / 1506.2±89.7
(715.6-2171.5) / 1556±165
(675-2202) / 1535±111
(642-2303) / 1532.4
Root Area (mm2) / 3756±190
(2305-6164) / 4077±370
(3087-5973) / 4072±232
(2559-6483) / 3968.3 / 3790±212
(1297-6049) / 3768±484
(2453-6087) / 3968±334
(1640-6027) / 3842 / - / - / - / - / - / - / - / -
Root Average Diameter (mm) / 1.984±0.05
(1.444-2.479) / 1.994±0.08
(1.713-2.358) / 1.930±0.04
(1.715-2.397) / 1.969 / 2.039±0.04
(1.456-2.454) / 2.01±0.1
(1.61-2.566) / 2.104±0.09
(1.56-3.035) / 2.051 / - / - / - / - / - / - / - / -
Root Length (mm) / 2396±167
(1314-4395) / 2367±215
(1542-3450) / 2501±284
(602-5373) / 2421.3 / 2077±172
(477-4114) / 2278±301
(1336-3378) / 3133±475
(1355-8106) / 2496 / - / - / - / - / - / - / - / -
Root Perimeter (mm) / 3524±173
(2207-5137) / 3675±339
(2872-5309) / 3853±222
(2260-6161) / 3684 / 3478±189
(1532-5483) / 3369±505
(2041-6364) / 3549±329
(1204-5994) / 3465.3 / - / - / - / - / - / - / - / -
Drought Susceptible Index / (NG-1) 1.062±0.39
(2.493-5.305) / (NG-2) 0.782±0.65
(-1.301-4.309) / (NG-3) 1.133±0.61
(-3.443-7.884) / 0.992 / (NG-1) 1.732±0.47
(-1.964-8.426) / (NG-2) 1.467±0.51
(0.012-4.171) / (NG-3) 1.182±0.28
(-0.611-2.993) / 1.46
Table S4 Analysis of Deviance (ANODA) for generalized linear model calculated by F-statistics of 8 yield contributing and 4 root traits of 48 Brassica juncea accessions across 2 years and 2 environments with 2 replications.
Source / Df / Plheight / Pmy branches / Secy branches / Pods/main shoot / Seeds/pod / Seed size / Yield / Root area / Rootdia / Root length / Rootperi / DSIYear / 1 / 103.53*** / 6.35* / 59.59*** / 9.14** / 1.90 / 39.95*** / 78.35*** / - / - / - / - / 1.99
Treatment / 1 / 0.72 / 77.77*** / 1.03 / 3.00 / 19.69*** / 5.81* / 0.05 / 0.34 / 7.78** / 0.03 / 2.27 / -
Replication / 1 / 12.39*** / 21.29*** / 31.27*** / 0.93 / 33.69*** / 22.55*** / 0.03 / 5.44* / 9.17** / 6.36* / 7.32** / 0.28
Genotype / 47 / 1.59* / 1.32 / 1.31 / 0.75 / 0.92 / 4.24*** / 3.41*** / 2.79*** / 3.2*** / 1.28 / 2.98*** / 1.39
Year × Environment / 1 / 12.87*** / 6.3* / 24.21*** / 44.33*** / 1.14 / 0.40 / 0.05 / - / - / - / - / -
Year × Replication / 1 / 0.13 / 35.32*** / 6.89** / 45.96*** / 0.06 / 30.91*** / 0.09 / - / - / - / - / 2.03
Year × Genotype / 47 / 1.21 / 0.81 / 0.90 / 0.75 / 0.94 / 2.12*** / 2.14*** / - / - / - / - / 1.01
Environment × Replication / 1 / 0.15 / 7.88** / 7.57** / 9.93** / 0.00 / 0.00 / 9.68** / 0.59 / 2.54 / 3.67 / 1.42 / -
Environment × Genotype / 47 / 0.86 / 0.93 / 0.70 / 0.87 / 0.82 / 1.14 / 0.52 / 2.17*** / 1.77** / 1.27 / 1.48 / -
Year × Environment × Genotype / 47 / 0.79 / 0.79 / 0.93 / 0.84 / 1.09 / 1.03 / 0.52 / - / - / - / - / -
Residuals / 189 / 189 / 189 / 189 / 189 / 189 / 189 / 189 / 94 / 94 / 94 / 94 / 94
*P < 0.05, **P < 0.01 and ***P < 0.001
Plant Height (Plheight), Primary Branches (Pmybranches), Secondary Branches (Secybranches), Pods on Main Shoot (Pods/mainshoot), Seed per Pod (Seeds/pod), Thousand Seed Weight (Seed size), Grain Yield (Yield), Root Area (Root area), Root Average Diameter (Rootdia), Root length (Root length), Root Perimeter (Rootperi) and Drought Susceptible Index (DSI)
Table S5 Coefficient of correlation (r) between yield contributing and root traits under control (C), restricted moisture (RM) condition and drought susceptible index (DSI) over the two years (2011-12 and 2012-13).
