(A) Normal frequency distribution of CCR2 periodicity in BxS individuals. Blue-colored bars represent periodicity after photic entrainment, and magenta-colored bars represent periodicity after …
Period estimates of CCR2::LUC expression in (A) three independent HIFs (57, 92, and 343) harboring either the Bay-0 or the Sha allele at QTL confidence interval (B) parental accessions and NIL-S …
Free-running profile of CCR2::LUC expression in Bay-0, Sha, and NIL in darkness (A), Left y-axis shows the luminescence measures of Bay and NIL, and the right y-axis shows the luminescence measures …
(A) Flowering time of HIF 89-S, HIF 539-B, NIL, and Bay-0 under long day (16L:8D) and short day (8L:16D). The flowering time was counted as the number of days at the appearance of 1 cm bolt. (B) …
(A) Schematic diagram explaining the different promoter-coding combinations used in (B). The Sha promoter of ELF3 fused with different coding regions is shown (for details see 'Materials and …
(A) Free-running profile of LHY::LUC expression in ELF3-Bay and ELF3-A362V in a 15-day continuous experiment under consecutive light and in dark conditions. The plants were entrained for 7 days …
(A–C) Scatter plot for R.A.E. against period showing estimates of individual ELF3-Bay and ELF3-A362V lines shown in (Figure 5A). Only lines with R.A.E. < 1.0 were plotted.
(A) Phase shifts in dark-adapted seedlings after resumption to LL. ELF3-Bay and ELF3-A362V plants entrained for 7 days under light/dark cycles (LD) were transferred in DD for 1 day and then …
Free-running period of Bay and NIL-S under different intensities of (A) red (B) blue and (C) red+blue lights (∼3:1). Plants were entrained for 7 days under 12 hr LD cycles (white light) before …
(A and G) CCA1::LUC, (B and H) LHY::LUC, (C and I) TOC1::LUC, (D and J) GI::LUC, (E and K) PRR7::LUC, and (F and L) PRR9::LUC. Error bars represent SEM and are shown on every third reading. Note …
Transcript accumulation of different clock genes in Bay-0, Sha, NIL-S and elf3-4 under LL. (A) CCA1::LUC, (B) LHY::LUC, (C) PRR7::LUC, and (D) PRR9::LUC, (E) GI::LUC, and (F) TOC1::LUC. Error bars …
(A) and (B) show maximum intensity projection of ELF3-YFP localization in root cells of ELF3-Bay-YFP (A) and ELF3-Sha-YFP (B). Arrows indicate the nuclei that are magnified four times and shown in …
Accumulation pattern of ELF3 transcript and encoded protein in ELF3-Bay-YFP and ELF3-Sha-YFP lines under LD (A and B), LL (C and D) and in DD (E and F). For LD, plants were grown under 12L:12D …
(A) Neighbor-joining tree showing the phylogenetic relationship of ELF3 coding sequence of 251 accessions. All accessions harboring ELF3-Sha allele were grouped in a single clade indicated by …
Circadian periodicity analysis of the BxS RILs after photic or thermal entrainment
Zeitgeber | Mean* | S. E | 95% confidence interval | ||
---|---|---|---|---|---|
Lower bound | Upper bound | ||||
BxS | LD | 26.702 | 0.035 | 26.633 | 26.771 |
TMP | 26.269 | 0.034 | 26.202 | 26.335 |
LD-TMP | BxS | |
---|---|---|
Pairwise comparisons | Mean difference (hr) | 0.433 |
S. E | 0.047 | |
Significance | <0.001 | |
Correlations | Correlation coefficient | 0.86 |
Significance | 0.001 |
LD stands for photic-zeitgeber and TMP for thermal-zeitgeber.
denotes the modified population marginal mean for the 95% Confidence Interval.
S.E. denotes standard error.
LD-TMP denotes the pairwise comparisons such that TMP period is subtracted from LD period.
Statistical analysis of CCR2 circadian periodicity after the two zeitgeber protocols for BxS population
Overall model | Univariate BxS | |
---|---|---|
Factor | F | P |
Genotype | 7.753 | <0.001 |
Environment | 36.413 | <0.001 |
Environment*Genotype | 2.183 | <0.001 |
Univariate LD | CV LD | Univariate TMP | CV TMP | ||||
---|---|---|---|---|---|---|---|
F | P | F | P | ||||
BxS | RIL | 10.387 | <0.001 | 18.043 | 7.382 | <0.001 | 16.498 |
TRANS (RIL) | 1.513 | <0.001 | 1.915 | <0.001 |
F = mean sum of squares\error sum of squares. P = significance value of the F-ratio.
