Table 5 Identification of Main Effect Qtls (MCIM) in QTLMAPPER MLM Module

SupplementationTable 1Identification of main effect QTLs (MCIM) in QTLMAPPER MLM module

Traita / QTL / Linkage group / Marker interval / Environment IDb / LODc / Ad / R2(%)e
NOP / QNOPH-1 / H / Sat_117-Satt191 / 4 / 3.90 / 0.79 / 12.92
NTP / QNTPI-1 / I / Sct_189-Satt330 / 4 / 3.77 / 1.14 / 14.73
QNTPD1b-1 / D1b / Sat_135-Satt537 / 6 / 3.56 / 1.13 / 15.34
QNTPB1-1 / B1 / Satt229-Sat_099 / 9 / 2.55 / -1.46 / 10.37
QNTPD1a-2 / D1a / Satt198-Satt273 / 11 / 4.09 / 1.33 / 21.00
NThP / QNThPD1a-1 / D1a / Satt495-Satt584 / 1 / 3.20 / 2.40 / 18.74
NTThP / QNTThPC2-1 / C2 / Satt289-Satt277 / 3 / 3.07 / -2.58 / 11.87
QNTThPC2-2 / C2 / Sat_092-Satt460 / 8 / 2.87 / -2.87 / 9.43
QNTThPB1-1 / B1 / Satt229-Sat_099 / 9 / 3.01 / -3.58 / 15.34
QNTThPB1-2 / B1 / Sat_099-Sat_113 / 11 / 4.37 / -2.43 / 13.25
QNTThPD1a-1 / D1a / Satt198-Satt273 / 11 / 4.26 / 3.09 / 21.43
QNThPD1a-2 / D1a / Satt220-Sat_112 / 3 / 4.04 / 2.27 / 14.31
NThFP / QNThFPA1-1 / A1 / Satt522-Satt571 / 7 / 4.47 / -1.99 / 12.38
QNThFPB1-1 / B1 / Sat_099-Sat_113 / 11 / 2.67 / -1.71 / 10.64
NTP / QNFPA1-1 / A1 / Sct_067-Satt545 / 5 / 4.13 / 0.76 / 14.92
QNFPB1-1 / B1 / Sat_113-Satt521 / 9 / 2.61 / -0.68 / 11.96
QNFPF-1 / F / Satt269-GMRUBP / 5 / 5.77 / -0.97 / 24.56
QNFPF-2 / F / Satt269-GMRUBP / 6 / 3.13 / -0.45 / 14.36
QNFPA1-3 / A1 / Sct_067-Satt545 / 8 / 3.33 / 0.76 / 13.91
QNFPA1-4 / A1 / Satt390-Satt218 / 10 / 3.15 / 0.48 / 9.88
SWPP / QSWPPA1-1 / A1 / Satt449-Satt155 / 1 / 3.56 / 1.04 / 6.99
QSWPPJ-1 / J / Satt431-Satt414 / 1 / 2.99 / -1.34 / 11.57
QSWPPD1a-1 / D1a / Satt373-Sat_062 / 1 / 2.83 / -1.08 / 13.10
QSWPPF-1 / F / Satt252-Satt269 / 5 / 3.79 / -1.10 / 19.79
QSWPPN-1 / N / Satt257-Satt551 / 7 / 2.87 / -1.28 / 15.48
QSWPPF-2 / F / Satt252-Satt269 / 8 / 5.86 / 2.48 / 30.22
NPPP / QNPPPB1-1 / B1 / Sat_099-Sat_113 / 11 / 2.93 / -2.53 / 10.83

a NOP, number of one-seed pod; NTP, number of two-seed pod; NThP, number of three-seed pod; NTThP, number of (two plus three)-seed per plant;

NFP, number of four-seed pod; NThFP, number of (three plus four)-seed pod; SWPP, seed weight per plant; NPPP, number of pod per plant.

bEnvironment ID 1-11: represent the 11 environments (2006 Harbin, 2006 HongXinglong, 2007 Harbin, 2007 HongXinglong, 2008 Harbin,

2008 HongXinglong, 2009 Harbin, 2009 HongXinglong, 2010 Harbin, 2010 HongXinglong, 2011 Harbin), respectively.

c LOD: log of odd.

d A: the additive effects contributed by QTL.

eR2 : R-square or phenotypic variation explained by QTL.

