<p>Mapping QTLs and meta-QTLs for two inflorescence architecture traits in multiple maize populations under different watering environments</p><p>Xiaoqiang Zhao1,2,3, Yunling Peng1,2,3*, Jinwen Zhang1,2,3, Peng Fang1,2,3, Boyang Wu1,2,3</p><p>1 Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China 2 Gansu Provincial Key Lab of Aridland Crop Science, Lanzhou 730070, China 3 College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China</p><p>* To whom correspondence should be addressed. Email: [email protected] Phone: 86-931-763-1145 Fax: 86-931-763-1145</p><p>1 Supplementary Table S1 Collection of corresponding original mapping datasets of QTLs for TBN and EN in maize</p><p>Populations Map length (cM) No. of QTLs References D types sizes NE SSRs RFLPs AFLPs TBN E</p><p>Mo17 x H99 F2:3 150 1 103 1420.4 Veldboom and Lee (1994) Agrama and Moussa SD34 x SD35 F 300 1 1 70 1589.3 3 (1996)</p><p>Ac7643S5 x Ac7729/TZSRWS5 F3 234 1 2 142 1760.0 Ribaut et al. (1997) Mo17 x B73 RILs 180 3 192 1695.1 6 Mickelson et al. (2002)</p><p>Zong3 x 87-1 F2:3 266 2 160 34 2531.6 14 Tang et al. (2005)</p><p>ILP x B73 B73S1 150 1 72 40 1146.0 2 Upadyayula et al (2006)</p><p>N87-1 x 9526 F3 183 1 1 103 1512.9 6 Gao et al. (2007)</p><p>DTP79 x B73 F3 116 1 1 33 192 9 8 Nikolic et al. (2011)</p><p>Qi319 x Huangzao4 F2:3 230 6 194 2493.7 40 Wang et al. (2011)</p><p>Ye478 x Huangzao4 F2:3 235 6 159 3169.0 22</p><p>T4 x T19 F2 (a) 330 1 192 1260.0 10 Zhang et al. (2013)</p><p>T4 x T19 F2:3 330 1 192 1260.0 4 CML444 x MALAWI RILs 234 1 2 160 2349.2 Almeida et al. (2014)</p><p>CML440 x CML504 F2:3 247 1 2 2712.3 </p><p>CML444 x CML441 F2:3 300 1 2 3558.3 </p><p>T4 x T19 F2 (b) 232 1 77 868.7 4 Zhang et al. (2014) N04 x Dan232 RILs 258 3 207 2408.8 14 Dong et al. (2015)</p><p>￡ Langhuang x TS141 F2:3 202 2 2 199 1542.5 11 This study (a)</p><p>￡ Chang7-2 x TS141 F2:3 218 2 2 205 1648.8 11 This study (b) Total 36 15 1,953 773 9 152 Mean 231.3 150.2 110.4 9 1940.4 11.7 ❈ Environment: NE: Normal environment; DE: Drought environment § Markers: SSRs: Simple sequence repeats; SNPs: Single nucleotide polymorphisms; RFLPs: Restricted fragment length polymorphisms; AFLPs: Amplified fragment length polymorphisms</p><p>∯ Approaches: IM: Interval mapping; MIM: Multiple interval mapping; CIM: Composite interval mapping; ICIM: Inclusive composite interval mapping</p><p>￡References: This study (a): Mapping information in LTpop in our study; This study (b): Mapping information in CTpop in our study</p><p>2 Supplementary Table S2 The phenotypic (rp; upper diagonal) and genetic (rg; lower diagonal) correlation coefficients among tested traits in the LTpop and CTpop, respectively Traits# TBN ASI EN EW KW EL</p><p>TBN ASI EN EW KW EL ……………………………………LTpop (No. of LTpop=202) ………………………………….