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Thank you for addressing the considerations submitted by the reviewers. A suggested couple of additional edits are listed below. The general shape of the manuscript appears acceptable for publication. In retrospect, in case you would like to strengthen the impact of your manuscript, you might consider adding gene ontology annotations to some of the gene classes.
LINE NO: / BEFORE / AFTER / [COMMENTS]
LINE 311: / Previos / Previous / [ . ]
LINE 341: / known of which / known which / [ . ]
Because the main focus of the manuscript deals with bioinformatics analysis, and that it focuses on a specific gene family, I would encourage a statement be added to point to known gene ontology (GO) annotations.
Journal manuscripts are often scanned by text-mining software that locates and extracts core data elements, like gene function. Adding standard ontology terms, such as the Gene Ontology (GO, geneontology.org) or others from the OBO fountry (obofoundry.org) can enhance the recognition of your contribution and description. This will also make human curation of literature easier and more accurate.
Congratulations.
In general the manuscript was well receved, except there appeared to be some points which can be further addressed as suggested by the reviewers. Please look at the reviews and make the adjustments accordingly. I have included below several spots where improvements may add to the readability. Considering that this is a drought stress related manuscript the measurement of what the conditions actually define are rather poor; though late to improve here something relative to percent moisture difference, or post-study dry weights help iron out measurements into meaningful terms rather than relative ones. I feel this manuscript will be well-received; however, there is a need to mention the differences found in this study relative to the quite different findings in other studies; a good literature review will in most cases help you catch the short-comings. I will classify this as requiring “minor edits”, but I would want you to add or fix the suggestions provided by the reviews. Thank you for this contribution.
Example of annotation:
LINE NO.: / PREVIOUS FORM / SUGGESTED FORM / [ADDITIONAL NOTES, NONE [.]]
30: / by NCBI CDD / by using the NCBI CDD / [.]
35: / with genome of rice, / with the genomes of rice, / [.]
57: / modifications resulted to address / modifications result to address / [.]
58: / especially the osmotic changes, / especially during osmotic changes, / [.]
69: / to drought, 16 early resonse / to drought conditions, 16 early responses / [.]
73: / imaging, Arabidopsis / imaging, an Arabidopsis / [.]
90: / characterized OSCA / characterized the OSCA / [.]
103: / harbor DUF221 / harbor the DUF221 / [.]
107: / then schematic was generated / then a schematic representation was generated / [.]
111: / on neighbor-joining method / on a neigbor-joining method / [.]
115: / from maize genome / from the maize genome / [.]
117: / Plant Genome / the Plant Genome / [.]
122: / subjected to dehydrate / subjected to dehydration / [.]
124: / well-watered plants / . / [How do you distinguish adequate vs. over-watered?]
124: / flag leaf came from / flag leaf which came from / [.]
133: / volume is 10ul / volume was 10ul / [.]
136: / Quantification method was / The quantification method used was / [.]
137: / expression derived / expression was derived / [.]
140: / phenotype reported / phenotypes reported / [.]
142: / marker is greater / marker was greater / [.]
143: / in the gene region of. / . / [The remaining end of the sentence is missing!]
144: / including general linear model / including the general linear model / [.]
204: / no Syntenic / no syntenic / [lower case.]
217: / protein domino / protein domain / [.]
248: / well-watered plants / . / [Not exacting to any degree; clarify measurements better!]
257: / further inquiry / further inquire / [.]
261: / genetic polymorphisms / genetic polymorphism / [.]
268: / relatedness) were / relatedness were / [.]
287: / . / . / [Can other stress related gene families be mentioned here?]
328: / study was done to detect the / study is known of which detects the / [.]
The manuscript "Genome-wide analysis of maize OSCA family members and their involvement in drought stress" described the maize OSCA family members in response to drought stress in maize. Furthermore, they focus on their involvement in drought. An association was observed between genetic variation in ZmOSCA4.1 and drought tolerance at the seedling stage. The manuscript is suited to the PeerJ as per aims and scope.
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(1) The authors constructed a phylogenic tree of OSCA genes in maize, sorghum, rice and Arabidopsis. However, no articles were cited for these genes. The authors should cite related literature or add methods used to identify these genes.
(2) The expression profiles of the ZmOSCA genes in different tissues should be introduced in MATERIALS and METHODS.
(3) Line 232 isn’t appropriate. Should the expression level be regulated?
(4) Semagn et al (2013) reported an article to reveale QTLs for drought resistance, and the article could be found at http://www.ncbi.nlm.nih.gov/pubmed/23663209. It is well known that association analysis and linkage positioning can be complementary. Could the authors compare the physical position of ZmOSCA4.1 with the reported drought-tolerant QTL in maize?
(5) The past sentence is highly recommended. For example, Line 236, 253, 275 etc should be in the past tense. The “Zea mays” in Table 1 should be italic. The author should pay more attention to the writing.
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This is a very nice study on identifying and characterizing maize OSCA gene family and their involvement in drought stress of maize. The authors have done a wide range of research works including phylogenetic analysis, synteny with the rice, maize, and sorghum genomes, expression profiles, et al. More importantly, a significant association between the natural variation in ZmOSCA4.1 and drought tolerance at the seedling stage was identified. Combine with it's expression changes in response to drought stress, the results suggest that this gene might play an important role in drought stress tolerance in maize. This paper provides a solide foundation for future study the functions of ZmOSCA genes in response to water deficit stress, as well as understanding of the natural variation in drought tolerance in maize. I can't find any technical problems in the work, it seems impressive. I recommend to publish in Peer J.
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In the paper entitled “Genome-wide analysis of maize OSCA family members and their involvement in drought stress”, Ding et al. identified 11 ZmOSCA genes from Maize based on the protein homology with Arabidopsis thaliana. The authors also identify the OSCA genes that upregulated or downregulated in response to drought stress at the deferent developmental stages. They also showed the difference homology between of the OCSA gene families from rice, sorghum, maize and Arabidopsis.
These findings advance our understanding of the homology between OSCA genes and would be importance for future functional and physiological studies.
However, few major and minor points should be addressed in the study:
1- The authors showed the protein domain and transmembrane regions of ZmOSCA based on the TMHMM Server V2 and they predicted OSCA has 9 transmembranes. Recently 4 different research articles were published on the structure of Arabidopsis OSCA1.1, OSCA1.2 OSCA3.1 and rice OSCA1.2 (Zhang et al., Jojoa-Cruz et al., Murthy et al and Maity et al). All those articles demonstrated that OSCA protein has 11 transmembranes. The authors did not mentioned those studies or make protein domain based on the known structure of OSCA. The authors should update figure 3 based on the structure of those 4 papers and include the new results and udpdate the discussion.
2- There have been many reported microarrays and RNA-Seq under drought stress on Arabidopsis and other plants and the data available publicly. The authors should compare their finding to the other plant.
Minor comments
1. In figure 1, the ZmOSCA 1.1a and ZmOSCA3.1 is small protein. Authors should make sure whether it is a real protein. Since, ZmOSCA 1.1a does not have full sequence in compare to others OSCA from maize or Arabidopsis, the change of expression level in figure 5 and 6 of that gene might not be real.
2. The scale bar of the heat map figure in 5A is not clear. Should be explained.
3. The relation between OSCA genes and drought were mentioned in the discussion. However, no literature have been cited.
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