SupplementationTable 2 Identification of additive effect QTLs (MCIM)and additive QTLs by environments interactions (AE) in QTLMAPPER MLM module

QTL a / Marker interval / AEi b / LODAEi c / VAEi(%)d / Additive QTLs by environments interactions (AE)e
AEi1 / AEi2 / AEi3 / AEi4 / AEi5 / AEi6 / AEi7 / AEi8 / AEi9 / AEi10 / AEi11
QNTPA1-1 / Sat_087-Satt200 / 0.41 / 3.15 / 0.27 / -0.06** / 0.13** / -0.01** / 0.01** / 0.07*
QNTPC2-1 / Sat_092-Satt460 / -0.34 / 2.98 / 0.32 / 0.27** / -0.21* / -0.46** / 0.01**
QNTPD1a-1 / Satt198-Satt273 / -0.12 / 3.95 / 2.50 / -1.43** / 0.26* / -0.17** / -0.21** / 0.77* / 0.96**
QNTPD1a-2 / Satt273-Satt502 / -0.55 / 4.21 / 0.73 / -0.55** / 0.33** / -0.21** / 0.19*
QNThPD1a-1 / Sat_112-Satt373 / 0.49 / 4.83 / 0.76 / 1.43* / 0.27* / -0.01** / -0.63**
QNTThPC2-1 / Sat_092-Satt460 / -0.68 / 3.26 / 0.29 / 0.03** / 0.71* / -0.95** / 0.02*
QNThFPD1b-1 / Sat_135-Satt537 / 0.91 / 4.33 / 1.02 / -0.22** / 0.09** / 0.07* / -0.11**
QNFPA1-1 / Sct_067-Satt545 / 0.28 / 3.11 / 1.34 / 0.15** / 0.31** / -1.13* / 0.09**
QNFPA1-2 / Satt390-Satt218 / 0.25 / 3.72 / 1.08 / 0.05* / 0.15** / 0.99* / -0.24** / -1.05*
QNFPB1-1 / Sat_113-Satt521 / -0.30 / 4.57 / 1.87 / 0.81** / 0.45* / 0.02** / 0.01*
QNFPF-1 / Satt252-Satt269 / -0.27 / 3.92 / 0.54 / 0.67** / -0.03 / -0.01** / 0.11** / -0.75**
QSWPPF-1 / Satt252-Satt269 / 0.06 / 3.61 / 2.58 / 0.03* / -1.02** / 2.04** / 1.02*
QNPPPO-1 / Satt331-Satt173 / -0.24 / 2.87 / 1.73 / 0.19** / 2.98* / -1.46** / -2.11* / -0.41**

a NTP, number of two-seed pod; NThP, number of three-seed pod; NFP, number of four-seed pod; NTThP, number of (two plus three)-seed per plant; SWPP, seed weight per plant; NPPP, number of pod per plant.

b AEi: the significant additive effects contributed by additive QTLs mapped in the environments.

c LODAEi: log of odd for additive effects byenvironment effect at the current scanning position.

d VAEi: Phenotypic variation explained by additive effects byenvironment interactions at the current scanning position.

e AEi1, AEi2, AEi3, AEi4, AEi5, AEi6, AEi7, AEi8, AEi9, AEi10, AEi11 represent the additive effects contributed by QTLs by multiple environments interactions among 11 environments (2006 Harbin, 2006 HongXinglong,

2007 Harbin, 2007 HongXinglong, 2008 Harbin, 2008 HongXinglong, 2009 Harbin, 2009 HongXinglong, 2010 Harbin, 2010 HongXinglong, 2011 Harbin), respectively.

**: indicates extremely significant difference at level of P＜0.01; *: indicates significant difference at level of P＜0.05.