</p><p>………………………………….CTpop (No. of CTpop=218) …………………………………. TBN 1 -0.369** -0.164* 0.361** 0.290** 0.272**</p><p>1 -0.317** -0.123* 0.300** 0.252** 0.205** ASI -0.404++ 1 0.255** -0.474** -0.144* -0.320**</p><p>-0.343++ 1 0.213** -0.418** -0.124* -0.389** EN -0.182++ 0.311++ 1 0.319** 0.330** 0.226**</p><p>-0.167++ 0.261++ 1 0.290** 0.294** 0.200** EW 0.390++ -0.542++ 0.375++ 1 0.702** 0.655**</p><p>0.328++ -0.466++ 0.316++ 1 0.517** 0.438** KW 0.347++ -0.216++ 0.389++ 0.811++ 1 -0.423**</p><p>0.294++</p><p>3 -0.155++ 0.328++ 0.580++ 1 -0.312** EL 0.313++ -0.416++ 0.270++ 0.695++ -0.503++ 1</p><p>0.246++ -0.447++ 0.243++ 0.521++ -0.390++ 1 # Traits: ASI (day): Anthesis-silking interval; EW (g): Ear weight; KW (g): 100-kernel weight; EL (cm): Ear length */** : Phenotypic correlation was significant at the 0.05 or 0.01 probability level +/++ : Genetic correlation exceeded was significant at the 0.05 or 0.01 probability level r201,0.05=0.138, r201,0.01=0.181, r217,0.05=0.119, r217,0.01=0.144</p><p>4 Supplementary Table S3 QTLs for TBN and EN were detected in LTpop and CTpop by single environment mapping with CIM</p><p>R2 QTL position Genetic effect Gene action d Traits QTLs Chr.a Env LODb (%) cM Marker interval Additivec Dominance |d/a| Type ………………………………………………………………………………………………….…LTpop (No. of LTpop=202) ………………………………………………………………………………………………….… TBN qTBN-Ch.3-1 3 S-W 59.1 umc1025-umc1174 4.65 1.07 -0.61 0.57 PD 6.56 qTBN-Ch.4-1 4 S-W 189.6 umc2287-umc2360 15.06 -4.09 3.15 0.77 PD 23.58 4 S-Z 189.6 umc2287-umc2360 14.94 -3.90 2.76 0.71 PD 23.24 qTBN-Ch.6-1 6 W-W 147.3 bnlg1702-umc1805 7.87 2.12 0.79 0.37 PD 13.79 6 W-Z 147.3 bnlg1702-umc1805 9.50 2.49 1.19 0.48 PD 15.01 qTBN-Ch.7-1 7 S-W 11.7 umc2177-umc1378 13.70 -2.91 3.57 1.23 OD 20.51 7 W-Z 13.6 umc2177-umc1378 5.28 -1.51 -2.68 1.77 OD 8.39 7 S-Z 11.7 umc2177-umc1378 10.00 -2.32 -2.98 1.28 OD 17.11 qTBN-Ch.7-2 7 W-W 110.7 umc1708-umc1768 4.19 -1.22 2.04 1.67 OD 6.16 7 W-Z 110.7 umc1708-umc1768 3.35 -0.16 -0.22 1.38 OD 4.29 qTBN-Ch.9-1 9 W-W 36.3 bnlg1730-umc1982 8.81 2.28 1.53 0.67 PD 14.62 EN qEN-Ch.1-1 1 W-W 61.4 umc1395-umc1356 18.09 -5.97 -0.78 0.13 A 26.95 1 W-Z 61.4 umc1395-umc1356 9.35 -2.40 -0.41 0.17 A 14.91 qEN-Ch.4-1 4 W-W 148.0 bnlg1621a-umc2027 3.97 -0.88 0.15 0.17 A 4.73 4 S-W 148.0 bnlg1621a-umc2027 9.09 -2.33 -0.36 0.15 A 15.00 4 S-Z 148.0 bnlg1621a-umc2027 12.36 -2.67 -0.99 0.37 PD 19.96 qEN-Ch.6-1 6 W-W 130.4 umc2040-bnlg1174a 3.07 0.18 0.21 1.17 D 4.12 6 S-W 130.4 umc2040-bnlg1174a 5.74 1.00 1.03 1.03 D 7.51 6 S-Z 130..3 umc2040-bnlg1174a 8.03 2.20 1.84 0.84 D 13.18 qEN-Ch.10-1 10 S-Z 13.8 bnlg1451-bnlg1337 3.41 -0.17 0.19 1.12 D 4.47 qEN-Ch.10-1 10 W-W 47.7 bnlg1655-umc1345 5.05 1.20 1.50 1.25 OD 7.11 ………………………………………………………………………………………………….…CTpop (No. of CTpop=218) ………………………………………………………………………………………………….