Table 3 Variation (SNPs and indels) found in aligned sequences of L. campestre, L. heterophyllum and L. hirtum as well as in aligned sequences of different L. campestre genotypes. The analyzed sequence length, number of polymorphism (Polym), number of nonsynonymous mutations (Non-syn), the number of species specific polymorphisms (Species spec. polym) and percent polymorphism per nucleotide (Polym/nt) are listed according to gene
Gene | Trait/gene function | Analyzed sequence lengtha | L. campestre + L. hirtum + L heterophyllum | L. campestre only | |||||
|---|---|---|---|---|---|---|---|---|---|
Polyma | Non-synb | Polym/nta (%) | Species spec. polyma,c | Polyma | Non-synb | Polym/nta (%) | |||
FRI | vernalization, flowering time | 606_498 | 13_8 | 6 | 2.1_1.6 | 0_0 (0) | 3_3 | 2 | 0.5_0.6 |
MAF2 | vernalization | 532_181 | 7_3 | 2 | 1.3_1.7 | 0_0 (0) | 7_3 | 2 | 1.3_1.7 |
MAF5 | vernalization | 365_206 | 4_4 | 1d | 1.1_1.9 | 0_1 (0) | 1_1 | 0 | 0.3_0.5 |
VIN3 | vernalization | 1347_1121 | 7_5 | 4 | 0.5_0.4 | 0_1 (1) | 0_0 | 0 | 0_0 |
VRN1 | vernalization | 1545_501 | 2_1 | 1 | 0.1_0.2 | 0_0 (0) | 2_1 | 1 | 0.1_0.2 |
VRN2 | vernalization | 1405_536 | 3_1 | 0 | 0.2_0.2 | 0_1 (0) | 0_0 | 0 | 0_0 |
FLC | vernalization, flowering time | 840_170 | 17_5 | 2 | 2_2.9 | 9_5 (3) | 0_0 | 0 | 0_0 |
AGL6 | flowering time | 570_182 | 2_0 | 0 | 0.4_0 | 1_0 (0) | 0_0 | 0 | 0_0 |
AGL16 | flowering time | 772_182 | 9_1 | 1d | 0.3_0 | 3_0 (1) | 1_0 | 0 | 0.13_0 |
AP2 | flowering time | 750_447 | 9_4 | 2 | 1.2_0.9 | 0_4 (0) | 0_0 | 0 | 0_0 |
SOC1 | flowering time | 797_290 | 6_1 | 1d | 0.8_0.3 | 0_0 (0) | 0_0 | 0 | 0_0 |
FUL | flowering time, pod shattering | 942_295 | 3_0 | 0 | 0.3_0 | 1_0 (1) | 0_0 | 0 | 0_0 |
RPL | flowering time, pod shattering | 560_524 | 1_1 | 1 | 0.2_0.2 | 0_0 (0) | 1_1 | 1 | 0.2_0.2 |
ADPG1 | pod shattering | 650_138 | 15_0 | 0 | 2.3_0 | 11_0 (2) | 0_0 | 0 | 0_0 |
ADPG2 | pod shattering | 465_212 | 4_3 | 0 | 0.9_1.4 | 0_0 (0) | 0_0 | 0 | 0_0 |
ALC | pod shattering | 849_321 | 7_1 | 1 | 0.8_0.3 | 3_0 (2) | 0_0 | 0 | 0_0 |
IND | pod shattering | 1025_440 | 11_5 | 3 | 1.1_1.1 | 0_3 (2) | 0_0 | 0 | 0_0 |
NAC012 | pod shattering | 400_305 | 1_0 | 0 | 0.3_0 | 0_0 (0) | 0_0 | 0 | 0_0 |
SHP1 | pod shattering | 1112_330 | 19_5 | 0 | 1.7_1.5 | 0_0 (0) | 11_3 | 0 | 1_0.9 |
SHP2 | pod shattering | 962_411 | 15_6 | 2 | 1.6_1.5 | 1_1 (1) | 1_1 | 1 | 0.1_0.2 |
FAD2 | oil quality | 710_416 | 5_4 | 2 | 0.7_1 | 0_0 (0) | 1_1 | 1 | 0.1_0.2 |
FAE1 | oil quality | 490_478 | 2_2 | 0 | 0.4_0.4 | 0_2 (0) | 0_0 | 0 | 0_0 |
KCS8 | oil quality | 1382_1362 | 12_9 | 5 | 0.9_0.7 | 0_0 (0) | 0_0 | 0 | 0_0 |
TAG1 | oil content | 962_414 | 15_5 | 0 | 1.6_0 | 1_0 (0) | 1_0 | 0 | 0.1_0 |
WRI1 | oil content | 1738_736 | 10_3 | 1 | 0.6_0.4 | 1_0 (1) | 0_0 | 0 | 0_0 |
AGL11 | seed dormancy | 587_253 | 8_1 | 0 | 1.4_0.4 | 1_0 (1) | 1_0 | 0 | 0.2_0 |
ATG5 | plant defense | 1672_392 | 11_0 | 0 | 0.7_0 | 5_0 (1) | 2_0 | 0 | 0.1_0 |
FER | disease resistance | 1112_1112 | 7_7 | 1 + 2d | 0.6_0.6 | 0_0 (0) | 2_2 | 1 | 0.2_0.2 |
GTR2 | glucosinolate transport | 1200_1016 | 7_6 | 1d | 0.6_0.6 | 1_3 (4) | 0_0 | 0 | 0_0 |
HAI2 | seed dormancy | 1034_865 | 11_4 | 1d | 1.1_0.5 | 1_1 (1) | 0_0 | 0 | 0_0 |
Total | Â | 27,381_14,334 | 243_95 | 40 | Â | 39_22 (21) | 34_16 | 9 | Â |
Mean | Â | Â | Â | Â | 0.9_0.8 | Â | Â | Â | 0.14_0.16 |