Exploring the Molecular Landscape of Nitrogen Use Efficiency in Potato (Solanum tuberosum L.) under Low Nitrogen Stress: A Transcriptomic and Metabolomic Approach

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

1. Introduction 

In order for this paper to provide a comprehensive overview of the issue of nitrogen use efficiency, the authors should also provide some details on the genetic diversity of the potato and the possible existence of resistant varieties/landraces. 

2.1. Plant Material and Treatment

Given that the experiments were conducted in the field, I suggest that the authors also give a brief description of the evolution of climatic factors in the year 2021 in the experiment areas. It is also important to mention the interventions with irrigation. Even if the analyses targeted in this paper address transcriptomics and metabolomics of nitrogen use efficiency in potato, epigenetics may play an important role in the phenotypic manifestation of different genes.

Author Response

Thank you for your patience to review our manuscript (Manuscript title: Exploring the Molecular Landscape of Nitrogen Use Efficiency in Potato (Solanum tuberosum L.) under Low Nitrogen Stress: A Transcriptomic and Metabolomic Approach. Manuscript ID: 3151848. Authors: Rui Xie, Xiaolei Jin, Jing Fang, Shuli Wei, Jie Ma, Ying Liu, Yuchen Cheng, Liyu Chen, Jiawei Liu, Yanan Liu, Zhigang Han, Binyu Guo, Jingshan Guo, Xiaoqing Zhao, Xiangqian Zhang and Zhanyuan Lu) and thanks to give the opportunity to have it revised. We have examined the paper carefully and seriously to make the statements and the concepts more exact and clear. The rewritten sentences or words are marked with red color. We agree with the reviewer’s comments and make the corresponding revisions according to their suggestions as best as we could. The list of changes is enclosed below and the corresponding revisions/corrections highlighted/in track changes in the re-submitted files. We hope that the revised manuscript is suitable for publication in Agronomy, section Plant-Crop Biology and Biochemistry. Thank you very much for your help! For specific modifications, please refer to the uploaded materials.

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

The manuscript is well-prepared. Unfortunately not fully addressed personally to me. In the area of ​​transcriptomics and metabolic I do not undertake an assessment of manuscript. This area requires specialist assessment.

 In the scope in which I can undertake to express a review.

 One-year field studies are definitely too short a time to prepare conclusions. I suggest conducting a second series of studies. My opinion this is one of the reasons for the negative assessment.

 I consider the recommended doses of nitrogen and other macronutrients to be very high. For some region (f.ex. Central Europe), especially for edible potato N dosses should not crossing 120 kg N per ha. Authors present that 300 kg/ha are recommended doses. Please explain why so high doses macronutrients and Nitrogen are recommended?

 Manuscript has many typo and punctuation errors. It should be read carefully and corrected before resubmitting to the editor.

 For example line 3. Latin name of crop should be Italicized.

 Line 16 remarks as above.

 Please explain why potato classified as cereals. Line 17 " ... significant grain crop."

 Line 37 and many others - no spaces before brackets with references numbers.

 What type of Nitrogen fraction plant utilized? Sentence need correction.

 Line 70 Latin name

Line 80 Latin name

Line 132 Please specify clearly: were the potatoes planted (using tubers) or sown (from seeds). In this rows used term sowing.

 Line 134 Instead irrigation I suggest used term fertigation.

 Please add some information about fertigation system and water dosses. Water viability is one of the main yielding factor.

Line 167 Sentence need correction.

 Line 243. Please correct and precise potato growing stages when tuber was harvest.

 The nitrogen utilization index isn't well explained. Effect of fertilization (treatment) applied in kg per ha was compared to the control. While uptake by plants was given in mg per plant. In addition, the nitrogen content in plants was determined at 45 DAP and tuber harvest at 85 DAP. My opinion efficiency of fertilization should be assessed at the same time as a tuber harvest?

Author Response

Thank you for your patience to review our manuscript (Manuscript title: Exploring the Molecular Landscape of Nitrogen Use Efficiency in Potato (Solanum tuberosum L.) under Low Nitrogen Stress: A Transcriptomic and Metabolomic Approach. Manuscript ID: 3151848. Authors: Rui Xie, Xiaolei Jin, Jing Fang, Shuli Wei, Jie Ma, Ying Liu, Yuchen Cheng, Liyu Chen, Jiawei Liu, Yanan Liu, Zhigang Han, Binyu Guo, Jingshan Guo, Xiaoqing Zhao, Xiangqian Zhang and Zhanyuan Lu) and thanks to give the opportunity to have it revised. We have examined the paper carefully and seriously to make the statements and the concepts more exact and clear. The rewritten sentences or words are marked with red color. We agree with the reviewer’s comments and make the corresponding revisions according to their suggestions as best as we could. The list of changes is enclosed below and the corresponding revisions/corrections highlighted/in track changes in the re-submitted files. We hope that the revised manuscript is suitable for publication in Agronomy, section Plant-Crop Biology and Biochemistry. Thank you very much for your help! For specific modifications, please refer to the uploaded materials.

