Table 3. Sequence features detected in genomes of maize and teosinte accessions.
| Inbred/accession | Endosperm colora | PZE0680879922b | Ccd1 copy numberc | Macro-transposon right junction (Tam3La-5') | Tam3La-3' junction | Macro-transposon left junction (Tam3Ld-3') | Tam3Lb-3 junction | Tam3Lc left junction | Tam3Lc retroelement junction | Tam3Lb/c right junction | Vacant Helitron 1 site (Wc progenitor) | Vacant Helitron 1 site (teosinte variant) | OH43 Helitron insertion | B73 Helitron 1 insertion site |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| B73:MZ | Y | TT | 1 | X | ||||||||||
| B97:MZ | Y | TT | 1 | X | ||||||||||
| BKN009:MZ | n.d. | CC | 1 | |||||||||||
| BKN010:MZ | n.d. | CC | 1 | |||||||||||
| BKN011:MZ | n.d. | TT | 1 | |||||||||||
| BKN014:MZ | n.d. | CC | 1 | X | ||||||||||
| BKN015:MZ | W | CC | 16 | X | X | X | X | X | X | |||||
| BKN016:MZ | Y | TT | 1 | X | ||||||||||
| BKN017:MZ | n.d. | CC | 3 | X | X | X | ||||||||
| BKN018:MZ | W | CC | 8 | X | X | X | X | X | X | |||||
| BKN019:MZ | n.d. | TT | 1 | |||||||||||
| BKN020:MZ | n.d. | TT | 1 | |||||||||||
| BKN022:MZ | n.d. | CC | 11 | X | X | X | X | X | X | X | X | |||
| BKN023:MZ | n.d. | CC | 1 | X | ||||||||||
| BKN025:MZ | n.d. | ./. | 13 | X | X | X | X | X | ||||||
| BKN026:MZ | n.d. | CC | 21 | X | X | X | X | X | X | X | ||||
| BKN027:MZ | n.d. | TT | 1 | X | ||||||||||
| BKN029:MZ | n.d. | CC | 15 | X | X | X | X | X | X | X | X | |||
| BKN030:MZ | n.d. | CC | 2 | X | ||||||||||
| BKN031:MZ | n.d. | CC | 4 | X | X | X | X | X | X | X | X | X | ||
| BKN032:MZ | n.d. | TT | 1 | X | ||||||||||
| BKN033:MZ | n.d. | CC | 1 | |||||||||||
| BKN034:MZ | n.d. | CC | 1 | |||||||||||
| BKN035:MZ | n.d. | CC | 23 | X | X | X | X | X | X | X | X | |||
| BKN040:MZ | W | CC | 14 | X | X | X | X | X | X | X | ||||
| CAU178:MZ | Y | TT | 1 | X | ||||||||||
| CAU478:MZ | Y | TT | 1 | X | ||||||||||
| CAU5003:MZ | Y | TT | 1 | |||||||||||
| CAUCHANG72:MZ | Y | TT | 1 | |||||||||||
| CAUMO17:MZ | Y | TT | 1 | X | ||||||||||
| CAUZHENG58:MZ | Y | TT | 1 | |||||||||||
| CML103:MZ | W | CC | 13 | X | X | X | X | X | X | X | X | |||
| CML133:MZ | W | CC | 1 | |||||||||||
| CML192:MZ | Y | TT | 1 | |||||||||||
| CML202:MZ | W | CC | 12 | X | X | X | X | X | ||||||
| CML206:MZ | W | ./. | 1 | |||||||||||
| CML228:MZ | Y | TT | 1 | Xd | X | |||||||||
| CML247:MZ | W | ./. | 1 | |||||||||||
| CML277:MZ | W | CC | 8 | X | X | X | X | X | X | |||||
| CML312SR:MZ | W | CC | 17 | X | X | X | X | X | X | |||||
| CML322:MZ | W | CC | 9 | X | X | X | X | X | X | X | ||||
| CML330:MZ | W | CC | 3 | X | X | X | X | X | ||||||
| CML333:MZ | W | CC | 2 | X | X | X | X | X | ||||||
| CML341:MZ | W | CC | 10 | X | X | X | X | |||||||
| CML411:MZ | Y | TT | 1 | X | ||||||||||