SupplementationTable 3 Identification of epistatic effect QTLs (MCIM)and epistatic QTLs by environments interactions (AAE) in QTLMAPPER MLM module

QTL a / Marker interval / QTL a / Marker interval / AAEij b / LODAAEij c / VAAEij(%)d / Epistasis by environments interactions (AAE) e
AAEij1 / AAEij2 / AAEij3 / AAEij4 / AAEij5 / AAEij6 / AAEij7 / AAEij8 / AAEij9 / AAEij10 / AAEij11
QNOPA1-1 / Satt200-Satt164 / QNOPG-1 / Satt199-Satt505 / 0.20 / 4.12 / 0.88 / 0.13* / -0.02** / -0.49* / -0.51** / 0.99**
QNOPA1-2 / Satt449-Satt155 / QNOPI-1 / Satt440-Sct_189 / 0.18 / 3.31 / 0.82 / 0.26** / -0.47* / -0.86** / 0.11**
QNTPB1-1 / Satt251-Satt229 / QNTPI-1 / Satt530-Satt440 / 0.19 / 3.17 / 1.53 / -0.03** / 0.07** / -0.15* / -0.28* / -0.43*
QNTPC2-1 / Satt289-Satt277 / QNTPD1a-2 / Satt182-Satt495 / 0.94 / 4.33 / 2.41 / 0.11** / 0.37** / 0.73* / 0.36**
QNTPC2-3 / Sat_120-Sat_103 / QNTPD1b-1 / Satt274-Satt459 / -0.68 / 3.95 / 1.07 / 0.05** / -0.26** / 0.45* / 0.33**
QNTPF-1 / Satt252-Satt269 / QNTPI-2 / Satt009-Satt530 / -2.17 / 3.61 / 1.39 / -0.89* / -0.24** / 0.81** / 0.01**
QNFPA1-1 / Sct_067-Satt545 / QNFPA1-2 / Satt164-Satt042 / -0.34 / 3.42 / 1.31 / -0.02** / -0.31** / -0.08** / -0.12*
QNFPA1-3 / Satt200-Satt164 / QNFPA1-4 / Satt300-Satt522 / -0.36 / 3.43 / 0.54 / 0.67** / 0.69** / 0.91** / -0.87**
QNFPA1-5 / Satt270-Satt390 / QNFPC2-1 / Satt372-Satt076 / 0.28 / 3.51 / 0.95
QNFPA1-6 / Satt390-Satt218 / QNFPD1b-1 / Satt266-Satt157 / -0.43 / 3.69 / 2.57 / 0.03** / 0.56** / 0.67** / 0.71** / 0.02**
QNFPA2-1 / Sat_036-Satt468 / QNFPG-1 / Satt505-Sat_088 / -0.33 / 3.32 / 0.78 / -0.09* / -0.35** / -0.26** / 0.91* / 0.57*
QNFPC1-1 / Satt195-Sat_042 / QNFPI-1 / Satt330-Satt292 / 0.17 / 4.27 / 0.72 / -0.21** / -0.57** / -0.62** / 0.83*
QNFPC2-2 / Sat_103-Sct_033 / QNFPD1a-1 / Sat_124-Sat_084 / -578.17 / 4.56 / 0.34 / 0.13** / 0.29** / 0.66** / 0.75* / 0.61**
QNFPC2-3 / Satt134-Satt289 / QNFPD1a-2 / Satt273-Satt502 / -0.56 / 5.13 / 0.21 / 0.33* / -0.61* / -0.86** / -0.77**
QNFPD1a-3 / Sat_124-Sat_084 / QNFPJ-1 / Satt244-Satt431 / -0.27 / 3.29 / 1.88 / 0.22* / 0.17** / -0.59** / -0.61**
QNFPD1a-4 / Satt495-Satt584 / QNFPG-2 / Satt394-Satt570 / -0.22 / 3.67 / 1.22 / -0.36** / 0.58* / 0.38** / -0.63** / 0.92*
QNFPD1a-5 / Satt584-Sat_124 / QNFPF-1 / Satt252-Satt269 / -0.19 / 5.22 / 1.12 / -0.34* / -0.02** / -0.87* / 0.69** / 0.71*
QNFPJ-2 / Satt414-Satt380 / QNFPN-1 / Satt445-Satt257 / 0.12 / 3.09 / 0.93 / -0.73* / 0.86** / -0.24** / -0.87* / -0.91**
QSWPPD1b-1 / Satt459-Sat_069 / QSWPPG-1 / Satt288-Satt012 / 0.62 / 3.49 / 1.78 / -.075** / -0.41** / -0.21** / 0.43**
QNTThPB2-1 / Sct_094-Sat_083 / QNTThPD1b-1 / Satt141-Satt041 / 0.83 / 3.16 / 0.78 / -0.36* / -0.63* / -0.67* / 0.56**
QNTThPC2-1 / Satt289-Satt277 / QNTThPL-1 / Satt278-Satt398 / 1.08 / 3.07 / 1.44 / 0.83* / 0.02** / 0.68* / -0.31* / -0.59**
QNTThPC2-2 / Satt277-Satt243 / QNTThPC2-3 / Sct_188-Satt335 / -1.01 / 4.09 / 0.60 / 0.63* / 0.52** / 0.93** / -0.82** / 0.61* / -0.11*

a NOP, number of one-seed pod;NTP, number of two-seed pod; NTThP, number of (two plus three)-seed per plant; NFP, number of four-seed pod.

