Peer review of: Arabidopsis FHY3 and FAR1 integrate light and strigolactone signaling to regulate branching (2020)

REVIEWERS' COMMENTS: 

Reviewer #1 (Remarks to the Author): 

The authors have addressed my comments. 

Reviewer #2 (Remarks to the Author): 

In this revised manuscript, the authors have addressed, or claimed to have addressed, all my 
criticisms from my previous review. 

However, I continue to have concerns about some of experiments and the incomplete 
documentation provided by the authors. Here is a sample of concerns: 

1) The manuscript uses a huge number of different transgenic Arabidopsis lines. How were these 
transformed? What strategy did they use to make stable T3 homozygous lines? How many 
independent transgenic lines did they examine for each construct? What percentage showed the 
phenotype? Which line did they pick for the final analysis, and why? 

Based on the speed at which they generated new constructs for this manuscript (e.g. 
pBRC1wt:gBRC1 and pBRC1m:gBRC1) -- less than 6 months -- the authors must have used T1 
lines for this analysis. Thus each "sample" of a transgenic line would have actually consisted of 
separate, independent T1 transgenic lines, with different genomic insertions and therefore effects 
on gene expression. Some of the lines would have no phenotype at all. It is simply not appropriate 
to perform phenotypic experiments on a collection of independent T1 lines. 

Is this also the case for all the other transgenic lines in the paper? Did the authors perform the 
experiments on a collection of freshly generated, independent T1 lines? Or did they use T3 lines? If 
I asked the authors for seed from the lines shown in the paper, would they actually be able to 
send me homozygous lines? 

All of this is completely standard experimental practice when using transgenic Arabidopsis, and 
important methodological information to provide. 

2) Statistics 
The majoriy of the statistical methodology provided in the paper just says: 
“Different letters indicate significant differences by two-way ANOVA (p<0.01). But ANOVA does not 
indicate where the differences occur, only that there are significant differences. So how did the 
authors assign these letters? 

Did the authors check their data for normality and use the appropriate non-parametric test where 
needed? (a core requirement for publishing in Nature journals). 

3) Figure manipulation 
I would also draw the authors attention to Figure 5B, where in the top row, exactly the same leaf 
has apparently been infiltrated with SMXL7-cLUC AND SMXL8-cLUC, in exactly the same splotch 
pattern, but with different signal intensities. Of course, these are just the same image with 
different exposures, masquerading as separate experiments. 

This is not a freak mistake, because on the lower row of Figure 5B, exactly the same leaf has 
apparently been infiltrated with SMXL6-cLUC AND SMXL7-cLUC, in exactly the same splotch 
pattern, but again with different signal intensities. Again, the same image with different exposures 
is being used to cover two experiments. 

I would suggest that the authors need to take a very careful look at all their images, to make sure 
there are no more occurrences of image duplication between experiments. Obviously this is not 
acceptable.