Supplementary Table S1 Primers of PCR-based insertion/deletion (InDel) markers for fine mapping

Name / Chromosome / Position (Mb）a / Forward primer（5'-3'） / Reverse primer（5'-3'）
M9 / 5 / 204,195,657 / TAGGCGATAAACTGGAAAGGAG / GGAGGGAGATGTAAATGTGCTG
M16 / 5 / 205,155,903 / ACATCCAGAAAGGGAAACAT / AGGAACAAACCTGAGGAATC
M29 / 5 / 206,532,842 / AGGTATGGCGTGCGACTATC / AACCCTCTAATAAATTACGTCTTG
K45 / 7 / 133,619,568 / AGAACTTTAGCTGAAGTCCG / CAGTGATGGTTACCTTTGAC
T25 / 7 / 134,076,918 / CGCTCACTGTCCTACGAGTA / GTGGACCAAATCAAAGATAAT
K54 / 7 / 137,706,137 / CTTGCTTTACTAACTCCACC / GATCAACTCATTTTATTCCA
K58 / 7 / 140,007,316 / GTGATGATTTAATATGTGCGT / TCTCAACTTCCAGGGTATAA
T79 / 7 / 141,694,058 / CCCGCCCCAAGCCACGAGAT / CCTGCCGTCAAAACCGCCAC
Y41 / 7 / 141,806,283 / TTGTCAGTTGTCACCCTCCTACC / GACAAGGCGAGCAAGATTGG
Y113 / 7 / 142,396,933 / GCTCCTCAAGCAGGTCAGTCA / TGCAAGAATCGGTCGATCATAT
T84 / 7 / 142,647,845 / TCCGAGTCCGATGGCACAAG / CAATGGCAGCAGCGACGAGA
T85 / 7 / 142,780,200 / ACAAATCCAAGAAAACCCCACA / ATGGCATTGGTAATTTCAGAGCAT
Y51 / 7 / 142,813,204 / GTGTATTGTGGTAGTATACAT / ATCATAGTAATGTTTGTCAT
Y53 / 7 / 142,908,358 / GATAGTCACTGCTTGGCTGAT / AGTTGCTCACGAGTCATTCATA
Y61 / 7 / 143,112,805 / ATCTACCGTTGGATACAGAT / ACATTACAACATGGCATACT
T44 / 7 / 143,337,228 / AGGTTTTGGCATTGTTCAGA / TGCGTTGTTTTACGATCCTATT
T48 / 7 / 145,457,637 / GAGGCTCCCCTTCCATAGTT / GATCGACCTTTTGTACCGAC
K18 / 7 / 146,595,135 / TAATCAATTCGAACGGGAAT / AGAAGGGGATACAGAGGAGC
K72 / 7 / 149,761,043 / GCTGCCAGTTCCAGACTGAG / AGCCATTGATTAGTGATTTGACC
K74 / 7 / 151,081,977 / ATAAAACCTGAAGTCCCACG / AATGAGTCCAAGATTCCAGAC
K30 / 7 / 152,399,819 / TTTTCAGTACCTAGTGCCATTT / TCCCACCACAGAAACATCATAC
T55 / 7 / 153,177,271 / CTGAGGCTGTGAGCGCTTTA / CGTTGAATCTGGACCCATTTC
T63 / 7 / 155,370,499 / TAGCCTATTTCTGGGATTTT / GTGATTTTCTTCTCAACCTT
K42 / 7 / 156,737,785 / GAGCCGAGTCCTACCAATAA / TAACATAGCTGGAGGCCAAA

a Markers position is based on the B73 genome (RefGen_V2)

Supplementary Table S2 Primers for quantitative real-time RT-PCR (qRT-PCR) validation