b AAEi: the significant epistatic effects contributed by epistatic QTLs mapped in the environments.

c LODAAEij: log of odd for additive and epistasis effects at the current scanning position.

d VAAEij: Phenotypic variation explained by epistasis byenvironment interactions at the current scanning position.

e AAEij1, AAEij2, AAEij3, AAEij4, AAEij5, AAEij6, AAEij7, AAEij8, AAEij9, AAEij10, AEij11 represent the epistatic effect contributed by QTLs by multiple environments interactions among 11 environments (2006 Harbin, 2006 HongXinglong, 2007 Harbin, 2007 HongXinglong, 2008 Harbin, 2008 HongXinglong, 2009 Harbin, 2009 HongXinglong, 2010 Harbin, 2010 HongXinglong, 2011 Harbin), respectively.

**: indicates extremely significant difference at level of P＜0.01; *: indicates significant difference at level of P＜0.05.

Trait a / QTL / Linkage group / Marker interval / Environment ID b / LOD / Ac / R2(%)d
NOP / QNOPH-1 / H / Sat_117-Satt191 / 4 / 4.12 / 0.81 / 12.32
NTP / QNTPD1b-1 / D1b / Sat_135-Satt537 / 6 / 3.46 / 0.97 / 10.69
QNTPB1-1 / B1 / Satt229-Sat_099 / 9 / 2.78 / -1.35 / 11.41
QNTPD1a-2 / D1a / Satt198-Satt273 / 11 / 4.24 / 1.62 / 15.62
NThP / QNThPA1-1 / A1 / Sat_087-Satt200 / 7 / 3.51 / -2.03 / 16.13
QNThPD1a-1 / D1a / Satt495-Satt584 / 1 / 3.67 / 2.47 / 17.24
NTThP / QNTThPB1-1 / B1 / Sat_099-Sat_113 / 11 / 3.82 / -2.56 / 10.53
QNTThPC2-1 / C2 / Satt289-Satt277 / 3 / 3.61 / -2.74 / 13.24
QNTThPC2-2 / C2 / Sat_092-Satt460 / 8 / 5.96 / -3.01 / 11.01
QNTThPG-1 / G / Satt505-Sat_088 / 10 / 3.75 / 0.52 / 11.34
NThFP / QNThFPA1-1 / A1 / Satt522-Satt571 / 7 / 4.21 / -2.07 / 12.43
QNThFPB1-1 / B1 / Sat_113-Satt521 / 1 / 3.93 / -1.21 / 15.66
NFP / QNFPA1-1 / A1 / Sct_067-Satt545 / 5 / 4.55 / 1.33 / 19.25
QNFPA1-3 / A1 / Satt390-Satt218 / 10 / 3.67 / 0.98 / 10.77
QNFPA2-1 / A2 / Sat_036-Satt468 / 9 / 2.98 / 1.01 / 9.98
QNFPB1-1 / B1 / Sat_113-Satt521 / 9 / 4.13 / -1.53 / 24.22
SWPP / QSWPPA1-1 / A1 / Satt449-Satt155 / 1 / 3.72 / 1.09 / 7.43
QSWPPD1a-1 / D1a / Satt373-Sat_062 / 1 / 3.11 / -2.31 / 14.12
QSWPPF-1 / F / Satt252-Satt269 / 8 / 3.25 / 1.24 / 11.79
QSWPPG-1 / G / Satt505-Sat_088 / 10 / 3.77 / 0.33 / 13.26
NPPP / QNPPPB1-1 / B1 / Satt229-Sat_099 / 11 / 4.02 / 0.41 / 9.34
QNPPPD1b-1 / D1b / Sat_135-Satt537 / 6 / 3.69 / -0.82 / 13.21

