Home » Reviews
In Silico Identification of Rice Gene Homologues in Brachypodium, Sorghum and Maize: Insight into Development of Gene Specific Markers
By Mr. Krishnanand P Kulkarni , Mr. Shantanu S Kulkarni , Mr. Mallik Gedda , Mrs. Manusha Bandevar , Dr. Humira Sonah , Dr. Raju N Gacche , Dr. Nilesh K Deshmukh , Dr. Rupesh K Deshmukh
Submited on: 12 Apr 2012 03:46:13 PM GMT
Published on: 13 Apr 2012 06:45:30 PM GMT
 
In Silico Identification of Rice Gene Homologues in Brachypodium, Sorghum and Maize: Insight into Development of Gene Specific Markers
Posted by Dr. Liliana D Godoy Olivares on 30 Jul 2012 05:35:46 PM GMT

  • What are the main claims of the paper and how important are they?

    A comparative analysis between cereal species seems a good approximation in case you want to generate genomic species with certain characteristics that confer resistance to adverse conditions. Authors should be more clear in their discussions.


  • Are these claims novel? If not, please specify papers that weaken the claims to the originality of this one.

    If it seems new, though to be unclear presentation of the results is not possible to appreciate the novel contributions to the subject.


  • Are the claims properly placed in the context of the previous literature?

    The above is insufiente to generate a good discussion.


  • Do the results support the claims? If not, what other evidence is required?

    There is not enough information (at least in the manuscript) that make this research a reliable contribution to the issue of genotyping and the search for molecular markers. Probably help a change in the presentation of results, including experiments with more number of replicas. Overall lack experimental information.


  • If a protocol is provided, for example for a randomized controlled trial, are there any important deviations from it? If so, have the authors explained adequately why the deviations occurred?

    Missing information to discuss.


  • Is the methodology valid? Does the paper offer enough details of its methodology that its experiments or its analyses could be reproduced?

    Missing information on methodological details used.


  • Would any other experiments or additional information improve the paper? How much better would the paper be if this extra work was done, and how difficult would such work be to do, or to provide?

    alignments and results include amplification of the sequencing primers designed as well as obtained.


  • Is this paper outstanding in its discipline? (For example, would you like to see this work presented in a seminar at your hospital or university? Do you feel these results need to be incorporated in your next general lecture on the subject?) If yes, what makes it outstanding? If not, why not?

    If the format of presentation of results had been different, and that would have improved the reception of the information delivered, ofcourse.


  • Other Comments:

    NA

  • Competing interests:
    None
  • Invited by the author to review this article? :
    No
  • Have you previously published on this or a similar topic?:
    No
  • References:

    NA

  • Experience and credentials in the specific area of science:

    NA

  • How to cite:  Godoy Olivares L D.In Silico Identification of Rice Gene Homologues in Brachypodium, Sorghum and Maize: Insight into Development of Gene Specific Markers [Review of the article 'In Silico Identification of Rice Gene Homologues in Brachypodium, Sorghum and Maize: Insight into Development of Gene Specific Markers ' by Deshmukh R].WebmedCentral 2012;3(7):WMCRW002148
1 2 3 4 5 6 7 8 9
Report abuse
 
Detailed analysis results are required.
Posted by Prof. Kazuo Ishii on 10 Jul 2012 05:56:04 AM GMT

  • What are the main claims of the paper and how important are they?

    The main claim of the paper is about novel comparative analysis among rice and Brachypodium, Sorghum and Maize. They claimed some homologues among them but they are obscure. The author should show clear and concise results.


  • Are these claims novel? If not, please specify papers that weaken the claims to the originality of this one.

    No, figures are not enough detail and difficult to understand.


  • Are the claims properly placed in the context of the previous literature?

    No, there is not enough evidence to discuss.


  • Do the results support the claims? If not, what other evidence is required?

    The results are not enough and not clear to discuss.


  • If a protocol is provided, for example for a randomized controlled trial, are there any important deviations from it? If so, have the authors explained adequately why the deviations occurred?

    The author should show the detail and clear results to discuss.


  • Is the methodology valid? Does the paper offer enough details of its methodology that its experiments or its analyses could be reproduced?

    The author showed the valid methodology. But the description is not enough in detail, and not clear to understand.


  • Would any other experiments or additional information improve the paper? How much better would the paper be if this extra work was done, and how difficult would such work be to do, or to provide?

    The author showed the valid methodology. But the description and figures are not enough in detail, and not clear to understand.


  • Is this paper outstanding in its discipline? (For example, would you like to see this work presented in a seminar at your hospital or university? Do you feel these results need to be incorporated in your next general lecture on the subject?) If yes, what makes it outstanding? If not, why not?

    The author should show the clear and concise results to discuss.


  • Other Comments:

    This theme is very interesting but the results are not enough to discuss and to understand. The author should improve the overall figures to clarify what is new.

