The paper deals with a very interesting topic and it provides important information and methodology to tackle with pollen contamination in pine seed orchards.

The introduction and the plot are well presented, trying to shed some light with updated and improved methods to quantify the amount of external pollen in the improved seed production. Selfing, as a different issue for inbreeding and genetic diversity reduction is considered as well.

The three sampling strategies used provide sound results on the problem studied, in particular the number of genotypes included in the study and the use of SNPs for it.

The variability of the results in the three orchards monitored is huge and it is properly discussed on the basis of distance of surrounding stands of the same species, pedological characteristics, age (intensity of flowering) of the ramets and meteorological factors (dryness).

In general, after reading the manuscript, the main idea is that pollen contamination is high, mean rate of 50% with peaks until 96%, and this mean value is reflecting the early? age of the three seed orchards (10-11 years old in the best case), so is it expected, perhaps, a higher contamination  in the near future when the orchards reach the maximum size, flowering intensity and productivity?. I suggest including some comment about it in conclusions.

The sentence “Assuming that the foreign pollen comes from unimproved stands, we calculated that the expected genetic gain would fall from 30% to 24%....” needs to be explained in deep. Is because the expected gg of 30 % took into account a similar rate of contamination that the obtained in the manuscript?

All in all IMHO,  if the las two raised questions could be elucidated, the draft is worth for publication in a high impact journal.

The manuscript offers an thorough experimental assessment on pollen contamination in Pinus pinaster seed orchards in France. From my limited expertise in this particular field, I believe the experimental design and data analysis are both flawless. The paper is well written in a correct, neutral style, so it generally reads well with the exceptions that will be deailed below.

My main concern about the manuscript is how the main questions, results and discussion is presented and organized, and also a (perhaps) excessive will to explain everything beyond the possibilities of the experiment.  

The reader finds too often relevant (or highly expectable) results that were not properly detailed in the objectives section at the end of the introduction. Fistly, the key effect of the sorrounding forest populations among the three seed orchards cannot be presented as a "finding" but rather as a confirmation of the expected result. Second, the effects of plant age and the location within the orchard are not even mentioned in the objectives, but they are mentioned both in the results and discussion. Similarly, environmental factors related to the yearly differences only pop up at the end of the discussion. Why not mentioning them from the very beggining?. 

This drawbacks are indeed related with a too long discussion, that could be shortened with a closer match between the results and hypotheses / expectations. Finally, the conclusions MUST be reduced considerably, such that only real conclusions are left, without repeating the argumentation of the discusion and keeping a lower level of speculation.

Specific comments:

Line 28: avoid too vague wording like "Several interpretative factors were highlighted". Declare exacly which ones instead. 

Line 33: Similarly: "considerable variability" is not specific enough

Line 35: Similarly "identifying new research perspectives" is too vague. Please, be more specific.

Line 62: This is the first mention of the core question of the paper. I find this is too demanding for the reader. An earlier mention would help

Line 74: "easy to multiplex", is this right??

Lines 79-84. This part needs a complete rewriting in the line stated above: declare hypotheses / expectations related to the effect of the sorrounding stands of the species, the environmental effects, the position within each orchard and the age of the orchard plants. 

Line 122 (Table). I think including here the distance to the nearest large maritime pine stands would improve the reading.

Line 192. Please avoid achronyms whenever not necessary. Here use "seed orchard" instead.

Line 197-198: This cannot be shown as something "unexpected", but rather the confirmation of a reasonable expectation.

Line 200: I think this result highlye relevant, and actually it is mentioned later on in the discussion. Threfore, I think enough importance should be given in the objectives, and showing the figures.

Line 230. Was this mentioned before as an objective??

Line 264-267: I recommend something more "catchy" to start the discussion, giving a clearer idea of your contribution beyond the previous knowledge.

Line 288: As expected....

Line 298-300: Again, highly expectable

Line 301. I suggest starting by declaring the evident importance of reproductive phenology, and then how the soil and climate conditions affects it.

Lines 308-309. As already stated, give plant age the necessary relevance throughout the work, or remove it!

Lines 318-319: The same thing about position within the orchard

Lines 328-332: Idem about yearly rainfall

Lines 351-352. Again, a totally new idea that had not been mentioned elsewhere (unless I'm wrong!)

Lines 357-390. Forgive me, but this is fine example of what IS NOT a Conclusions section. Extremely long and little conclusive. Please, reduce it to one fourth, and let it be real conclusions.