Gene / Forward primer（5'-3'） / Reverse primer（5'-3'）
GRMZM5G899476 / CGCCAAGAGGAGAACAGG / TTTCAGAGCCGCCGAAGC
GRMZM2G338928 / TTCCGAATAGTTGGTTTGA / GCCCTCTAGTTGGGATGTA
GRMZM2G143718 / GCGGACGATCTGCGATGT / TCCTGGAAATTCAACCCT
GRMZM2G048131 / CGAGACGAGCGAGGAAGAAC / TGCACGAGGACACGAACATC

Supplementary Table S3 Kernel cracking scores for 1192A and its recurrent parent B73 across different environments

Environment a / Line / Range / Mean / Std
2015CP / 1192A / 3-9 / 7.83 / 1.65
B73 / 0-3 / 0.45 / 0.94
2015GL / 1192A / 3-9 / 6.46 / 1.47
B73 / 0-3 / 0.25 / 0.62
2015XX / 1192A / 3-9 / 6.67 / 1.18
B73 / 0-3 / 0.28 / 0.64
2016CP / 1192A / 5-9 / 7.44 / 1.46
B73 / 0-3 / 0.60 / 0.83
2016FS / 1192A / 5-9 / 7.82 / 1.47
B73 / 0-3 / 0.53 / 1.01
2016XX / 1192A / 3-9 / 6.42 / 1.50
B73 / 0-3 / 0.41 / 0.84

a Environment is labeled with the last two digits of year and the abbreviation of location (GL, Gongzhuling of Jilin Province, China; XX, Xinxiang of Henan Province, China; CP, Changping in Beijing, China; FS, Fangshan in Beijing, China)

Supplementary Table S4 Kernel cracking scores for the reciprocal crosses and their parental lines in the environment of 2016CP

Cross type / Generation / Total number / Ear number
0 / 1 / 3 / 5 / 7 / 9
1192AU / 18 / 0 / 0 / 1 / 2 / 7 / 8
1192A(♀)×B73(♂) / F0 / 8 / 0 / 0 / 0 / 1 / 4 / 3
1192A(♀)×B73(♂) / F1 / 17 / 3 / 2 / 3 / 5 / 3 / 1
B73(♀)×1192A(♂) / F1 / 18 / 2 / 2 / 3 / 4 / 5 / 2
B73(♀)×1192A(♂) / F0 / 7 / 5 / 2 / 0 / 0 / 0 / 0
B73U / 15 / 11 / 4 / 0 / 0 / 0 / 0

Supplementary Table S5 RNA-sequencing data statistics

Samplea / Raw reads / Clean reads (CR/RRb) / Total Mapped (TM/CRc) / Multiple mapped (MM/CRd) / Uniquely mapped (UM/CRe) / Error rate
A8_1 / 49298160 / 46325322 (93.97%) / 38683118 (83.5%) / 858824 (1.85%) / 37824294 (81.65%) / 2%
A8_2 / 55732920 / 52618670 (94.41%) / 44158679 (83.92%) / 997359 (1.9%) / 43161320 (82.03%) / 3%
A10_1 / 45793690 / 42752502 (93.36%) / 35641451 (83.37%) / 945064 (2.21%) / 34696387 (81.16%) / 2%
A10_2 / 48562662 / 45934356 (94.59%) / 39250688 (85.45%) / 928490 (2.02%) / 38322198 (83.43%) / 2%
A12_1 / 48216200 / 46543342 (96.53%) / 40684891 (87.41%) / 877286 (1.88%) / 39807605 (85.53%) / 2%
A12_2 / 57534652 / 54712424 (95.09%) / 46248533 (84.53%) / 1001923 (1.83%) / 45246610 (82.7%) / 2%
A14_1 / 46176810 / 43997326 (95.09%) / 37506758 (85.25%) / 838878 (1.91%) / 36667880 (83.34%) / 2%
A14_2 / 42705166 / 40028388 (93.93%) / 33653446 (84.07%) / 848834 (2.12%) / 32804612 (81.95%) / 2%
B8_1 / 52380026 / 49482334 (94.47%) / 41702326 (84.28%) / 958895 (1.94%) / 40743431 (82.34%) / 2%
B8_2 / 48248624 / 44795584 (92.84%) / 37234706 (83.12%) / 876994 (1.96%) / 36357712 (81.16%) / 2%
B10_1 / 44285596 / 42566410 (96.12%) / 37000136 (86.92%) / 833779 (1.96%) / 36166357 (84.96%) / 2%
B10_2 / 49645526 / 46975088 (94.62%) / 39748618 (84.62%) / 891712 (1.9%) / 38856906 (82.72%) / 2%
B12_1 / 53423028 / 50738012 (94.97%) / 43271816 (85.28%) / 1010352 (1.99%) / 42261464 (83.29%) / 3%
B12_2 / 52809832 / 50500552 (95.63%) / 43332058 (85.81%) / 977178 (1.93%) / 42354880 (83.87%) / 2%
B14_1 / 43889858 / 42173096 (96.09%) / 36612137 (86.81%) / 836059 (1.98%) / 35776078 (84.83%) / 2%
B14_2 / 42654024 / 41000038 (96.12%) / 35974286 (87.74%) / 835876 (2.04%) / 35138410 (85.7%) / 1%
Total / 781356774 / 741143444 (94.85%) / 630703647 (85.10%) / 14517503 (1.96%) / 616186144 (83.14%)