Traits / RM / RM / C / C2011-12 / 2012-13 / 2011-12 / 2012-13
Plant Height (cm) / 0.531*** / 0.574*** / NS / NS
Primary Branches / 0.673*** / NS / 0.528*** / 0.338*
Secondary Branches / NS / 0.919*** / NS / 0.532***
Pods on Main Shoot / 0.795*** / 0.564*** / 0.432** / 0.928***
Seeds per Pod / 0.671*** / 0.612*** / NS / 0.819***
Thousand Seed Weight (gm) / 0.828*** / NS / 0.379* / 0.799***
Grain Yield (kg/ha) / NS / NS / 0.662*** / NS
Root Area (mm2) / NS / - / 0.447** / -
Root Average Diameter (mm) / 0.994*** / - / 0.35* / -
Root Length (mm) / NS / - / 0.401** / -
Root Perimeter (mm) / NS / - / 0.309* / -
NS not significant
* P < 0.05, ** P < 0.01, *** P < 0.001
Table S6 Canonical coefficients between co-variables (Traits) and cononical variables (drought susceptible index; DSI).
Traits / RM / RM / C / C2011-12 / 2012-13 / 2011-12 / 2012-13
Plant Height (cm) / 0.027 / -0.034 / 0.039 / 0.007
Primary Branches / 0.699 / 1.634 / -0.871 / -0.687
Secondary Branches / 0.034 / -0.334 / 0.196 / 0.305
Pods on Main Shoot / -0.029 / 0.024 / 0.025 / 0.015
Seeds per Pod / 0.000 / -0.004 / -0.032 / 0.006
Thousand Seed Weight (gm) / 0.523 / -0.094 / 0.714 / 0.949
Grain Yield (kg/ha) / 0.545 / -0.001 / 0.001 / 0.002
Root Area (mm2) / 0.000 / - / -0.001 / -
Root Average Diameter (mm) / 0.557 / - / -0.396 / -
Root Length (mm) / 0.001 / - / 0.000 / -
Root Perimeter (mm) / 0.000 / - / 0.001 / -
Table S7 Details of SSR molecular markers.
Chromosome / Number of markers / Number of double alleles / Average Inter-Marker Distance (standard deviation) / Number of Associated markersUnmapped / 34 / 55 / Unmapped / 2
A1 / 11 / 18 / 41.2(28.3) / 0
A2 / 5 / 5 / 57.8(13.0) / 1
A3 / 11 / 16 / 67.0(48.8) / 1
A4 / 7 / 8 / 44.3(32.6) / 0
A5 / 10 / 15 / 63.6(34.2) / 0
A6 / 5 / 8 / 83.0(24.1) / 2
A7 / 7 / 14 / 74.4(19.5) / 1
A8 / 7 / 18 / 50.3(13.6) / 0
A9 / 11 / 14 / 67.3(42.3) / 0
A10 / 5 / 8 / 48.0(36.1) / 0
B1 / 6 / 9 / 42.4(23.9) / 0
B2 / 4 / 6 / 25.3(47.5) / 1
B3 / 6 / 7 / 48.2(38.0) / 3
B4 / 8 / 13 / 47.2(26.5) / 0
B5 / 7 / 9 / 25.6(21.6) / 1
B6 / 6 / 6 / 58.0(31.9) / 0
B7 / 4 / 4 / 40.6(17.5) / 0
B8 / 3 / 6 / 43.9(20.9) / 1
Average / 6.8 / 10.2 / 51.6(15.4)
Table S8 Results from FDR program QVALUE in four models.
Model / π0 / π1 ≡ 1 - π0GLM (Q) / 0.98037 / 0.01963
MLM (Q+K) / 1 / 0
GLM (PC) / 0.97928 / 0.02072
MLM (PC+K) / 0.96762 / 0.03238
π0 = overall proportion of true null hypotheses (FDR)
π1 = proportion of significant results