SupplementationTable 4Identification of main effect QTLs (MCIM) in QTLNETWORK MLM module

a NOP, number of one-seed pod; NTP, number of two-seed pod; NThP, number of three-seed pod; NTThP, number of (two plus three)-seed per plant;

NFP, number of four-seed pod; NThFP, number of (three plus four)-seed pod; SWPP, seed weight per plant; NPPP, number of pod per plant.

bEnvironment ID 1-11: represent the 11 environments (2006 Harbin, 2006 HongXinglong, 2007 Harbin, 2007 HongXinglong, 2008 Harbin,

2008 HongXinglong, 2009 Harbin, 2009 HongXinglong, 2010 Harbin, 2010 HongXinglong, 2011 Harbin), respectively.

c LOD: log of odd.

d A: the additive effects contributed by QTL.

eR2 : R-square or phenotypic variation explained by QTL.

SupplementationTable 5 Identification of additive effect QTLs (MCIM)and additive QTLs by environments interactions (AE) in QTLNETWORK MLM module

QTL a / Marker interval / AEi b / LODAEi c / VAEi(%)d / Additive QTLs by environments interactions (AE)e
AEi1 / AEi2 / AEi3 / AEi4 / AEi5 / AEi6 / AEi7 / AEi8 / AEi9 / AEi10 / AEi11
QNTPA1-1 / Sat_087-Satt200 / 0.52 / 3.47 / 0.31 / 0.63* / -0.09** / 0.32** / -0.04** / 0.03** / 0.05*
QNTPA2-1 / Satt468-Satt327 / 0.12 / 0.43 / 1.71 / -1.99** / -0.53** / 0.01** / -1.21* / 1.38**
QNTPD1a-1 / Satt198-Satt273 / -0.77 / 0.93 / 1.21 / -1.01** / 0.33* / 0.02* / -0.21** / -0.34** / 0.56* / 0.87**
QNThPD1a-2 / Sat_112-Satt373 / 0.57 / 5.01 / 0.92 / 1.43* / 0.27* / -0.01** / -0.63**
QNThPO-1 / Satt173-Satt581 / -0.52 / 0.65 / 0.98 / 0.63** / 0.13** / 0.36* / 0.21* / -0.31** / 0.26**
QNTThPC2-1 / Sat_092-Satt460 / -0.81 / 3.64 / 0.37 / -0.07** / 0.06** / 0.557* / 0.41** / -0.82** / 0.03*
QNThFPD1b-1 / Sat_135-Satt537 / 0.98 / 4.62 / 1.33 / -0.43** / 0.07** / 0.02* / 0.17* / -0.15**
QNFPA1-1 / Satt545-Sat_087 / 0.32 / 2.30 / 1.24 / -0.41** / -0.30* / -0.37* / 0.37* / 0.3241* / 0.18**
QNFPB1-1 / Sat_113-Satt521 / -0.36 / 2.23 / 1.86 / 0.54** / -0.03** / -0.27** / 0.07** / -0.23**
QNFPF-1 / Satt252-Satt269 / -0.46 / 4.21 / 0.63 / -0.32** / 0.73** / -0.05* / -0.09** / 0.79** / -0.81**

b AEi: the significant additive effects contributed by additive QTLs mapped in the environments.

c LODAEi: log of odd for additive effects byenvironment effect at the current scanning position.

d VAEi: Phenotypic variation explained by additive effects byenvironment interactions at the current scanning position.

2007 Harbin, 2007 HongXinglong, 2008 Harbin, 2008 HongXinglong, 2009 Harbin, 2009 HongXinglong, 2010 Harbin, 2010 HongXinglong, 2011 Harbin), respectively.

**: indicates extremely significant difference at level of P＜0.01; *: indicates significant difference at level of P＜0.05.

