Table 2.
FT genes in rice, sorghum, foxtail millet, brachypodium, barley, and bread wheat.
| Gene | Chr (Mbp) | Gene modela | Exons | Protein (aa) | Closest rice FTL homolog | Homology to rice gene: e-value (% identity)c |
|---|---|---|---|---|---|---|
| O. sativa | ||||||
| OsFTL1 | 1 (6.50) | Os01g11940.1 | 4 | 276 | N/A | N/A |
| OsFTL2 | 6 (2.95) | Os06g06320.1 | 4 | 179 | N/A | N/A |
| OsFTL3 | 6 (2.93) | Os06g06300.1 | 4 | 178 | N/A | N/A |
| OsFTL4 | 9 (19.98) | Os09g33850.1 | 4 | 173 | N/A | N/A |
| OsFTL5 | 2 (23.59) | Os02g39064.1 | 4 | 174 | N/A | N/A |
| OsFTL6 | 4 (24.39) | Os04g41130.1 | 4 | 174 | N/A | N/A |
| OsFTL7 | 12 (7.24) | Os12g13030.1 | 4 | 177 | N/A | N/A |
| OsFTL8 | 1 (5.65) | Os01g10590.1 | 4 | 169 | N/A | N/A |
| OsFTL9 | 1 (31.34) | Os01g54490.1 | 4 | 175 | N/A | N/A |
| OsFTL10 | 5 (25.67) | Os05g44180.1 | 4 | 174 | N/A | N/A |
| OsFTL11 | 11 (10.74) | Os11g18870.1 | 4 | 174 | N/A | N/A |
| OsFTL12 | 6 (20.97) | Os06g35940.1 | 4 | 173 | N/A | N/A |
| OsFTL13 | 2 (7.49) | Os02g13830.1 | 4 | 185 | N/A | N/A |
| S. bicolor | ||||||
| SbFT1 | 10 (3.46) | Sb10g003940.1 | 4 | 179 | OsFTL2 | 4e-68 (91.1) |
| SbFT2 | 3 (1.51) | FGENESH00000046519 | 5 | 173 | OsFTL1 | 2e-64 (88.9) |
| SbFT3* | 9 (55.15) | Sb09g025760.1* | 4* | 118* | OsFTL10l | 6e-18 (86.5) |
| SbFT4 | 10 (48.39) | Sb10g021790.1 | 4 | 173 | OsFTL12 | 5e-43 (86.8) |
| SbFT5 | 3 (62.75) | Sb03g034580.1 | 4 | 177 | OsFTL9l | 1e-37 (83.9) |
| SbFT6A | 4 (9.46) | Sb04g008320.1 | 4 | 182 | OsFTL13 | 1e-77 (91.5) |
| SbFT6B | 6 (33.53) | Sb06g012260.1 | 4 | 185 | OsFTL13 | 8e-42 (86.0) |
| SbFT7 | 8 (15.21) | Sb08g008180.1 | 4 | 177 | OsFTL7 | 1e-80 (92.3) |
| SbFT9 | 6 (50.27) | Sb06g020850.1 | 4 | 174 | OsFTL6 | 2e-51 (86.2) |
| SbFT10 | 2 (64.81) | Sb02g029725.1 | 4 | 173 | OsFTL4 | 2e-73 (92.5) |
| SbFT11 | unknown | Sb0010s003120.1 | 4 | 174 | OsFTL11 | 1e-31 (83.7) |
| SbFT12 | 4 (55.04) | Sb04g025210.1 | 4 | 174 | OsFTL5 | 2e-66 (91.3) |
| S. italica | ||||||
| SiFT1A | 4 (5.21) | Si008517m.g | 4 | 178 | OsFTL2 | 3e-84 (92.2) |
| SiFT1B | 4 (12.52) | Si007366m.g | 4 | 177 | OsFTL2 | 3e-66 (90.4) |
| SiFT1C | 4 (9.10) | Si008120m.g | 4 | 165 | OsFTL2 | 3e-38 (86.7) |
| SiFT2 | 5 (13.59) | De novo predictionb | 4 | 173 | OsFTL1 | 4e-62 (89.2) |
| SiFT3 | 3 (13.16) | De novo predictionb | 4 | 199 | OsFTL10k | 2e-27 (82.3) |
| SiFT4 | 4 (29.10) | Si007376m.g | 4 | 173 | OsFTL12 | 7e-39 (85.2) |
| SiFT5 | 5 (36.83) | Si005012m.g | 4 | 179 | OsFTL9 | 3e-41 (86.3) |