… TBN qTBN-Ch.2-1 2 W-G 37.2 umc2363-umc1024 8.71 -2.63 -3.17 1.21 OD 12.08 2 S-G 37.0 umc2363-umc1024 3.90 -0.98 1.24 1.27 OD 5.22 qTBN-Ch.4-1 4 S-G 143.6 umc2287-umc2360 11.35 -3.50 2.16 0.62 PD 17.85 4 S-J 143.6 umc2287-umc2360 10.09 -2.97 1.19 0.40 PD 15.00 qTBN-Ch.5-1 5 W-J 232.6 umc2216-umc1072 3.04 0.45 -0.32 0.71 PD 4.22 5 S-J 232.6 umc2216-umc1072 4.47 1.42 -0.58 0.41 PD 6.53 qTBN-Ch.6-1 6 W-G 100.3 umc2040-bnlg1174a 6.95 2.25 0.91 0.40 PD 10.07 qTBN-Ch.7-1 7 S-G 0.5 umc2177-umc1378 8.79 -2.64 3.23 1.22 OD 12.11 7 W-J 0.5 umc2177-umc1378 6.11 -1.96 2.67 1.36 OD 9.05 7 S-J 0.5 umc2177-umc1378 9.03 -2.87 -3.48 1.21 OD 13.03 qTBN-Ch.9-1 9 W-G 82.7 dupssr29-bnlg469a 10.00 -2.91 1.26 0.43 PD 14.92 EN qEN-Ch.3-1 3 W-G 16.8 umc1780-umc2376 6.87 -2.05 -0.12 0.06 A 9.35 3 W-J 16.6 umc1780-umc2376 4.14 -0.14 0.11 0.79 A 6.18 qEN-Ch.6-1 6 S-G 94.2 umc2040-bnlg1174a 8.91 -2.67 0.45 0.17 D 12.63 6 W-J 94.2 umc2040-bnlg1174a 11.07 -3.21 0.37 0.12 D 17.42 6 S-J 94.2 bnlg2191-mmc0523 7.86 2.73 2.20 0.81 D 11.85 a Chr.: Chromosome 1 to 10 b LOD: Logarithm of odds c Genetic effect: Additive effect: positive values indicated that the TS141 (male parent) carries the allele for an increase in TBN and EN, while negative values indicated that Langhuang/Chang7-2 (female parent) contributed the allele for an increase in TBN and EN d R2 (%): Phenotypic variance explained by the QTL The same as below</p><p>5 Supplementary Table S4 Summary of stable QTLs (sQTLs) for all investigated traits in LTpop and CTpop </p><p>Trait sQTL Population Env. QTL Bin Marker interval R2(%) TBN sQTL1 LTpop, CTpop JointФ qTBN-J1-1 1.08-1.10 mmc0041-phi308707 7.41-13.35 sQTL2 CTpop W-G, S-G, Joint qTBN-Ch.2-1 2.01-2.04 umc2363-umc1024 5.14-12.08 sQTL3 LTpop, CTpop S-W, S-Z, S-G, S-J, Joint qTBN-Ch.4-1 4.09-4.09 umc2287-umc2363 6.40-23.58 sQTL4 CTpop W-J, S-J, Joint qTBN-Ch.5-1 5.06-5.07 umc2216-umc1072 3.58-6.53 sQTL5 LTpop W-W, W-Z, Joint qTBN-Ch.6-1 6.05-6.05 bnlg1702-umc1805 6.98-15.01 sQTL6 LTpop, CTpop S-W, W-Z, S-Z, S-G, W-J, S-J, Joint qTBN-Ch.7-1 7.00-7.00 umc2177-umc1378 8.39-20.51 sQTL7 LTpop W-W, W-Z, Joint qTBN-Ch.7-2 7.04-7.04 umc1708-umc1768 4.29-6.16 EN sQTL8 LTpop W-W, W-Z, Joint qEN-Ch.1-1 1.05-1.07 umc1395-umc1356 13.24-26.95 sQTL9 LTpop, CTpop Joint qEN-J1-1, qEN-J1-2 1.08-1.10 mmc0041-phi308707 6.16-10.12 sQTL10 CTpop W-G, W-J, Joint qEN-Ch.3-1 3.01-3.01 umc1780-umc2376 6.18-9.35 sQTL11 LTpop W-W, S-W, S-Z, Joint qEN-Ch.4-1 4.06-4.06 bnlg1621a-umc2027 3.14-19.96 sQTL12 LTpop, CTpop W-W, S-W, S-Z, S-G, W-J, S-J, Joint qEN-Ch.6-1 6.05-6.05 umc2040-bnlg1174a 4.12-17.42 Ф: Joint: the joint QTLs were identified across all water environments by the QTL Network version 2.0</p><p>6 Supplentary Table S5 Epistatic interactions were detected in LTpop and CTpop with MCIM Trait Env. QTL(i) Marker interval(i) Bin(i) QTL(j) Marker interval(j) Bin(j) AAe ADf h2(AA)(%)g h2(AD)(%)h …………………………………………………………………………………………………………………………...…..…LTpop (No. of LTpop=202) …………………………………….………………….………….. ………………………………………………………….