SupplementationTable 6 Identification of epistatic effect QTLs (MCIM)and epistatic QTLs by environments interactions (AAE) in QTLNETWORK MLM module

QTL a / Marker interval / QTL a / Marker interval / AAEij b / LODAAEij c / VAAEij(%) d / Epistasis by environments interactions (AAE) e
AAEij1 / AAEij2 / AAEij3 / AAEij4 / AAEij5 / AAEij6 / AAEij7 / AAEij8 / AAEij9 / AAEij10 / AAEij11
QNOPA1-1 / Satt200-Satt164 / QNOPG-1 / Satt199-Satt505 / 0.23 / 4.57 / 0.96 / 0.17* / -0.05** / -0.87* / -0.62** / 0.03** / 0.24**
QNTPB1-1 / Satt251-Satt229 / QNTPI-1 / Satt530-Satt440 / 0.34 / 3.45 / 1.67 / -0.05** / 0.09** / 0.17** / -0.55* / -0.43* / -0.36* / -0.67*
QNTPC2-1 / Satt289-Satt277 / QNTPD1a-1 / Satt182-Satt495 / 1.02 / 4.56 / 2.98 / 0.19** / 0.57** / 0.65* / 0.43** / -0.42**
QNTPA2-1 / Satt468-Satt327 / QNTPD1a-2 / Satt198-Satt273 / -0.28 / 0.04 / 0.56 / 2.31** / -0.13* / 0.43* / 0.12** / 0.14**
QNThPD1a-1 / Satt273-Satt502 / QNThPI-1 / Satt009-Satt530 / 0.39 / 0.33 / 1.35 / -0.05** / 1.0095* / -0.12** / -1.08** / 0.77* / -0.16**
QNFPA1-1 / Satt390-Satt218 / QNFPD1b-1 / Satt266-Satt157 / -0.55 / 3.72 / 3.41 / 0.07** / 0.41** / 0.76** / 0.01** / 0.55** / 0.21**
QNFPA2-1 / Sat_036-Satt468 / QNFPG-1 / Satt505-Sat_088 / -0.52 / 3.47 / 0.93 / -0.11* / -0.34** / -0.65** / 0.87* / 0.61*
QNFPC1-1 / Satt195-Sat_042 / QNFPI-1 / Satt330-Satt292 / 0.19 / 4.37 / 0.85 / -0.53** / -0.02** / -0.61** / -0.43** / 0.01** / 0.77*
QNFPC2-1 / Sat_103-Sct_033 / QNFPD1a-1 / Sat_124-Sat_084 / -0.57 / 4.67 / 0.68 / 0.07* / 0.52** / 0.73** / 0.94** / 0.81* / 0.30**
QNFPC2-2 / Satt134-Satt289 / QNFPD1a-2 / Satt273-Satt502 / -0.79 / 6.27 / 0.64 / 0.41* / 0.37* / -0.56* / -0.23** / -0.51**
QNFPD1a-3 / Sat_124-Sat_084 / QNFPJ-1 / Satt244-Satt431 / -0.73 / 3.63 / 1.67 / 0.45* / 0.53** / -1.01** / -1.25**
QNFPD1a-4 / Satt495-Satt584 / QNFPG-2 / Satt394-Satt570 / -0.17 / 3.55 / 1.32 / -1.33** / 0.77* / 0.21** / -0.06** / 0.47*
QNFPD1a-5 / Satt584-Sat_124 / QNFPF-1 / Satt252-Satt269 / -0.32 / 5.77 / 1.69 / -0.51* / -0.13** / -0.05* / 0.87** / 0.76*
QNFPH-1 / Satt191-Satt293 / QNFPN-1 / Sat_095-Sat_091 / 0.05 / 1.21 / 0.48 / 0.44* / 0.65** / 0.68** / -0.38* / -0.56** / -0.25**
QNTThPC2-1 / Satt289-Satt277 / QNTThPL-1 / Satt278-Satt398 / 1.67 / 3.23 / 1.57 / 0.51* / 0.13** / 0.93* / -0.87* / -0.65**
QNTThPC2-2 / Satt277-Satt243 / QNTThPC2-3 / Sct_188-Satt335 / -1.33 / 4.28 / 0.91 / 0.35* / 0.49** / 0.83** / -0.67** / 0.52* / -0.03*
QSWPPC2-1 / Satt372-Satt076 / QSWPPI-1 / Satt530-Satt440 / 0.13 / 1.21 / 2.33 / 0.05** / 0.21* / -0.86* / 1.59** / -0.13**

a NOP, number of one-seed pod;NTP, number of two-seed pod; NTThP, number of (two plus three)-seed per plant; NFP, number of four-seed pod.

b AAEi: the significant epistatic effects contributed by epistatic QTLs mapped in the environments.

c LODAAEij: log of odd for additive and epistasis effects at the current scanning position.

d VAAEij: Phenotypic variation explained by epistasis byenvironment interactions at the current scanning position.