| CML418:MZ | W | CC | 10 | X | X | X | X | X | X | |||||
| CML479:MZ | Y | TT | 1 | X | ||||||||||
| CML504:MZ | W | CC | 16 | X | X | X | X | X | X | X | ||||
| CML505:MZ | W | CC | 10 | X | X | X | X | X | X | X | ||||
| CML511:MZ | W | CC | 16 | X | X | X | X | X | ||||||
| CML52:MZ | Y | TT | 1 | X | ||||||||||
| CML52R:MZ | Y | ./. | 1 | |||||||||||
| CML69:MZ | Y | TT | 2 | X | X | X | X | X | ||||||
| CML84:MZ | W | CC | 11 | X | X | X | X | X | ||||||
| CML85:MZ | W | CC | 1 | |||||||||||
| CML96:MZ | W | CC | 1 | |||||||||||
| CML99:MZ | W | CC | 11 | X | X | X | X | X | X | X | ||||
| H16:MZ | W | CC | 1 | |||||||||||
| HP301:MZ | Y | TT | 1 | |||||||||||
| IL14H:MZ | W | ./. | 1 | X | ||||||||||
| KI11:MZ | Y | TT | 1 | |||||||||||
| KI3:MZ | Y | TT | 1 | X | ||||||||||
| KY21:MZ | W | CC | 13 | X | X | X | X | |||||||
| M162W:MZ | W | CC | 7 | X | X | X | X | X | X | X | ||||
| M37W:MZ | W | CC | 1 | |||||||||||
| MO17:MZ | Y | TT | 1 | X | ||||||||||
| MO18W:MZ | W | CC | 6 | X | X | X | X | X | X | X | ||||
| MS71:MZ | Y | TT | 1 | X | ||||||||||
| NC350:MZ | Y | TT | 8 | X | X | X | X | X | X | X | ||||
| NC358:MZ | Y | TT | 1 | X | ||||||||||
| OH43:MZ | Y | TT | 1 | Xd | X | |||||||||
| OH7B:MZ | Y | ./. | 1 | X | ||||||||||
| P1:MZ | W | CC | 16 | X | X | X | X | X | X | X | X | |||
| P39:MZ | Y | TT | 1 | X | ||||||||||
| TIL01:TEO | n.d. | CC | 1 | X | ||||||||||
| TIL02:TEO | n.d. | CC | 1 | X | ||||||||||
| TIL03:TEO | n.d. | CC | 1 | X | ||||||||||
| TIL04-TIP285:TEO | n.d. | CC | 1 | |||||||||||
| TIL05:TEO | n.d. | CC | 1 | |||||||||||
| TIL06:TEO | n.d. | CC | 1 | X | ||||||||||
| TIL07:TEO | n.d. | CC | 1 | X | ||||||||||
| TIL08:TEO | n.d. | CC | 1 | X | ||||||||||
| TIL09:TEO | n.d. | CC | 1 | X | ||||||||||
| TIL10:TEO | n.d. | CC | 1 | X | ||||||||||
| TIL11:TEO | n.d. | CC | 1 | |||||||||||
| TIL12:TEO | n.d. | CC | 1 | X | ||||||||||
| TIL15:TEO | n.d. | CC | 1 | |||||||||||
| TIL16:TEO | n.d. | CC | 1 | |||||||||||
| TIL17:TEO | n.d. | TT | 1 | X | ||||||||||
| TIL25:TEO | n.d. | CC | 1 | X | ||||||||||
| TIL04-TIP454:TEO | n.d. | CC | 1 | |||||||||||
| TIL06:TEO | n.d. | CC | 1 | |||||||||||
| TIL14:TEO | n.d. | CC | 1 | X | ||||||||||
| TX303:MZ | Y | TT | 1 | X | ||||||||||
| TZI8:MZ | W | CC | 12 | X | X | X | X | X | X | X | ||||
| VL0512447:MZ | W | CC | 1 | |||||||||||
| VL05128:MZ | W | CC | 12 | X | X | X | X | X | X | |||||
| VL054178:MZ | W | ./. | 12 | X | X | X | X | X | X | X | ||||
| VL05610:MZ | W | CC | 1 | |||||||||||
| VL056883:MZ | W | CC | 17 | X | X | X | X | X | X | X | ||||
| VL062784:MZ | W | CC | 14 | X | X | X | X | X | ||||||
| W22:MZ | Y | TT | 1 | X | ||||||||||
| W64A:MZ | Y | TT | 1 | X |
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.