a A8-A14 and B8-B14: transcriptomes of 1192A and B73 at 8-14 day after pollination respectively, _1 and _2: reduplicate 1 and 2

b CR/RR: Clean reads/Raw reads

c TM/CR: Total mapped/Clean reads

d MM/CR: Multiple mapped/Clean reads

e UM/CR: Uniquely mapped / Clean reads

Supplementary Table S6 Pearson correlations for the RNA-sequencing results among different samples

Samplea / A8_1 / A8_2 / A10_1 / A10_2 / A12_1 / A12_2 / A14_1 / A14_2 / B8_1 / B8_2 / B10_1 / B10_2 / B12_1 / B12_2 / B14_1 / B14_2
A8_1 / 1 / 0.98 / 0.93 / 0.88 / 0.82 / 0.84 / 0.81 / 0.76 / 0.96 / 0.96 / 0.88 / 0.85 / 0.83 / 0.80 / 0.80 / 0.80
A8_2 / 0.98 / 1 / 0.93 / 0.87 / 0.82 / 0.84 / 0.81 / 0.75 / 0.96 / 0.95 / 0.88 / 0.84 / 0.83 / 0.80 / 0.80 / 0.80
A10_1 / 0.93 / 0.93 / 1 / 1 / 0.92 / 0.91 / 0.89 / 0.85 / 0.94 / 0.89 / 0.96 / 0.94 / 0.91 / 0.89 / 0.87 / 0.88
A10_2 / 0.88 / 0.87 / 0.97 / 1 / 0.96 / 0.95 / 0.94 / 0.91 / 0.89 / 0.84 / 0.97 / 0.97 / 0.95 / 0.93 / 0.92 / 0.93
A12_1 / 0.82 / 0.82 / 0.92 / 0.96 / 1 / 0.96 / 0.97 / 0.95 / 0.84 / 0.79 / 0.95 / 0.95 / 0.97 / 0.97 / 0.96 / 0.97
A12_2 / 0.84 / 0.84 / 0.91 / 0.95 / 0.96 / 1 / 0.98 / 0.95 / 0.86 / 0.81 / 0.93 / 0.95 / 0.96 / 0.94 / 0.95 / 0.95
A14_1 / 0.81 / 0.81 / 0.89 / 0.94 / 0.97 / 0.98 / 1 / 0.97 / 0.83 / 0.78 / 0.92 / 0.94 / 0.96 / 0.96 / 0.96 / 0.96
A14_2 / 0.76 / 0.75 / 0.85 / 0.91 / 0.95 / 0.95 / 0.97 / 1 / 0.78 / 0.73 / 0.88 / 0.92 / 0.95 / 0.95 / 0.96 / 0.96
B8_1 / 0.96 / 0.96 / 0.94 / 0.89 / 0.84 / 0.86 / 0.83 / 0.78 / 1 / 0.96 / 0.91 / 0.88 / 0.86 / 0.83 / 0.83 / 0.82
B8_2 / 0.96 / 0.95 / 0.89 / 0.84 / 0.79 / 0.81 / 0.78 / 0.73 / 0.96 / 1 / 0.85 / 0.83 / 0.81 / 0.78 / 0.78 / 0.77
B10_1 / 0.88 / 0.88 / 0.96 / 0.97 / 0.95 / 0.93 / 0.92 / 0.88 / 0.91 / 0.85 / 1 / 0.96 / 0.95 / 0.94 / 0.93 / 0.93
B10_2 / 0.85 / 0.84 / 0.94 / 0.97 / 0.95 / 0.95 / 0.94 / 0.92 / 0.88 / 0.83 / 0.96 / 1 / 0.96 / 0.95 / 0.93 / 0.94
B12_1 / 0.83 / 0.83 / 0.91 / 0.95 / 0.97 / 0.96 / 0.96 / 0.95 / 0.86 / 0.81 / 0.95 / 0.96 / 1 / 0.99 / 0.98 / 0.98
B12_2 / 0.80 / 0.80 / 0.89 / 0.93 / 0.97 / 0.94 / 0.96 / 0.95 / 0.83 / 0.78 / 0.94 / 0.95 / 0.99 / 1 / 0.98 / 0.98
B14_1 / 0.80 / 0.80 / 0.87 / 0.92 / 0.96 / 0.95 / 0.96 / 0.96 / 0.83 / 0.78 / 0.93 / 0.93 / 0.98 / 0.98 / 1 / 0.99
B14_2 / 0.80 / 0.80 / 0.88 / 0.93 / 0.97 / 0.95 / 0.96 / 0.96 / 0.82 / 0.77 / 0.93 / 0.94 / 0.98 / 0.98 / 0.99 / 1

a A8-A14 and B8-B14: transcriptomes of 1192A and B73 at 8-14 day after pollination respectively, _1 and _2: reduplicate 1 and 2