| SiFT6A | 1 (2.32) | Si020173m.g | 4 | 184 | OsFTL13 | 6e-64 (88.8) |
| SiFT6B | 7 (17.29) | Si011866m.g | 4 | 184 | OsFTL13 | 1e-52 (87.8) |
| SiFT7 | 3 (5.97) | Si025116m.g | 3 | 175 | OsFTL7 | 3e-90 (94.1) |
| SiFT9 | 7 (23.45) | Si012372m.g | 4 | 174 | OsFTL6 | 3e-56 (87.0) |
| SiFT10 | 2 (37.13) | De novo predictionb | 4 | 173 | OsFTL4 | 2e-67 (89.6) |
| SiFT11 | 8 (14.74) | Si027589m.g | 4 | 174 | OsFTL11 | 5e-43 (85.9) |
| SiFT12 | 1 (30.15) | Si020105m.g | 4 | 174 | OsFTL5 | 6e-61 (87.9) |
| B. distachyon | ||||||
| BdFT1 | 1 (47.49) | Bradi1g48830.1 | 4 | 177 | OsFTL2 | 2e-76 (90.8) |
| BdFT2 | 2 (5.40) | Bradi2g07070.1 | 4 | 173 | OsFTL1 | 2e-71 (90.2) |
| BdFT3 | 2 (17.34) | Bradi2g19670.1 | 4 | 180 | OsFTL10 | 4e-28 (83.3) |
| BdFT4 | 1 (34.32) | Bradi1g38150.1 | 4 | 173 | OsFTL12 | 2e-57 (88.5) |
| BdFT5 | 2 (49.83) | Bradi2g49795.1 | 4 | 177 | OsFTL9 | 2e-29 (84.7) |
| BdFT6 | 3 (7.00) | Bradi3g08890.1 | 4 | 182 | OsFTL13 | 1e-58 (89.2) |
| BdFT8A | 4 (44.37) | Bradi4g39750.1 | 4 | 171 | OsFTL7 | 1e-55 (87.9) |
| BdFT8B | 4 (44.37) | Bradi4g39760.1 | 4 | 172 | OsFTL7 | 3e-69 (90.9) |
| BdFT8C | 4 (44.36) | Bradi4g39730.1 | 4 | 173 | OsFTL7 | 2e-66 (89.8) |
| BdFT9 | 5 (17.44) | Bradi5g14010.1 | 4 | 174 | OsFTL6 | 2e-64 (88.7) |
| BdFT10 | 4 (40.55) | Bradi4g35040.1 | 4 | 173 | OsFTL4 | 1e-86 (93.2) |
| BdFT12 | 3 (49.57) | Bradi3g48036.1 | 4 | 174 | OsFTL5 | 2e-66 (91.3) |
| H. vulgare | ||||||
| HvFT1 | 7H (41.48) | MLOC_68576.1 | 3 | 177 | OsFTL2 | 7e-73 (90.9) |
| HvFT2 | 3H (45.99)h | DQ297407 | 4 | 178 | OsFTL1 | 2e-70 (90.4) |
| HvFT3 | 1H (419.42)i | HM133572 | 4 | 180 | OsFTL9k | 9e-20 (81.2) |
| HvFT4 | 2H (71.03) | MLOC_74854.1 | 4 | 173 | OsFTL12 | 1e-40 (85.0) |
| HvFT5 | 4H (2.99)j | EF012202.1 | 4 | 180 | OsFTL10 | 1e-15 (93.2) |
| HvFT6 | 6H (175.57) | Morex_contig_54196d | 4 | 182 | OsFTL13 | 6e-61 (88.3) |
| HvFT7 | 5H (302.12) | Morex_contig_1573409e | 4 | 178 | OsFTL7 | 2e-67 (90.2) |
| HvFT8A | 2H (601.97) | Morex_contig_37453d | 4 | 173 | OsFTL7 | 1e-49 (86.4) |
| HvFT8B | 2H (609.86) | Morex_contig_1560712e | 4 | 173 | OsFTL7 | 1e-49 (86.4) |
| HvFT8C | 2H (589.61) | Morex_contig_158449e | 4 | 172 | OsFTL7 | 3e-47 (86.1) |
| HvFT9 | 2H (390.11) | MLOC_58552.3 | 4 | 174 | OsFTL6 | 2e-70 (90.0) |
| HvFT10 | 5H (457.04) | Morex_contig_44860b | 4 | 172 | OsFTL4 | 2e-79 (91.9) |
| HvFT11 | 4H (155.44) | MLOC_57326.1 | 4 | 179 | OsFTL11 | 1e-24 (82.0) |