**: indicates extremely significant difference at level of P＜0.01; *: indicates significant difference at level of P＜0.05.

SupplementationTable 7 Identification of epistatic effect QTLs (ICIM) in ICIM BIP-EPI module (two-dimension scanning)

QTL a / Marker interval / QTL a / Marker interval / AA b / LODAAc / VAAj(%)d
QNTPA1-1 / Sat_087-Satt200 / QNTPB2-1 / Satt020-Sct_094 / 0.67 / 3.61 / 5.49
QNTPB1-1 / Satt251-Satt229 / QNTPI-1 / Satt530-Satt440 / -0.85 / 4.23 / 7.61
QNTPB2-2 / Satt168-Satt020 / QNTPD1b-1 / Satt266-Satt157 / 0.23 / 3.59 / 5.63
QNTPB2-3 / Satt168-Satt020 / QNTPD1a-1 / Satt198-Satt273 / -0.41 / 3.67 / 4.32
QNTPC2-1 / Satt289-Satt277 / QNTPD1a-2 / Satt182-Satt495 / 0.37 / 5.23 / 7.66
QNTPD1a-3 / Satt182-Satt495 / QNTPI-2 / Sct_189-Satt330 / -0.15 / 4.69 / 8.13
QNTPD1a-4 / Satt220-Sat_112 / QNTPF-1 / Satt252-Satt269 / -0.21 / 3.24 / 6.75
QNTPF-2 / Satt252-Satt269 / QNTPI-3 / Satt009-Satt530 / -0.42 / 5.71 / 5.32
QNTPF-3 / GMRUBP-Satt030 / QNTPJ-1 / Satt414-Satt380 / 0.31 / 6.42 / 5.64
QNTPJ-2 / Satt414-Satt380 / QNTPL-1 / Satt278-Satt398 / 0.12 / 3.77 / 8.95
QNFPA1-1 / Satt042-Satt449 / QNFPB2-1 / Satt168-Satt020 / -0.53 / 4.53 / 7.29
QNFPA1-2 / Satt390-Satt218 / QNFPC2-1 / Sct_188-Satt335 / -0.47 / 4.67 / 9.27
QNFPA1-3 / Satt390-Satt218 / QNFPD1b-1 / Satt266-Satt157 / -0.65 / 5.31 / 8.93
QNFPA2-1 / Sat_036-Satt468 / QNFPG-1 / Satt505-Sat_088 / -0.36 / 8.62 / 9.06
QNFPB1-1 / Satt509-Satt197 / QNFPD1b-2 / Satt266-Satt157 / 0.72 / 4.17 / 7.31
QNFPB1-2 / Satt509-Satt197 / QNFPG-2 / Satt394-Satt570 / -0.91 / 5.34 / 5.18
QNFPC2-2 / Sat_103-Sct_033 / QNFPD1a-1 / Sat_124-Sat_084 / -0.25 / 3.97 / 7.51
QNFPD1a-2 / Sat_001-Sat_114 / QNFPD1b-3 / Sat_135-Satt537 / 0.43 / 4.53 / 4.19
QNFPD1a-3 / Satt495-Satt584 / QNFPG-3 / Satt394-Satt570 / -0.61 / 3.79 / 5.12
QNFPD1a-4 / Satt584-Sat_124 / QNFPF-1 / Satt252-Satt269 / -0.51 / 5.86 / 5.24
QNFPD1a-5 / Satt273-Satt502 / QNFPH-1 / Satt191-Satt293 / -0.17 / 6.91 / 7.31
QNFPD1b-4 / Satt428-Satt266 / QNFPL-1 / Satt398-Sat_134 / 0.76 / 7.02 / 7.24
QNTThPC2-1 / Satt289-Satt277 / QNTThPL-1 / Satt278-Satt398 / 0.26 / 6.73 / 6.89

a NOP, number of one-seed pod; NTP, number of two-seed pod; NThP, number of three-seed pod; NTThP, number of (two plus three)-seed per plant;

NFP, number of four-seed pod; NThFP, number of (three plus four)-seed pod; SWPP, seed weight per plant; NPPP, number of pod per plant.

b AA: the significant epistatic effects contributed by epistatic QTLs interactions.

c LODAA: log of odd for epistatic effects at the current scanning position.

d VAA: Phenotypic variation explained by epistaticQTLsinteractions at the current scanning position.