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Table 2 Chromosome localization of the identified wheat carotenoid biosynthetic/catabolic genes on the durum [29] and bread wheat [28] consensus maps and allele frequency in the tetraploid wheat collection of 233 genotypes

From: The carotenoid biosynthetic and catabolic genes in wheat and their association with yellow pigments

Gene Enzyme SNP name SNP id   Wheat map position Allele frequency
  Chrom. Durum map Bread map Whole collection Durum sub-population
PSY1 Phytoene synthase 1 BS00022137_51 IWB6923 A/G 7AL 203.2 - 0.26–0.74 0.12–0.88
BobWhite_c4483_603 IWB3406 A/G 7AL - 226.1 monomorphic monomorphic
CAP7_c12398_110 IWB13781 T/G 7BL 200.1 164.2 failed failed
BS00010747_51 IWB6281 T/G 7BL 200.1 164.2 failed failed
BS00084631_51 IWB11376 T/G 7DL - -   
Kukri_rep_c105287_311 IWB49080aa T/C 7DL   208.1   
PSY2 Phytoene synthase 2 BobWhite_c339_247 IWB2660 G/T 5AS - 15.6 0.83–0.17 0.84–0.16
RAC875_c51670_117 IWB58766 C/T 5AS - 15.6 0.77–0.23 0.87–0.13
Excalibur_c2922_3416 IWB24805a C/T 5AS 46.6 15.6 monomorphic monomorphic
Excalibur_c30273_138 IWB24947 C/T 5BS - 19.7 0.29–0.71 0.13–0.87
Kukri_c23694_370 IWB42850 A/G 5BS - 19.7 0.75–0.25 0.87–0.13
GENE-3207_610 IWB33289 C/T 5BS - 19.7 0.72–0.28 0.87–0.13
GENE-3207_134 IWB33287 A/G 5BS - 19.7 failed failed
Excalibur_c3948_1315 IWB26051a C/T 5BS 15.8 19.7 0.43–0.57 0.48–0.52
GENE-3207_174 IWB33288 A/G 5DS - -   
PSY3 Phytoene synthase 3 CAP7_c7840_316 IWB14264 A/G 5 L - - monomorphic monomorphic
BS00077855_51 IWB10965a C/T 5AL 126.8 82.0 0.74–0.26 0.88–0.12
PDS Phytoene desaturase BobWhite_c3609_361 IWB2819 A/G 4AS - - 0.01-0.99 monomorphic
Tdurum_contig11560_383 IWB67151 C/T 4BL - - monomorphic monomorphic
IACX725 IWB36188 A/G 4BL - - monomorphic monomorphic
Kukri_c20125_281 IWB42264a C/T 4BL 83.1 75.6 0.81–0.19 0.90–0.10
Ra_c72128_236 IWB52568 A/G 4DL - -   
Z-ISO cis-zeta-carotene isomerase - -       
ZDS Zeta-carotene desaturase CAP11_c754_335 IWB13046 A/G 2AS - - monomorphic monomorphic
JD_c52783_234 IWB37604 C/T 2BS - - monomorphic monomorphic
Kukri_c23475_1485 IWB42817 A/G 2BS - - monomorphic monomorphic
RFL_Contig3540_283 IWB64386 A/C 2BS - - monomorphic monomorphic
Ra_c5594_569 IWB52265 A/G 2DS - -   
D_contig22022_580 IWB16076 T/G 2DS - -   
CRTISO (CISO) Carotenoid isomerase IAAV5931 IWB35115 A/G 1AS - 66.9 0.98–0.02 monomorphic
IAAV2888 IWB34631a A/G 1AS 43.3 66.3 0.12–0.88 monomorphic
CAP11_c292_249 IWB12814 T/C 1BS - - monomorphic monomorphic
LYCB (LCYB) Lycopene beta-cyclase CAP7_rep_c12997_415 IWB14395 A/G 6S - - monomorphic monomorphic
Excalibur_c9273_1271 IWB29407a T/C 6DS - -   
LYCE (LCYE) Lycopene epsilon-cyclase wsnp_Ex_c48136_53140385 IWA4009 T/C 3AL - 85.4 monomorphic monomorphic
RAC875_c2375_132 IWB55558 A/G 3AL - - monomorphic  
IAAV4785 IWB34923a G/T 3AL 65.9 85.4 0.29–0.71 0.35–0.65
Excalibur_c34554_312 IWB25473a C/T 3BL 67.2 64.4 0.31–0.69 0.16–0.84
D_contig37716_635 IWB16739 A/G 3DL - -   