Supplementary Table S7 Over-represented genes in GO enrichment

Gene ID / Gene description / GO term / Expression difference
DAPa / 1192A / B73 / Log2Fcb / Significantc
AF546187.1_FG007 / alpha zein 19kDa D2 / nutrient reservoir activity / 8 / 0.62d / 1.35 / -1.17 / NS
10 / 0.77 / 1.62 / -1.23 / NS
12 / 4.65 / 331.53 / -6.29 / DOWN
14 / 172.56 / 213.62 / -0.09 / NS
AF546188.1_FG001 / alpha-zein protein / nutrient reservoir activity / 8 / 0.91 / 0.59 / 0.6 / NS
10 / 0.86 / 14.13 / -4.15 / NS
12 / 37.91 / 264.8 / -2.93 / DOWN
14 / 136.97 / 224.11 / -0.56 / NS
AF546188.1_FG002 / alpha-zein protein / nutrient reservoir activity / 8 / 1.54 / 1.47 / 0.05 / NS
10 / 2.72 / 28.15 / -3.5 / NS
12 / 70.84 / 540.37 / -3.06 / DOWN
14 / 343.28 / 526.6 / -0.44 / NS
AF546188.1_FG003 / alpha-zein protein / nutrient reservoir activity / 8 / 0.48 / 0.76 / -0.68 / NS
10 / 1.25 / 19.22 / -4.07 / NS
12 / 31.31 / 208.24 / -2.87 / DOWN
14 / 120.37 / 199.82 / -0.55 / NS
GRMZM2G026703 / globulin2 / nutrient reservoir activity / 8 / 0.12 / 0.02 / 2.89 / NS
10 / 0.07 / 0.28 / -2.02 / NS
12 / 0.29 / 2.11 / -3 / DOWN
14 / 5.36 / 9.88 / -0.69 / NS
GRMZM2G026939 / zein-alpha 19A2-like / nutrient reservoir activity / 8 / 0.42 / 0.48 / -0.21 / NS
10 / 0.71 / 8.57 / -3.73 / NS
12 / 22.53 / 181.58 / -3.14 / DOWN
14 / 107.43 / 148.17 / -0.28 / NS
GRMZM2G059620 / Zein-alpha 19B1 / nutrient reservoir activity / 8 / 33.16 / 25.48 / 0.35 / NS
10 / 33.61 / 194.08 / -2.67 / NS
12 / 449.52 / 7436.64 / -4.17 / DOWN
14 / 8067.13 / 9693.5 / -0.05 / NS
GRMZM2G388461 / alpha-zein protein / nutrient reservoir activity / 8 / 0.35 / 0.31 / 0.16 / NS
10 / 0.3 / 0.58 / -1.07 / NS
12 / 4.88 / 88.72 / -4.32 / DOWN
14 / 40.38 / 74.31 / -0.68 / NS
GRMZM2G174883 / Legumin 1 / nutrient reservoir activity / 8 / 26.58 / 85.25 / -1.69 / NS
10 / 1065.99 / 1923.3 / -0.96 / NS
12 / 1595.45 / 2641.59 / -0.82 / DOWN
14 / 1717.05 / 2310.26 / -0.3 / NS
GRMZM2G097059 / MADS-domain transcription factor 4 / specification of floral organ identity / 8 / 262.75 / 318.4 / -0.32 / NS
