Supplementary Table 3. Candidate genes for the biparental population Hi27 x A272.

Chromosome / Candidate Gene / RefGen V2 / RefGen V2 / Maize Reference genome V2
ORF Start / ORF Stop
1 / hyd8 ‒ hydroxylase 8 / 6,353,416 / 6,354,652 / GRMZM5G826824
1 / nced1 ‒ 9-cis-epoxycarotenoid dioxygenase 1 / 250,892,567 / 250,895,242 / GRMZM2G014392
1 / ao3 – aldehyde oxidase 1 / 286,358,278 / 286,366,211 / GRMZM2G019799
1 / ao1 – aldehyde oxidase 1 / 286,448,581 / 286,456,365 / GRMZM2G141535
1 / ao4 – aldehyde oxidase 1 / 286,506,118 / 286,513,080 / GRMZM2G141473
2 / hyd4‒ carotene hydroxylase / 15,865,938 / 15,868,219 / GRMZM2G164318
2 / ccd7 ‒ carotenoid cleavage dioxygenase 7 / 19,458,968 / 19,461,625 / GRMZM2G158657
2 / crti2 – carotene isomerase 2 / 226,366,352 / 226,371,341 / GRMZM2G106531
2 / nced4 ‒ 9-cis-epoxycarotenoid dioxygenase 4 / 234,574,835 / 234,576,854 / GRMZM2G408158
3 / dxr1 – deoxyxylulosereductoisomerase 1 / 30,226,804 / 30,233,358 / GRMZM2G056975
3 / ggh2 – geranyl hydrogenase 2 / 40,062,008 / 40,064,270 / GRMZM2G419111
3 / nced3 ‒ 9-cis-epoxycarotenoid dioxygenase 3 / 87,344,791 / 87,346,554 / GRMZM5G858784
4 / cyp15 – cytochrome P450 15 / 235,724,340 / 235,728,875 / GRMZM2G010221
4 / hyd7‒ hydroxylase 7 / 236,023,117 / 236,025,051 / GRMZM2G163683
5 / nced9 ‒ 9-cis-epoxycarotenoid dioxygenase 9 / 16,850,172 / 16,851,977 / GRMZM5G838285
5 / lcyB ‒ lycopene beta cyclase / 100,700,176 / 100,702,026 / GRMZM5G849107
5 / hds1 – Hydroxymethylbutenyl diphosphate synthase 1 / 182,124,005 / 182,130,631 / GRMZM2G137409
5 / mecs2 – methyl erythritolcyclodiphosphate synthase 2 / 196,279,295 / 196,281,037 / AC209374.4_FG002
5 / nced8 ‒ 9-cis-epoxycarotenoid dioxygenase 8 / 200,687,176 / 200,689,579 / GRMZM2G150363
5 / ggh1 – geranylgeranyl hydrogenase 1 / 206,890,298 / 206,892,838 / GRMZM2G105644
5 / cyp13 – cytochrome P450 13 / 215,827,224 / 215,831,730 / GRMZM5G837869
6 / y1 – phytoeno synthase / 82,017,148 / 82,021,007 / GRMZM2G300348
6 / dxs1 – deoxyxylulose phosphate synthase 1 / 146,378,393 / 146,382,661 / GRMZM2G137151
6 / ippi3 – isopentenyl pyrophosphate isomerase 3 / 147,131,116 / 147,136,679 / GRMZM2G133082
7 / zds1 – zeta-carotene desaturase1 / 17,470,585 / 17,479,020 / GRMZM2G454952
7 / ggps2 – geranylgeranyl pyrophosphate synthase 2 / 160,531,537 / 160,533,586 / GRMZM2G102550
8 / lcyE ‒ lycopene epsilon cyclase1 / 138,882,594 / 138,889,812 / GRMZM2G012966
9 / dxs3 – deoxyxylulose phosphate synthase 3 / 14,077,852 / 14,081,075 / GRMZM2G493395
10 / crtRB1 ‒ Beta-carotene hydroxylase / 136,057,100 / 136,060,219 / GRMZM2G098676

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