  • Competing interests:
    No
  • Invited by the author to review this article? :
    No
  • Have you previously published on this or a similar topic?:
    No
  • References:
  • Experience and credentials in the specific area of science:

    Genome sequencing and transcriptome analysis.

  • How to cite:  Ishii K .Detailed analysis results are required.[Review of the article 'In Silico Identification of Rice Gene Homologues in Brachypodium, Sorghum and Maize: Insight into Development of Gene Specific Markers ' by Deshmukh R].WebmedCentral 2012;3(7):WMCRW002057
1 2 3 4 5 6 7 8 9
Report abuse
 
gene specific mark based on microsatellite sequences? a good try.
Posted by Dr. Feng Feng on 20 Jun 2012 08:09:58 PM GMT

  • What are the main claims of the paper and how important are they?

    in this manuscript, the authors proposed to use the comparative mapping approach to detect the Rice gene homologues in 3 different cereal species.  They also proposed to design gene-specific markers based on the microsatellite repeat motif identified gene sequences. This work could be of an impact on genetyping genes in these cereal species.


  • Are these claims novel? If not, please specify papers that weaken the claims to the originality of this one.

    the claim seems novel, but the results and conclusion are not very convincing.


  • Are the claims properly placed in the context of the previous literature?

    n/a


  • Do the results support the claims? If not, what other evidence is required?

    the manuscript has not provided enough results to convince the readers, or at least not in a correct or clear format. The authours should show results of at least one set of such primers, and also show that the primers designed by this way really could work to correctly genetype the desired genes. So far no such results have been shown. In addition, the figures in the manuscript are not clear to see anything at all.


  • If a protocol is provided, for example for a randomized controlled trial, are there any important deviations from it? If so, have the authors explained adequately why the deviations occurred?

    n/a


  • Is the methodology valid? Does the paper offer enough details of its methodology that its experiments or its analyses could be reproduced?

    the methodology seems valid, but no enought detail is provided, especially the results of those analyses are not provided.


  • Would any other experiments or additional information improve the paper? How much better would the paper be if this extra work was done, and how difficult would such work be to do, or to provide?

    except the in silico design of primers, some experimental verificantions of the desinged primers are necesary. Otherwise, the conclusion is not convincing.

     


  • Is this paper outstanding in its discipline? (For example, would you like to see this work presented in a seminar at your hospital or university? Do you feel these results need to be incorporated in your next general lecture on the subject?) If yes, what makes it outstanding? If not, why not?

    it is hard to evaluate its importance of this paper since not enough detail is available or not in a correct/obvious format. 


  • Other Comments:

    n/a

  • Competing interests:
    n/a
  • Invited by the author to review this article? :
    No
  • Have you previously published on this or a similar topic?:
    No
  • References:
    None
  • Experience and credentials in the specific area of science:

    na

  • How to cite:  Feng F .gene specific mark based on microsatellite sequences? a good try.[Review of the article 'In Silico Identification of Rice Gene Homologues in Brachypodium, Sorghum and Maize: Insight into Development of Gene Specific Markers ' by Deshmukh R].WebmedCentral 2012;3(6):WMCRW001949
1 2 3 4 5 6 7 8 9
Report abuse
 
Development of Gene Specific Markers for breeding
Posted by Prof. Ke-Lin Du on 17 Apr 2012 10:53:24 AM GMT

1 Is the subject of the article within the scope of the subject category? Yes
2 Are the interpretations / conclusions sound and justified by the data? Yes
3 Is this a new and original contribution? Yes
4 Does this paper exemplify an awareness of other research on the topic? No
5 Are structure and length satisfactory? Yes
6 Can you suggest brief additions or amendments or an introductory statement that will increase the value of this paper for an international audience? No
7 Can you suggest any reductions in the paper, or deletions of parts? No
8 Is the quality of the diction satisfactory? Yes
9 Are the illustrations and tables necessary and acceptable? No
10 Are the references adequate and are they all necessary? Yes
11 Are the keywords and abstract or summary informative? No
  • Other Comments:

    9. The figures 2 and 3 are not clear at all. 

     

    11. Keywards are missing. 

  • Invited by the author to review this article? :
    No
  • Have you previously published on this or a similar topic?:
    No
  • References:
    None
  • Experience and credentials in the specific area of science:

    I have knowledge in data mining in bioinformatics. 

  • How to cite:  Du K .Development of Gene Specific Markers for breeding[Review of the article 'In Silico Identification of Rice Gene Homologues in Brachypodium, Sorghum and Maize: Insight into Development of Gene Specific Markers ' by Deshmukh R].WebmedCentral 2012;3(4):WMCRW001694
1 2 3 4 5 6 7 8 9
Report abuse
 
 
 
We use cookies on this website to measure and improve performance. By continuing to browse the site, you are agreeing to our use of cookies.