Kukri_c196_184 IWB42160 AC 3DL - -   
BCH1 (CHYB1, HYD1) Carotenoid β-ring hydroxylase (β-hydroxylase 1) BobWhite_c34273_67 IWB2683 A/nulli 2AL 133.3 - 0.81–0.19 monomorphic
Tdurum_contig5114_319 IWB72154a C/T 2AL - 112.1 0.51–0.49 0.30–0.70
RFL_Contig329_957 IWB64290 T/nulli 2BL - - 0.90–0.10 monomorphic
RFL_Contig329_877 IWB64289 A/G 2BL - - monomorphic monomorphic
BCH2 (CHYB2, HYD2) Carotenoid β-ring hydroxylase (β-hydroxylase 2) Tdurum_contig12547_293 IWB67643 T/C 4BL, 4DL, 5AL - - monomorphic monomorphic
CYP97A3 (LUT5) Carotenoid β-ring hydroxylase (Cytochrome P450-type monooxygenase CYP97A3) wsnp_JD_c7795_8868122 IWA6182 C/T 6AL - 138.3 0.04–0.96 0.01–0.99
wsnp_BF291974A_Ta_2_1 IWA441a C/T 6AL 122.7 138.0 0.58–0.42 0.55–0.45
Tdurum_contig569_263 IWB72540 A/G 6BL 145.3 108.9 0.77–0.23 0.75–0.25
CAP11_c816_470 IWB13062a A/G 6BL 145.3 - 0.54–0.46 0.33–0.67
GENE-3988_631 IWB33711 A/G 6BL 145.8 - 0.04–0.96 monomorphic
BobWhite_c12032_371 IWB293 T/C 6DL - 133.54   
CYP97C1 (LUT1) Carotenoid ε ring -hydroxylase (Cytochrome P450-type monooxygenase CYP97C1) Kukri_rep_c111979_282 IWB49532 T/C 1AL -    
Excalibur_c29401_543 IWB24832 A/G 1BL -    
CCD7 (MAX3) Carotene (9,10) cleavage dioxygenase - -       
CCD8 (MAX4) (13,14) cleavage dioxygenase - -       
CCD1 (NC5) (5,6) (5′,6′) (9,10) (9′,10′) carotenoid cleavage dioxygenase wsnp_Ex_c6209_10838456 IWB4445 A/G 5AS - -   
CAP11_c2357_97 IWB12774 T/C 5BS - -   
TA004832-0873 IWB65889 A/G 5BS 0.7 8.7   
BobWhite_rep_c53718_103 IWB5053 T/C 5DS - -   
CYP711A1 (MAX1) Cytochrome P450-type monooxygenase CYP711A1 - -    - -   
ZEP (ABA1) Zeaxanthin epoxidase RAC875_c856_92 IWB60810 A/C 2DL - -   
CAP7_c4349_243 IWB14103 A/G 2DL - -   
D_GBF1XID01ASYXD_209 IWB18346 A/G 2DL - -   
VDE Violaxanthin de-epoxidase wsnp_Ex_c11728_18862431 IWA1533 A/G 2AL - - 0.87–0.13 monomorphic
wsnp_Ex_rep_c69465_68405569 IWA5610 C/T 2BL - 99.8 0.08–0.92 0.02–0.98
wsnp_Ex_c39862_47046812 IWA3696 C/T 2BL - 99.6 0.01–0.99 monomorphic
wsnp_Ex_c9805_16183499 IWA4965a C/T 2BL 94.2 99.8 0.07–0.93 0.02–0.98
Kukri_c52435_163 IWB46254 A/G 2BL - - monomorphic monomorphic
NXS Neoxanthin synthase - -       
NCED4 (CCD4) 9-cis-epoxycarotenoid dioxigenase 4 wsnp_RFL_Contig4424_5193532 IWA8592a C/T 6AL 62.8 82.4 0.24–0.76 0.07–0.93
CAP11_c4654_171 IWB12893 A/G 6DL - -   
NCED9 (NC2; CCD9) 9-cis-epoxycarotenoid dioxigenase CAP11_c5699_107 IWB12966 T/C 6DL - -   
CAP7_c6372_329 IWB14194 A/G 6DL - -   
ABA2 (SDR) Short-chain alcohol dehydrogenase Tdurum_contig13608_72 IWB68029 T/G 5AL - - failed failed
RFL_Contig4520_749 IWB64707 A/G 5BL 157.5 137.1 0.70–0.30 0.54–0.46
Tdurum_contig13608_195 IWB68027 T/C 5DL - -   
AAO3 Abscisic aldehyde oxidase RAC875_c64451_465 IWB59875 C/T 7AL 180.3 - 0.76–0.24 0.70–0.30
Kukri_c5789_1029 IWB46699 T/C 7AL 180.3 - failed failed
Ku_c5789_1180 IWB39660 G/T 7BL 155.7 120.8 0.37–0.63 0.24–0.76
Excalibur_rep_c112889_341 IWB30603 A/G 7DL - 184.18   
  1. aSNP comigrating or mapping in the same contig of the gene sequence