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I see that you have completed all the changes for acceptance for publication. Congratulations
[# PeerJ Staff Note - this decision was reviewed and approved by Robert Winkler, a PeerJ Section Editor covering this Section #]
You've largely made the changes requested by reviewers, but you still need to corrects some deficiencies. I found the first paragraph you added to the introduction to the manuscript irrelevant. This information is already known and has been repeated dozens of times in articles. Just write "Seed vigor is an important agronomic trait in determining wheat (Triticum aestivum) yields as in other crops".
In addition, if you correct the very minor formal and spelling errors noted by the reviewers, your manuscript will be ready for acceptance.
I requested the corresponding author to change the in-text citations so that only the phrase "et al." is italicized. However, the author has italicized the entire citation, including the author names and years. For example, in the citation "Çelik et al., 2023," only the "et al." should be italicized. If the author corrects these, I have no further issues. The paper can be published, as the corresponding author has made commendable revisions in response to my critiques.
no comment
no comment
Same as my previous review report
Same as my previous review report
Same as my previous review report
I have made 3-4 annotations in the attached file for the author's reference. Other than that, the authors have provided a valid response to the queries raised by me. Hence, I believe that MS is ready for acceptance.
Best regards
To extend, authors accepted all my suggestions and significantly improved the manuscript. At this point I have no critical remarks and can suggest the manuscript for publication.
Experimental design is enough clear now, all requested changes were made.
To my extend, findings are valid. All required underlying data was provided, as well as the results were supported with statistic tests.
None
The reviewers have made necessary recommendations for improving your manuscript. I agree with them. Your research is well structured in general terms, but the English language needs some correction and please pay attention to terminology. In the conclusion section, it would be more appropriate to briefly summarize your findings and offer your suggestions rather than repeating them.
**PeerJ Staff Note:** Please ensure that all review and editorial comments are addressed in a response letter and that any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate.
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In the introduction section, the first two sentences required citation. Firstly, we highly recommend that the authors give some information related to the importance of Wheat and after continuing the gap. You are studying the genetic mapping of the Wheat introgression population so the wheat ploidy, chromosome number, and so on... required. For insurance, for example, ı think that these phrases were not so appreciated. But generally well-structured. Abbreviations are required or you must give the long name of short usage such as QTL, cM, SSR, and so on...
This trial was conducted about 4 years ago. Why did you wait until now, so long time is not acceptable but we can easily see that you are making more to do Quantitative trait loci (QTL) analysis. What is the pattern of trial design? How about the “standard germination method”? Can you please give a citation?
The “Calculation of traits related to wheat seed vigor” this section has required a citation.
Please upload the phenotypic data and genomic data as supplementary table
In line 216, minor-polygene, On what basis are you saying this? Is this an assumption? A high LOD value increases the probability that the QTL sought is the QTL sought. Still, it also strengthens the possibility that QTLs with a high r square value and a high p probability value are the QTLs responsible for the relevant feature. Therefore, it would be beneficial to keep markers with low LOD values.
Please cite the figures and tables included in supplementary tables in the main text.
Line 404-409. In order to effectively......seed vigor during seed aging, this needs citations.
Line 462-464. Needs citation/s
Line 466. For example, not appreciated in here
Line 467-468. Similarly, Shi et al. (2020) (Shi, et al., 2020) duplicated.
Line 472. Same problem. Shi et al (2020) (Shi, et al., 2020) m
(Shi, et al., 2020), the comma is in the wrong place, please correct it.
In the citation, name et al. (year), the et should be written italics in the whole text
Line 482. Li et al. (Li et al., 2014). Please correct it.
PLEASE CITE THE FIGURES IN THE RESULTS AND DISCUSSION SECTIONS.
The MS in question, "QTL mapping for seed vigor-related traits under artificial aging in common wheat by two introgression line(IL) populations by Zhenrong et al. attempts to define QTLs related to seed vigor related traits in two wheat populations.
Important strengths that make this story interesting are:
1. Use of two populations
2. Use of IL populations
3. Use of different ageing durations
4. Candidate genes reporting and detection of epistasis
Article English is of sufficient quality that makes it publishable. However, I have made several comments in the PDF file attached with this review for the author to consider and provide answers.
All the relevant literature is cited and now stone is left unturned.
I have, however, one comment about the figures 3 and 4. The authors used different symbols to indicate various QTLs belonging to different traits. My suggestion is that the trait is already indicated in the QTL name. It is better to color the names of QTLs according to the ageing duration. For example, mapchart is equipped with 9 colors from C1 to C9. You can give color to your QTL names accroding to the treatment. This will make the figures 3 and 4 more appealing and the readers will spend less time to located where are the QTLs as vibrant colors are more easily noted than simple black toned colors. In additions, various symbols of different traits can be removed because the QTL name already carries the trait acronym.