Genotype denotes RIL, ENVIRONMENT denotes the different entrainments, TRANS denotes independent transformants of each genotype.
denotes the testing of an interaction between two factors, whereas B(A) denotes the testing main factor A in which a factor B is nested.
CV is the coefficient of genetic variation, LD stands for photic and TMP stands for thermal entrainment.
NS denotes nonsignificance.
Localization of the main QTLs for the BxS population after photic vs thermal zeitgeber protocols
Zeitgeber | H2 | Chromosome | Position | LOD score (*) | % expl variance | F | p value | 2a |
---|---|---|---|---|---|---|---|---|
(cM) | (h) | |||||||
LD | 0.76 | I | 63.7 | 3.21 | 14.9 | 7.704 | 0.007 | −0.614 |
II | 34.5 | 5.72 | 27.3 | 20.784 | <0.001 | 1.003 | ||
IV | 69.9 | 3.89 | 17.1 | 14.003 | <0.001 | 0.833 | ||
TMP | 0.73 | II | 34.5 | 4.56 | 25.5 | 25.033 | <0.001 | 0.988 |
IV | 69.9 | 3.26 | 16.2 | 6.501 | 0.014 | 0.508 |
H2 denotes broad sense heritability.
(cM) denotes centiMorgan.
(*) LOD- score threshold was determined at 2.4.
% expl variance is the percent of explained variance.
F = mean sum of squares\error sum of squares.
P denotes the significance value of the F-ratio.
2a denotes the additive effect of Bay allele when the effect of the Sha allele on period is subtracted.
(h) denotes the effect in hours.
− denotes that the Sha allele displayed longer period than that of Bay allele.
Geographical location of the 15 accessions with ELF3-Sha allele
Abbreviation | Name | Stock ID | Country | Location | Latitude | Longitude | Altitude |
---|---|---|---|---|---|---|---|
ICE130 | Kolyvan/Kly-4 | CS76384 | Russia | Kolyvan | 51.32 | 82.55 | 505 |
ICE138 | Lebjashje/Leb-3 | CS76426 | Russia | Altaijskij Kraj | 51.65 | 80.82 | 301 |
ICE70 | Borskoje/Borsk-2 | CS76421 | Russia | Samarskaja Oblast | 53.04 | 51.75 | 75 |
ICE71 | Shiguljovsk/Shigu-1 | CS76375 | Russia | Samarskaja Oblast | 53.33 | 49.48 | 181 |
ICE72 | Shiguljovsk/Shigu-2 | CS76374 | Russia | Samarskaja Oblast | 53.33 | 49.48 | 181 |
Kar1 | Karakol | CS76522 | Kyrgyzstan | Susamyr village/West Karakol river | 42.3 | 74.36 | 2503 |
Kondara | Kondara | CS76532 | Tadjikistan | Khurmatov | 38.5 | 68.5 | 815 |
Kz9 | Kazakhstan | CS76537 | Kazakhstan | Karagandy | 49.67 | 73.33 | 535 |
Nemrut | Nemrut-1 | CS76398 | Turkey | Nemrut Dag | 38.64 | 42.23 | 2249 |
Neo6 | Neo6 | CS76560 | Tajikistan | Jawshangoz village | 37.35 | 72.46 | 3467 |
Rubenzhoe | Rubenzhoe-1 | CS76594 | Ukraine | Rubezhnoe | 49.01 | 38.36 | 56 |
Sha | Shakdara | CS76382 | Tadjikistan | Pamiro-Alay | 38.90 | 69.05 | 3439 |
Sorbo | Sorbo | CS22653 | Tadjikistan | 38.82 | 69.48 | 1751 | |
Westkar4 | West Karakol | CS76629 | Kyrgyzstan | Karakol valley | 42.3 | 74 | 2187 |
Zal1 | Zal1 | CS76634 | Kyrgyzstan | Tchong-Kemin valley/Djachyl-Kul lake | 42.8 | 76.35 | 2230 |
RIL periodicity of CCR2::LUC in BxS after photic entrainment.
RIL periodicity of CCR2::LUC in BxS after thermal entrainment.
Detail of primers used.