specification of organ identity / 10 / 154.66 / 202.95 / -0.47 / NS
specification of floral organ number / 12 / 111.56 / 205.93 / -1 / NS
cell fate specification / 14 / 56.45 / 168.26 / -1.53 / DOWN
maintenance of floral meristem identity
GRMZM2G099522 / MADS-box transcription factor 1-like / specification of floral organ identity / 8 / 75.53 / 81.34 / -0.16 / NS
specification of organ identity / 10 / 45.26 / 53.55 / -0.31 / NS
cell fate specification / 12 / 24.4 / 39.95 / -0.84 / NS
maintenance of floral meristem identity / 14 / 4.45 / 23.26 / -2.31 / DOWN
GRMZM2G102161 / MADS14 / specification of floral organ identity / 8 / 243.65 / 226.01 / 0.06 / NS
specification of organ identity / 10 / 117.76 / 99.63 / 0.16 / NS
cell fate specification / 12 / 61.86 / 73.4 / -0.35 / NS
maintenance of floral meristem identity / 14 / 34.36 / 59.24 / -0.72 / DOWN
GRMZM2G129034 / MADS27 / specification of floral organ identity / 8 / 277.72 / 244.01 / 0.14 / NS
specification of organ identity / 10 / 148.54 / 135.4 / 0.06 / NS
specification of floral organ number / 12 / 97.31 / 122.94 / -0.45 / NS
cell fate specification / 14 / 51.08 / 98.66 / -0.9 / DOWN
GRMZM2G159397 / MADS6 / specification of floral organ identity / 8 / 496.63 / 375.67 / 0.36 / NS
specification of organ identity / 10 / 218.26 / 205.07 / 0.01 / NS
specification of floral organ number / 12 / 122.87 / 161.97 / -0.51 / NS
cell fate specification / 14 / 71.98 / 135.21 / -0.85 / DOWN
maintenance of floral meristem identity
AC190909.3_FG004 / callose synthase 3-like / glucosyltransferase activity / 8 / 3.96 / 2.61 / 0.56 / NS
UDP-glucosyltransferase activity / 10 / 8.73 / 14.29 / -0.76 / NS
12 / 13.82 / 18 / -0.51 / NS
14 / 7.67 / 18.04 / -1.18 / DOWN
GRMZM2G004087 / callose synthase / glucosyltransferase activity / 8 / 1.35 / 1.44 / -0.13 / NS
UDP-glucosyltransferase activity / 10 / 3.49 / 7.19 / -1.09 / NS
12 / 6.34 / 8.57 / -0.56 / NS
14 / 3.51 / 9.42 / -1.32 / DOWN
GRMZM2G011240 / sucrose synthase 4 / glucosyltransferase activity / 8 / 0.61 / 0.56 / 0.07 / NS