… TBN S-W qTBN-J1-1 mmc0041-phi308707 1.08-1.10 qTBN-Ch.4-1 umc2287-umc2360 4.09-4.09 -1.04 6.15</p><p>S-Z qTBN-J1-1 mmc0041-phi308707 1.08-1.10 qTBN-Ch.4-1 umc2287-umc2360 4.09-4.09 -0.97</p><p>6.03</p><p>EN S-W qEN-J1-2 mmc0041-phi308707 1.08-1.10 qEN-J2-1 umc1165-umc1823 2.01-2.02 -0.62</p><p>5.64</p><p>S-Z qEN-J1-2 mmc0041-phi308707 1.08-1.10 qEN-Ch.4-1 bnlg1621a-umc2027 4.06-4.06 -0.75</p><p>5.79</p><p>W-W qEN-Ch.1-1 umc1395-umc1356 1.05-1.07 qEN-Ch.6-1 umc2040-bnlg1174a 6.05-6.05</p><p>0.42</p><p>3.94 ………………………………………………………………………………………………………………….……..…..…CTpop (No. of CTpop=218) ……………………………………………………………………………………………………………………..……..…..… TBN S-G qTBN-J1-1 mmc0041-phi308707 1.08-1.10 qTBN-Ch.4-1 umc2287-umc2360 4.09-4.09 -0.92</p><p>7 5.07</p><p>EN W-G qEN-J1-2 mmc0041-phi308707 1.08-1.10 qEN-Ch.3-1 umc1780-umc2376 3.01-3.01 -0.64</p><p>3.71 eAA: The additive by additive epistatic interaction effect fAD: The additive by dominance epistatic interaction effect g h2(AA): Percentage of phenotypic variance explained by the additive by additive epistatic interaction effect h h2(AD): Percentage of phenotypic variance explained by the additive by dominance epistatic interaction effect</p><p>8 Supplementary Table S6 Consensus map information and projected QTLs for TBN and EN in the consensus map</p><p>Tot Items❄ Chr. 1 Chr. 2 Chr. 3 Chr. 4 Chr. 5 Chr. 6 Chr. 7 Chr. 8 Chr. 9 Chr. 10 al No. of Markers (No.) 99 60 73 73 71 55 55 63 51 53 653 No. of TBN-QTLs (Original) 17 18 22 25 9 7 22 14 6 12 152 No. of TBN-QTLs (Projected) 15 13 20 16 3 7 14 9 3 3 103 No. of EN-QTLs (Original) 15 5 10 5 3 11 6 3 3 5 61 No. of EN-QTLs (Projected) 10 5 7 3 1 6 1 2 1 1 37 7,2 1,141.3 Map Length (cM) 721.44 828.90 725.60 709.10 643.44 644.14 628.20 641.20 561.49 46. 9 90 ❄ Items: No. of TBN/ EN QTLs (Original): No. of original TBN/EN QTLs in 19 original QTL mapping studies; No. of TBN/EN QTLs (Projected): No. of projected TBN/EN QTLs in the consensus map</p><p>9 Supplementary Fig. S1 The rate of changes of tested traits in three parents and two F2:3 populations under water-stressed environments, respectively</p><p>10 Supplementary Fig. S2 Frequency distribution of TBN and EN in LTpop under four different watering environments (A and B) and CTpop (C and D); Partitioning variations for TBN (E) and EN (F) across LTpop and CTpop</p><p>11 Supplementary Fig. S3 Information on 19 original progeny populations: TBN (A) and EN (B) (Red/Green: Female parents under normal/drought environment; Blue/Yellow: Male parents under normal/drought environment; Pink/White: Progeny populations under normal/drought environment); H2 of TBN (Yellow) and EN (Gray) (C); Mid-parent heterosis () of TBN (Red) and EN (Purple) and over-parent heterosis () of TBN (Green) and EN (Brown) (D); Distribution of TBN/EN-QTLs on chromosomes (E); Distribution of Gene action for TBN/EN-QTLs (F). Distribution of LOD score for TBN/EN-QTLs (Red box /Green triangle) (G); Distribution of phenotypic variation (R2) for TBN/EN-QTLs (Red box/Green triangle) (H) </p><p>12 Supplementary Fig. S4 The consensus map was constructed across 19 original mapping datasets and the corresponding mQTLs were detected in the consensus map</p><p>13</p>