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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

From: Identification of genes regulating traits targeted for domestication of field cress (Lepidium campestre) as a biennial and perennial oilseed crop

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   27,381_14,334 243_95 40   39_22 (21) 34_16 9  
Mean      0.9_0.8     0.14_0.16
  1. aValues to the left of the underscore are for full length of the sequenced regions whereas values to the right of the underscore are only for the coding regions; b = applies only to the coding regions; c = values within parentheses refer to the total number of polymorphisms unique to L. campestre; d = polymorphism predicted as deleterious for protein function