UDP-glucosyltransferase activity / 10 / 2.31 / 9.46 / -2.05 / NS
12 / 8.68 / 20.19 / -1.36 / NS
14 / 5.02 / 33.93 / -2.71 / DOWN
GRMZM2G018241 / cellulose synthase-9 / glucosyltransferase activity / 8 / 3.57 / 3.41 / 0.01 / NS
UDP-glucosyltransferase activity / 10 / 2.32 / 3.15 / -0.5 / NS
12 / 2.58 / 4.31 / -0.88 / NS
14 / 1.09 / 3.75 / -1.7 / DOWN
GRMZM2G082580 / probable cellulose synthase A catalytic subunit 6 / glucosyltransferase activity / 8 / 11.18 / 10.95 / -0.01 / NS
UDP-glucosyltransferase activity / 10 / 11.13 / 11.32 / -0.09 / NS
12 / 11.22 / 11.7 / -0.16 / NS
14 / 6.58 / 14.11 / -1.05 / DOWN
GRMZM2G152908 / sucrose synthase 1 / glucosyltransferase activity / 8 / 161.22 / 140.87 / 0.16 / NS
UDP-glucosyltransferase activity / 10 / 257.23 / 480.49 / -0.97 / NS
12 / 321.14 / 312.73 / -0.06 / NS
14 / 169.46 / 284.7 / -0.68 / DOWN
GRMZM2G311182 / sucrose synthase 4 / glucosyltransferase activity / 8 / 4.89 / 4.49 / 0.09 / NS
UDP-glucosyltransferase activity / 10 / 19.33 / 38.34 / -1.09 / NS
12 / 31.32 / 43.85 / -0.6 / NS
14 / 32.44 / 64.35 / -0.89 / DOWN
GRMZM2G370162 / UDP-glucose: glycoprotein glucosyltransferase / glucosyltransferase activity / 8 / 3.2 / 2.86 / 0.12 / NS
UDP-glucosyltransferase activity / 10 / 3.51 / 4.98 / -0.57 / NS
12 / 4.47 / 5.85 / -0.51 / NS
14 / 2.41 / 5.59 / -1.15 / DOWN
GRMZM2G553532 / callose synthase / glucosyltransferase activity / 8 / 3.06 / 2.4 / 0.3 / NS
UDP-glucosyltransferase activity / 10 / 4.54 / 9.11 / -1.06 / NS
12 / 9.18 / 12.59 / -0.59 / NS
14 / 5.83 / 13.04 / -1.1 / DOWN
GRMZM5G875238 / sucrose phosphate synthase 1 / glucosyltransferase activity / 8 / 17.69 / 9.78 / 0.82 / NS
UDP-glucosyltransferase activity / 10 / 8.95 / 10 / -0.21 / NS
12 / 9.14 / 14.4 / -0.77 / NS
14 / 4.48 / 9.06 / -0.96 / DOWN
Novel00008 / callose synthase 9-like / glucosyltransferase activity / 8 / 2.83 / 2.01 / 0.45 / NS
UDP-glucosyltransferase activity / 10 / 4.81 / 7.77 / -0.75 / NS
12 / 8.39 / 10.9 / -0.5 / NS
14 / 5.16 / 11.51 / -1.08 / DOWN

a Days after pollination