Author Response File: Author Response.pdf

Reviewer 3 Report

Comments and Suggestions for Authors

The problem addressed in the presented manuscript is relevant, especially in connection with significant pollution of arable land. Potato is one of the main vegetable crops (but not grain - 17). When spawning potato varieties that exhibit different dependence on the amount of added N, the authors identified effective pathways for the biosynthesis of some nitrogen-containing compounds and their metabolite pathways. The results obtained are valuable for the further creation of new potato varieties with effective nitrogen assimilation.

1. It is desirable to shorten the introduction, since there are repetitions

2. Why were fertilizers applied both in liquid and solid form and in such a ratio?

3 - provide an equation (coefficients) for determining chlorophylls. The method of extracting chlorophylls with 95% ethanol is non-standard. The same authors also use extraction with 80% acetone.

219 - 2−^ΔΔCt

4 - In tables S2 and S3 it is desirable to provide captions

5 - In figure S4 provide the same designations as in other figures and in the text -PC1 and PC2

296 - PC1 and PC2 - is this the principal component or variety or treatment N?

6 - Figure 3A and 3B - how do they differ, where are the roots and where are the leaves? Also to figure 3F

7- Figure 3D - what does the LN/NN ratio mean. Provide the calculation of this parameter in Materials and Methods.

341 - provide the full names of the enzymes

8 - In figure 6 indicate where the PCA results are for the leaves, where for the roots.

9- Figure S4 does not have the R2Y and Q2Y indicators, which are indicated in -408. What are these parameters?

10- in the upper left corner of figure 9, the corresponding colors are probably not shown.

605 - If nitrogen deficiency promotes accumulation of carbohydrates, including starch, then why does the weight of potato tubers decrease according to your data with nitrogen deficiency, if one of the components of tubers is starch?

11 - double numbering of references.

Author Response

Thank you for your patience to review our manuscript (Manuscript title: Exploring the Molecular Landscape of Nitrogen Use Efficiency in Potato (Solanum tuberosum L.) under Low Nitrogen Stress: A Transcriptomic and Metabolomic Approach. Manuscript ID: 3151848. Authors: Rui Xie, Xiaolei Jin, Jing Fang, Shuli Wei, Jie Ma, Ying Liu, Yuchen Cheng, Liyu Chen, Jiawei Liu, Yanan Liu, Zhigang Han, Binyu Guo, Jingshan Guo, Xiaoqing Zhao, Xiangqian Zhang and Zhanyuan Lu) and thanks to give the opportunity to have it revised. We have examined the paper carefully and seriously to make the statements and the concepts more exact and clear. The rewritten sentences or words are marked with red color. We agree with the reviewer’s comments and make the corresponding revisions according to their suggestions as best as we could. The list of changes is enclosed below and the corresponding revisions/corrections highlighted/in track changes in the re-submitted files. We hope that the revised manuscript is suitable for publication in Agronomy, section Plant-Crop Biology and Biochemistry. Thank you very much for your help! For specific modifications, please refer to the uploaded materials.

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

Congratulations to the authors for all their research work and for writing this paper!

Author Response

Dear Reviewer,

Thank you very much for your kind words and for taking the time to review our manuscript.  We are truly grateful for your positive feedback and encouragement regarding our research work and the paper we have written.

Best regards,

Rui Xie

Reviewer 2 Report

Comments and Suggestions for Authors

The manuscript submitted for evaluation concerns the efficiency of nitrogen use in potato production. If the Authors have results from the previous year (2019-2020) of the studies, why did they not include them in the manuscript?

I suggest correcting and supplementing the manuscript in the scope concerning the evaluation of the XS6 and NS7 varieties in earlier years.

Author Response

Dear Reviewer,

Thank you for your patience to review our manuscript (Manuscript title: Exploring the Molecular Landscape of Nitrogen Use Efficiency in Potato (Solanum tuberosum L.) under Low Nitrogen Stress: A Transcriptomic and Metabolomic Approach. Manuscript ID: 3151848. Authors: Rui Xie, Xiaolei Jin, Jing Fang, Shuli Wei, Jie Ma, Ying Liu, Yuchen Cheng, Liyu Chen, Jiawei Liu, Yanan Liu, Zhigang Han, Binyu Guo, Jingshan Guo, Xiaoqing Zhao, Xiangqian Zhang and Zhanyuan Lu) and thanks to give the opportunity to have it revised. We have examined the paper carefully and seriously to make the statements and the concepts more exact and clear. The rewritten sentences or words are marked with blue color. We agree with the reviewer’s comments and make the corresponding revisions according to their suggestions as best as we could. The list of changes is enclosed below and the corresponding revisions/corrections highlighted/in track changes in the re-submitted files. We hope that the revised manuscript is suitable for publication in Agronomy, section Plant-Crop Biology and Biochemistry. Thank you very much for your help!

Best regards,
Rui Xie

Author Response File: Author Response.pdf