| HvFT12 | 6H (245.55) | MLOC_64619.2 | 4 | 174 | OsFTL5 | 4e-68 (89.2) |
| T. aestivumm | ||||||
| TaFT1-A1 | 7A | Traes_7AS_EBD5F1F54.1 | 3 | 177 | OsFTL2 | 6e-61 (88.6) |
| TaFT1-B1* | 7B | Traes_7BS_581AA844D.1* | 3* | 148* | OsFTL2 | 2e-42 (86.7) |
| TaFT1-D1* | 7D | Traes_7DS_12C14942B.1* | 3* | 155* | OsFTL2 | 6e-42 (88.7) |
| TaFT2-A1* | 3A | Traes_3AS_6D1315D0A.3* | 3* | 94* | OsFTL1 | 5e-63 (92.5) |
| TaFT2-B1 | 3B | Traes_3B_2A454DB62.1 | 2* | 102* | OsFTL1 | 4e-82 (92.7) |
| TaFT3-A1 | 1A | Traes_1AL_4F90FEB36.1 | 4 | 180 | OsFTL10 | 1e-25 (82.8) |
| TaFT3-B1 | 1B | Traes_1BL_2C43B822A.1 | 4 | 180 | OsFTL9 | 3e-29 (83.1) |
| TaFT3-D1 | 1D | Traes_1DL_CE737E359.1 | 4 | 179 | OsFTL10 | 2e-30 (85.1) |
| TaFT4-A1 | 2A | Traes_2AS_64063A59B.1 | 4 | 173 | OsFTL12 | 3e-50 (86.9) |
| TaFT4-A2 | 7A | 7AL_4533105f | 4 | 171 | OsFTL12 | 3e-41 (86.1) |
| TaFT4-B1 | 2B | Traes_2BS_43A8E1EC8.1 | 4 | 173 | OsFTL12 | 8e-48 (86.4) |
| TaFT4-D1 | 2D | Traes_2DS_81D62E5E9.1 | 4 | 173 | OsFTL12 | 5e-49 (87.2) |
| TaFT5-A1 | 5A | Traes_5AL_20DFB725B.1 | 4 | 178 | OsFTL10 | 1e-25 (84.1) |
| TaFT5-A2 | 5A | 5AL_2805675d | 6 | 189 | OsFTL10 | 3e-26 (83.1) |
| TaFT5-B1 | 4B | Traes_4BL_EBE908323.1 | 4 | 180 | OsFTL10 | 2e-26 (83.1) |
| TaFT5-B2* | 4B | 4BL_6996269*g | 2* | 133* | OsFTL10 | 6e-19 (81.2) |
| TaFT5-D1 | 4D | Traes_4DL_C4A99BB83.1 | 4 | 179 | OsFTL10 | 2e-26 (83.1) |
| TaFT5-D2 | 4D | Traes_4DL_CF206DAA3.1 | 4 | 180 | OsFTL10 | 6e-24 (82.5) |
| TaFT5-D3* | 4D | 4DL_14405941*g | 2* | 133* | OsFTL10 | 2e-07 (82.8) |
| TaFT5-D4 | 4D | Traes_4DL_FC267A763.1 | 4 | 180 | OsFTL10 | 3e-16 (81.9) |
| TaFT6-A1 | 6A | Traes_6AS_B3C246E08.1 | 4 | 183 | OsFTL13 | 2e-70 (90.1) |
| TaFT6-B1* | 6B | 6BS_1200904*f | 3* | 104* | OsFTL12 | 5e-14 (91.7) |
| TaFT6-D1 | 6D | Traes_6DS_00E3E39411.1 | 4 | 183 | OsFTL13 | 1e-77 (90.1) |
| TaFT6-D2 | 6D | Traes_6DS_00E3E3941.1 | 4 | 183 | OsFTL13 | 1e-77 (90.1) |
| TaFT7-A1* | 5A | Traes_5AL_1AF8FD33F.1* | 4* | 156* | OsFTL7 | 2e-20 (98.2) |
| TaFT7-B1 | 5B | Traes_5BL_9A27C4A75.1 | 4 | 178 | OsFTL7 | 2e-60 (88.8) |
| TaFT7-D1* | 5D | Traes_5DL_53D0B5EED.1* | 4* | 129* | OsFTL7 | 9e-20 (82.4) |
| TaFT8-A1 | 2A | Traes_2AL_552AE18AD.1 | 4 | 173 | OsFTL7 | 2e-11 (88.2) |
| TaFT8-A2 | 2A | Traes_2AL_2F198B97C.1 | 4 | 171 | OsFTL7 | 2e-36 (84.3) |
| TaFT8-B1 | 2B | Traes_2BL_879586172.1 | 4 | 172 | OsFTL7 | 3e-47 (86.1) |
| TaFT8-B2 | 2B | Traes_2BL_2A9A178A1.1 | 4 | 164 | OsFTL7 | 1e-49 (88.0) |
