A Metropolis-Hastings algorithm was used to sample σgi from its distribution conditional on y*, p σgi | y*), where y* denotes the data y corrected for the mean and all other genetic effects except the marker effect (gi) [ 15].
The key roles played by GI are evident when analyzing the effect of gi mutants over leaf movement and gene expression rhythms of multiple clock controlled and flowering genes, including GI itself [21], [22].
Given σgi, marker effects, gi was sampled from a Normal distribution as prior and using Gibbs sampling [ 16].
After overnight induction, PIN1 and PIN3 abundance was significantly increased in inflorescences of the pAlcA:HEC1 line compared with the respective GUS control and this effect was further enhanced by auxin co-treatment (Fig. 4A,B).
The variance of the marker effects (σ gi ) was estimated for every marker using a relevant prior distribution, which was a mixture of an inverted chi-squared distribution and a discrete probability mass at σgi = 0.
This was consistent with previous reports on the effect of gi mutations on SOC1 expression in whole seedlings [ 23, 24].
A much greater effect of gi mutations on SOC1 expression in the shoot apex would be expected as there is strong up regulation of SOC1 in the shoot apex in LD [ 23, 24], but this would be greatly diluted in our experiments as we examined SOC1 expression in total aerial parts of young plants.
Both gi-3 lov1-4 double mutants and gi-3 single mutants showed a similar flowering time (average leaf number: 26.7±1.3 vs. 27.0±2.2, respectively), indicating that lov1-4 mutation failed to suppress the late flowering of gi-3 mutants and that de-repression of CO expression in the absence of LOV1 function would not be sufficient to overcome the effect of gi-3 mutations.
Mixing by vortex with carborundum and separation by centrifugation appeared to have the greatest effect on GUS expression in switchgrass.
Some effects of gi mutations on TOC1 transcript accumulation were reported previously, but these experiments were carried out under very different light or temperature regimes from this work [ 6, 8].
