Identification of Associations between SSR Markers and Quantitative Traits of Maize (Zea mays L.)
Round 1
Reviewer 1 Report
In this manuscript, the authors tried to find a correlation between DNA marker profiles (using SSR markers) and quantitative traits of maize. The authors evaluated 26 traits in13 selected cultivars, and the maize plants were compared between two different years (2016 and 2017).
From my point of view the manuscript shows some flaws and it is necessary a deep edit.
- The introduction needs to be more exhaustive; In particular, the authors can explain how these molecular markers can be useful for the evaluation of crop species between 2 different (or more) years. I suppose this was the author's main purpose. I suggest improving it to better explain what the meaning of this study is.
- Please edit the Material and methods. My suggestion is to divide it into different paragraphs. This can help the reader to catch all the protocols used by the authors.
- The authors used microsatellite markers, but they did not report the sequences. I suggest reporting (in SM) the SSR motifs.
Author Response
Response to Reviewer 1 Comments
Reviewer #1
Point 1:
The introduction needs to be more exhaustive; In particular, the authors can explain how these molecular markers can be useful for the evaluation of crop species between 2 different (or more) years. I suppose this was the author's main purpose. I suggest improving it to better explain what the meaning of this study is.
Response: We corrected Introduction section. We added text “Possible associations between SSR markers and some QTLs in order to furnish elements are very important for breeders to perform Marked Assisted Selection in order to speed up selection process to obtain varieties with improved characteristics and contribute to the genotyping.”
Point 2: Please edit the Material and methods. My suggestion is to divide it into different paragraphs. This can help the reader to catch all the protocols used by the authors.
Response: We divided Material and methods section to six subsections: “2.1. Plant material”, “2.2. Field experiment”, “2.3. Quantitative traits”, “2.4. DNA extraction”, “2.5. Microsatellite markers analysis” and “2.6. Statistical analysis”.
Point 3: The authors used microsatellite markers, but they did not report the sequences. I suggest reporting (in SM) the SSR motifs.
Response: We added Table S1 in Supplementary Materials with Simple sequence repeat (SSR) markers motifs (https://www.maizegdb.org/).
Author Response File: 
Author Response.docx
Reviewer 2 Report
Brocianowski et al. 2020 identified associations between SSR markers and quantitative traits in thirteen maize cultivars grown in the field in the years 2016 and 2017. Thirty SSR primers were tested and 112 SSR markers were detected for 26 quantitative traits, which explained up to 78% of the phenotypic variance. Twenty-two of the total SSR markers were significantly associated with the same traits in both growing seasons. Furthermore, the authors provided comprehensive lists of marker trait associations in the supplement tables, which can be used as a resource for the science and breeding community.
Minor suggestions:
- 111 – 112: Dividing by 2 and multiplying by 2 cancels itself out. Either the authors compute the average from three replicates, or they just state that the thousand grain weight was calculated from the sum of two random samples of 500 kernels.
- 124: Please add the concentration of the primers used.
- 149 + 158: The authors stated that they found a total of 112 SSR markers, but found associations of 160 SSR markers in 2016 and 125 markers in 2017. I assume the authors calculated the 112 markers from a joint model and the other numbers from single models for each year. Please add one more explaining sentence to make it easier for the reader to distinguish between the numbers. This also applies to the abstract.
- 168: Please reword the sentence. The authors did not introduce “the” 22 markers earlier in the manuscript and the sentence could be misinterpreted in its current version.
- 216: In the supplemental tables some markers are highlighted in bold letters. Please provide an explanation in the description.
Author Response
Response to Reviewer 2 Comments
Reviewer #2
Point 1: Brocianowski et al. 2020 identified associations between SSR markers and quantitative traits in thirteen maize cultivars grown in the field in the years 2016 and 2017. Thirty SSR primers were tested and 112 SSR markers were detected for 26 quantitative traits, which explained up to 78% of the phenotypic variance. Twenty-two of the total SSR markers were significantly associated with the same traits in both growing seasons. Furthermore, the authors provided comprehensive lists of marker trait associations in the supplement tables, which can be used as a resource for the science and breeding community.
Response: Thank you very much.
Minor suggestions:
Point 2: 111 – 112: Dividing by 2 and multiplying by 2 cancels itself out. Either the authors compute the average from three replicates, or they just state that the thousand grain weight was calculated from the sum of two random samples of 500 kernels.
Response: We corrected this sentence. New sentence is: “The thousand grain weight was calculated from the sum of two random samples of 500 kernels each.”