| TaFT8-B3 | 3B | TRAES3BF053100340CFD_t1 | 4 | 175 | OsFTL7 | 3e-41 (85.1) |
| TaFT8-B4 | 3B | Traes_25121009B.1 | 4 | 175 | OsFTL7 | 5e-20 (86.5) |
| TaFT8-D1* | 2D | Traes_2DL_16EDF0CD2* | 1* | 65* | OsFTL7 | 7e-49 (87.6) |
| TaFT9-A1 | 2A | 2AL_6350768f | 4 | 174 | OsFTL6 | 4e-68 (89.2) |
| TaFT9-B1 | 2B | Traes_2BL_8DB6CE516.1 | 4 | 174 | OsFTL6 | 1e-65 (88.7) |
| TaFT9-D1 | 2D | Traes_2DL_485183B12.1 | 4 | 174 | OsFTL6 | 2e-63 (88.3) |
| TaFT10-A1 | 5A | Traes_5AL_EFB6E50C9.2 | 5 | 178 | OsFTL4 | 2e-85 (93.2) |
| TaFT10-B1 | 5B | Traes_5BL_52911E1E4.2 | 4 | 173 | OsFTL4 | 2e-82 (92.7) |
| TaFT10-D1* | 5D | 5DL_4544439*d | 2* | 73* | OsFTL4 | 2e-65 (91.9) |
| TaFT11-A1 | 4A | Traes_4AL_68B60F6AA.1 | 4 | 179 | OsFTL11 | 1e-40 (84.8) |
| TaFT11-B1 | 4B | Traes_4BS_DCCAE937D.1 | 4 | 179 | OsFTL11 | 2e-33 (83.4) |
| TaFT11-D1 | 4D | Traes_4DS_2D08DBB36.1 | 4 | 179 | OsFTL11 | 1e-40 (84.8) |
| TaFT12-A1 | 6A | Traes_6AL_66B24F155.1 | 4 | 174 | OsFTL5 | 1e-65 (88.7) |
| TaFT12-B1 | 6B | Traes_6BL_DA76A4429.1 | 4 | 174 | OsFTL5 | 2e-66 (91.3) |
| TaFT12-D1 | 6D | Traes_6DL_62A8C29E0.1 | 4 | 174 | OsFTL5 | 4e-65 (91.2) |
No BdFT7 gene was identified in B. distachyon accession BD21. No SbFT8 gene was identified in S. bicolour accession BTx623.
*
Partially truncated gene/pseudogene.
a
For foxtail millet, barley and wheat, genomic contigs accession numbers are listed where no previously annotated gene models existed. In these cases, de novo gene models were made via FGENESH, using the species parameters listed below.
b
Manually edited gene prediction. FGENESH gene prediction using the following parameters:
c
rice model.
d
monocot model.
e
barley model.
f
bread wheat model.
g
B. distachyon model. Chromosomal Mb position determined via DNA homology with:
h
Morex_contig_136243.
i
Morex_contig_2551337.
j
Morex_contig_1572474.
k
E-value hits for OsFTL10 marginally lower than to OsFTL9. However, the length of alignment is longer for OsFTL10 compared to OsFTL9, and so OsFTL10 is listed in the table.
l
While the highest BLASTn hits for OsFT9 and OsFT10 in sorghum are SbFT3 and SbFT5, respectively, investigation of wider colinearity finds the orthologous relationships to be OsFLT9-SbFT5 and OsFTL10-SbFT3 (see Figure 4; Paterson et al., 2009).
m
For wheat, PGSB/MIPS version 2.2 gene models are listed, where available. Note, OsFTL11 and its homologs were not included in the analysis due to its previously reported differentiation from the true FT-gene family (Faure et al., 2007).