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In view of the short study period and despite our best efforts, the value of a statistical analysis of the seedling data is possibly ambiguous.
This was further supported by the 7 d old seedling data where growth of the rice seedlings was significantly reduced after 100 μM Cr (VI) treatment.
EXPRSS has 64% overlap with leaf disc data (236/370), 49% overlap with seedling data (181/372) and 23% overlap with leaf data (45/199) for downregulated genes.
For upregulated genes EXPRSS has 92% overlap with leaf disc data (487 out of 529), 77% overlap with seedling data (626 out of 808) and 74% overlap with leaf data (445 out of 604).
The MIM model based on score as a significance threshold was not able to detect this QTL, but a minor effect QTL was detected using the Bayesian Information Content threshold with LOD 1.8 and explaining 6.5%% of the total variance for the total P content in the seedling (data not shown).
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Germination and seedling emergence data was collected at the beginning of the season.
These seedlings were used not only for our research in this paper but also for root respiration, biomass, and N concentration of seedling foliage (data not shown).
The ranking of plots based on 16S beta diversity were highly correlated with those based on seedling community data (r=0.75; p<0.02).
To identify differential transcript abundance during the functional transition of the cotyledon during seedling development, data obtained from scans of 8 oligo chips obtained for each of 6 time-point comparisons (see Figure 1, Methods) was quantified, uploaded into GeneSpring 7.2 (Silicon Genetics, CA), and then transformed, filtered and normalized (see Methods).
The lse2 seedlings rarely survived under full-sun field conditions, requiring heavily shaded environments (e.g., surrounding one lse2 seedling with WT seedlings; data not shown) to persist.
In addition, P. aeruginosa (PA14) is highly susceptible to gentamycin at concentrations less than 10 µg/ml in MS medium alone or in conditioned medium, i.e., after growth of seedlings (data not shown).
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