Table 3 Sequence features detected in genomes of maize and teosinte accessions
Inbred/accessionEndosperm coloraPZE0680879922bCcd1 copy numbercMacro-transposon right junction (Tam3La-5')Tam3La-3' junctionMacro-transposon left junction (Tam3Ld-3')Tam3Lb-3 junctionTam3Lc left junctionTam3Lc retroelement junctionTam3Lb/c right junctionVacant Helitron 1 site (Wc progenitor)Vacant Helitron 1 site (teosinte variant)OH43 Helitron insertionB73 Helitron 1 insertion site
B73:MZYTT1X
B97:MZYTT1X
BKN009:MZn.d.CC1
BKN010:MZn.d.CC1
BKN011:MZn.d.TT1
BKN014:MZn.d.CC1X
BKN015:MZWCC16XXXXXX
BKN016:MZYTT1X
BKN017:MZn.d.CC3XXX
BKN018:MZWCC8XXXXXX
BKN019:MZn.d.TT1
BKN020:MZn.d.TT1
BKN022:MZn.d.CC11XXXXXXXX
BKN023:MZn.d.CC1X
BKN025:MZn.d../.13XXXXX
BKN026:MZn.d.CC21XXXXXXX
BKN027:MZn.d.TT1X
BKN029:MZn.d.CC15XXXXXXXX
BKN030:MZn.d.CC2X
BKN031:MZn.d.CC4XXXXXXXXX
BKN032:MZn.d.TT1X
BKN033:MZn.d.CC1
BKN034:MZn.d.CC1
BKN035:MZn.d.CC23XXXXXXXX
BKN040:MZWCC14XXXXXXX
CAU178:MZYTT1X
CAU478:MZYTT1X
CAU5003:MZYTT1
CAUCHANG72:MZYTT1
CAUMO17:MZYTT1X
CAUZHENG58:MZYTT1
CML103:MZWCC13XXXXXXXX
CML133:MZWCC1
CML192:MZYTT1
CML202:MZWCC12XXXXX
CML206:MZW./.1
CML228:MZYTT1XdX
CML247:MZW./.1
CML277:MZWCC8XXXXXX
CML312SR:MZWCC17XXXXXX
CML322:MZWCC9XXXXXXX
CML330:MZWCC3XXXXX
CML333:MZWCC2XXXXX
CML341:MZWCC10XXXX
CML411:MZYTT1X
CML418:MZWCC10XXXXXX
CML479:MZYTT1X
CML504:MZWCC16XXXXXXX
CML505:MZWCC10XXXXXXX
CML511:MZWCC16XXXXX
CML52:MZYTT1X
CML52R:MZY./.1
CML69:MZYTT2XXXXX
CML84:MZWCC11XXXXX
CML85:MZWCC1
CML96:MZWCC1
CML99:MZWCC11XXXXXXX
H16:MZWCC1
HP301:MZYTT1
IL14H:MZW./.1X
KI11:MZYTT1
KI3:MZYTT1X
KY21:MZWCC13XXXX
M162W:MZWCC7XXXXXXX
M37W:MZWCC1
MO17:MZYTT1X
MO18W:MZWCC6XXXXXXX
MS71:MZYTT1X
NC350:MZYTT8XXXXXXX
NC358:MZYTT1X
OH43:MZYTT1XdX
OH7B:MZY./.1X
P1:MZWCC16XXXXXXXX
P39:MZYTT1X
TIL01:TEOn.d.CC1X
TIL02:TEOn.d.CC1X
TIL03:TEOn.d.CC1X
TIL04-TIP285:TEOn.d.CC1
TIL05:TEOn.d.CC1
TIL06:TEOn.d.CC1X
TIL07:TEOn.d.CC1X
TIL08:TEOn.d.CC1X
TIL09:TEOn.d.CC1X
TIL10:TEOn.d.CC1X
TIL11:TEOn.d.CC1
TIL12:TEOn.d.CC1X
TIL15:TEOn.d.CC1
TIL16:TEOn.d.CC1
TIL17:TEOn.d.TT1X
TIL25:TEOn.d.CC1X
TIL04-TIP454:TEOn.d.CC1
TIL06:TEOn.d.CC1
TIL14:TEOn.d.CC1X
TX303:MZYTT1X
TZI8:MZWCC12XXXXXXX
VL0512447:MZWCC1
VL05128:MZWCC12XXXXXX
VL054178:MZW./.12XXXXXXX
VL05610:MZWCC1
VL056883:MZWCC17XXXXXXX
VL062784:MZWCC14XXXXX
W22:MZYTT1X
W64A:MZYTT1X
  • Y, yellow; W, white.

  • a n.d., not determined.

  • b HapMap2 SNP genotype data (Chia et al. 2012).

  • c Copy number rounded to nearest positive integer.

  • d Features detected by single sequence reads in CML228 and OH43, respectively. Absence of corroborating evidence of other Wc features in these inbreds suggested that the single reads were most likely of spurious origin.