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Thank you very much for carefully revising the manuscript.
# PeerJ Staff Note - this decision was reviewed and approved by Gerard Lazo, a PeerJ Section Editor covering this Section #
Solid,, and with acknowledged challenges that are clearly described.
Well done and clear.
I felt like the revisions were done well.
Please consider to greatly shorten this paper and minimize your speculations. In addition, you should take into account the advice from reviewer #2 about a de novo assembly of the reads that don't map, to identify genes in the teosinte parent that are missing from the reference. If you think this is beyond the scope of this manuscript, you should at least discuss that this option is missing here.
Overall, this manuscript reads like a Master’s thesis that was re-worked into a manuscript. Unfortunately, the manuscript is overly long making it difficult to distill the key data and interpretation from the manuscript. The manuscript could easily be trimmed to 1/3rd of its length and be stronger.
Page 24 has different line #’s
‘where’ to ‘were’
‘form’ to ‘from’
I am concerned there are a lot of interpretations from what is really a small number of indivduals. The authors should comment on the power to make interpretations, and the significance of these interpretations, with data from so few indivdiduals.
Line 29: I think it is a misnomer to use the term ‘novel whole-genome sequence data’
Line 154: The authors used v3 of the B73 genome. The current version is v4. I am sure this is because they started the work before v4 was officially available. I am fine with this but the authors should make a note as to why they used v3.
Line 171: The authors refer to Table S17. I did not have the supplemental tables. And these should be cited in order
Line 192-203: The number of markers for the map seems exceptional low. This is why the QTLs are so large. Can the authors comment on this?
Line 352: It is highly problematic to project SNPs onto a reference genome annotation as shown in Arabidopsis. Thus, the authors should put their SnpEff data in that context. My guess is that a lot of these are artifacts and if they had annotation of their query genomes, then an alternative splice form will alleviate the SNP.
While the authors findings are technically sound, the low power of the entire study warrants text to let the reader know this.
This is all quite well done - the writing is clear, references are appropriate, and results are well explained.
There are important and clear research goals, and most of the approaches are well carried out.
My only concern is that the analysis is mainly focused on SNPs called against the reference genome. Additional analysis that would be useful would be to identify any sequences where introgression has lead to copy number variation or (especially) novel genes introgressed. With increasing appreciation for the importance of gene sequences that are missing from the reference genome, I would advocate a "pan genome" style approach to understand this aspect of introgression better.
There are various approaches, but the easiest would simply be to de novo assemble the reads that don't map, to identify genes in the teosinte parent that are missing from the reference. Ideally, the mapping population could be used to place some/all of these sequences onto chromosomes as well, if there are obvious protein-coding or otherwise likely functional genes.
This may be beyond the scope of this current paper, but it should at least be acknowledged that a SNP based approach might be missing something here, and this should be investigated as much as possible here and/or in other papers. At the least, it would be useful to look at copy number variation between the parents based on mapping to the reference genome, and to identify if any regions that were introgressed would lead to gene deletion / duplication, as well as identifying the gene sequences that are novel in the teosente parent even if they can't be placed easily.
Findings are well stated and clear. My only additional suggestion is that there are many important traits that were not measured, and it is likely that because of this key phenotypes were missed. Also, as briefly mentioned, there are many traits that could be expressed differently in the highland environment.
It would be ideal to re-do the mapping in the highland environment, obviously for a future paper no this one. IF this is done, I would expect that biotic interactions as well as abiotic factors are important, and lead to higher fitness (yield) in the highlands with certain introgressions. There are likely insects, pathogens, and other organisms that differ substantially between these environments, and could play an important role.
For instance, in sunflower it was found that resistance to local herbivores was driving introgression at key genomic regions during a natural range expansion into texas, leading to the origin of the subspecies H. annuus texanus
Quantitative trait locus mapping identifies candidate alleles involved in adaptive introgression and range expansion in a wild sunflower
KD Whitney et al.
Molecular ecology 24 (9), 2194-2211
This is a nice paper, and adds important new understanding to how Maize and Teosinte have interacted in the areas where they coexist, and how selection may have acted / be acting. The fact that phenotypes associated with this introgression have not yet been identified is not too surprising, since it may be something you didn't measure, as discussed above, or that is only expressed in the highland environment.
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