Point 3: 124: Please add the concentration of the primers used.
Response: We added: “primers concentration 0.28 mM” in the manuscript text.
Point 4: 149 + 158: The authors stated that they found a total of 112 SSR markers, but found associations of 160 SSR markers in 2016 and 125 markers in 2017. I assume the authors calculated the 112 markers from a joint model and the other numbers from single models for each year. Please add one more explaining sentence to make it easier for the reader to distinguish between the numbers. This also applies to the abstract.
Response: We corrected manuscript in Results section: “The number of molecular markers associated with observed traits ranged from 1 (for number of kernels in row, ears weight and fresh weight of one plant) to 14 (for damage of maize caused by P. nubilalis) in 2016 as well as from 1 (for SPAD, number of grains in ear and fresh weight of one plant) to 12 (for carotenoids content) in 2017 (Table 2, S2-S27). The total of significant associations of 160 SSR markers with at least one trait in 2016 as well as 125 in 2017 were found on the basis of regression analysis (Tables 2, S2-S27)” and in Abstract: “The number of molecular markers associated with observed traits ranged from 1 (for number of kernels in row, ears weight and fresh weight of one plant) to 14 (for damage of maize caused by P. nubilalis) in 2016 as well as from 1 (for SPAD, number of grains in ear and fresh weight of one plant) to 12 (for carotenoids content) in 2017. The total of significant associations of 160 SSR markers with at least one trait in 2016 as well as 125 in 2017 were found on the basis of regression analysis”.
Point 5: 168: Please reword the sentence. The authors did not introduce “the” 22 markers earlier in the manuscript and the sentence could be misinterpreted in its current version.
Response: We corrected this sentence: “Twenty two SSR markers performed significant effect on at least one tested trait in both years of experiment (Tables 2 and 3).”
Point 6: 216: In the supplemental tables some markers are highlighted in bold letters. Please provide an explanation in the description.
Response: We added in the supplementary tables text: “# ‑ SSR markers with significant effect in both years of experiment were marked by bold”.
Author Response File: Author Response.docx
Reviewer 3 Report
The paper "Identification of Association between SSR Marker and Quantitative Traits of Maize (Zea mays L.) shows the results concerning two year experiments to determine the possible association between SSR and some QTLs in order to furnish elements, for breeders, to perform Marked Aiisted Selection in order to speed up selection process to obtain varietie with improved characteristics and contribute to the genotyping. The experiments are conducted in an appropriate way, the statistical and informatics analyses are correct and the results correctly presented and interpreted. In general, also if the results are not very strong, the walking to associate QTL to molecular marker is very long and this research may be considered one of the necessary steps. I think that might explained, in the appropriate context, the choice of QTL investigated in order to understand if they are selected before (and why) or are choosen ex post with some degree of significance in relation to the SSR markers. I also think that a light revisione by a native speaker may improve the quality of paper.
Author Response
Response to Reviewer 3 Comments
Reviewer #3
Point 1: The paper "Identification of Association between SSR Marker and Quantitative Traits of Maize (Zea mays L.) shows the results concerning two year experiments to determine the possible association between SSR and some QTLs in order to furnish elements, for breeders, to perform Marked Aiisted Selection in order to speed up selection process to obtain varietie with improved characteristics and contribute to the genotyping. The experiments are conducted in an appropriate way, the statistical and informatics analyses are correct and the results correctly presented and interpreted. In general, also if the results are not very strong, the walking to associate QTL to molecular marker is very long and this research may be considered one of the necessary steps. I think that might explained, in the appropriate context, the choice of QTL investigated in order to understand if they are selected before (and why) or are choosen ex post with some degree of significance in relation to the SSR markers. I also think that a light revisione by a native speaker may improve the quality of paper.
Response: Thank you very much. We corrected manuscript and added text: “SSR markers which have significant effects of quantitative traits are probably linked with QTLs which determined these traits. Microsatellite markers detected in both years of study should contribute to improved understanding of the genetic of yield and other quantitative traits.”. The manuscript was corrected by a native speaker.
Author Response File: Author Response.docx
Round 2
Reviewer 1 Report
Thanks to the authors for their efforts to improve the manuscript.
Author Response
Response to Reviewer 1 Comments
Reviewer #1
Point 1: Thanks to the authors for their efforts to improve the manuscript.
English language and style are fine/minor spell check required.
Response: Thank you very much. We corrected English language of the manuscript.
Best regards,
Jan Bocianowski
Author Response File: Author Response.docx