Several other comments are made in the MS attached.
The replicates are fine, and I find no ambiguity in following the MS. Appropriate software were used and visualized in a nice way. Methods are described appropriately and can be replicated in other cases.
QTL mapping of seed vigor related traits is really hard to perform because the seeds need to be grown, harvested, post harvest operations and then performing the experiments. Thus, it takes atleast double the time to perform seed vigor related experiments in crop plants as compared to other traits. Hence, the current study offers a new insight into this wonderful trait. In addition, the data being published will add to the already existing but meager knowledge related to these traits. The conclusions are well defined, though the paragraph is long, but needs to be brought to scientific community.
This paper reports QTL mapping of seed vigor-related traits using two wheat introgression line populations. Researchers identified 26 additive QTL and 72 pairs of epistatic QTL from several chromosomes and identified a set of candidate genes to be involved in seed vigor traits. The paper is written well; however, minor edits for language will be needed. My major comments on this paper are given below:
QTL mapping of seed vigor traits in wheat has been published previously by several researchers (L101-121); therefore, it is not any new research. The use of introgression lines, i.e. a different type of mapping population, also does not bear much novelty – unless fine mapping of the QTL has been performed using the introgression lines. Several QTL detected from this study have already been published by other researchers (L461-499). Correlation analysis from this paper also agreed with the results reported by Shi, et al. (2020) (L422).
You carried out a search in the QTL regions for putative candidate genes. Today, the identification of putative genes from the QTL regions cannot be considered much in-depth research. In this regard, Fig 5 and 6 do not add much solid information to our knowledge; research on the validation of the genes whether playing a role in the control of these traits could have extended our knowledge. Validation of at least a few of the QTL markers for co-segregation with the trait in a different population could have also provided information for the use of the markers in breeding, and this would have been valuable information. Thus, the current version of the paper does not add much new information that can extend our knowledge, or information that can be used in breeding or other applications.
In M&M section, you mentioned that the populations were grown in an experiment field (37°252N, 112°252E) of Shanxi Agricultural University (Taigu, China) in the growing season of 2019-2020. Based on your earlier publications, it seems that significant variation existed in the two populations for days to heading, and I assume that variation also existed for days to maturity. If the seeds were harvested at the same time from the field plots, this could have affected the seed quality traits, i.e. induced non-genetic variation between the lines. If this is the case, this non-genetic difference might have affected the results. Some of the QTL you are claiming to be new; given the fact that the majority of the QTL showed minor effects on the traits, it will be difficult to prove if they are real QTL.
L219-229: You provided some information on the parents based on data collected at 0 h (control) and 72 h aging. I am not sure why you did not include the results of the parents from all time points and present this together with data of the introgression lines to show whether the parents differ for these traits or not; this is an additional lacking of the paper.
M&M: How the Introgression lines were developed should have been described in brief (should not have only referred to the previous publications).
L145-153: Genetic background of IL populations. How the genome contents have been measured - brief information was needed (should not only refer to the previous publications). The proportion of genome - of which? Is it donor parent genome?
Other comments:
L88-100: Detailed review on other crops such as rice, maize, and barley is not relevant here; unnecessarily increased the volume of the paper.
Results: The first part of the 1st paragraph is mostly M&M - avoid repetition.
L233- 343: Detection of additive QTL for seed-vigor traits: Reading this section was boring - should have been shortened.
Discussion: "Phenotypic variation and genetic basis of seed-vigor traits" and "Comparison of QTLs detected between the two IL populations of wheat" sections: Discussion is very weak - largely included the rationale for this work and the results.
Tables and Figures should stand-alone – this is missing in many cases. For example, Fig 2, in which crops? What does IL mean?
For language edits, I listed a few as an example:
L28 & Other places: QTL is plural - why you add 's' and make it plural again?
L47: Should be agronomic traits.
L48-49: "Great germination rate, small germination rate" - not good wording.
L60: Increasing reports showed that seed aging/deterioration sophisticated biological trait involving ........ - not sure what you mean here by the word sophisticated.
L62-65: missing words need to be added for better clarity.
L126: What is MA method?
L132: Is it 160 plants or 160 lines? Should be lines.
Added above
Added above
Added above
The manuscript by Zhenrong et al. is devoted to identification of QTLs, associated with vigor-related traits in hexaploid wheat. The manuscript is well-written and, to my extend, meets the journal criteria.
The experimental design and procedures are provided in clear and sequential manner. I have a few specific comments, which will be listed below.
Author provided all necessary data in the manuscript as well as the source data in the supplementary files. The majority of finding are supported with the respective statistics.
Here I provide some specific comments to the manuscript:
Lines 134-138 – Provide references for the described characteristics of the cultivars;
Lines 142-143 – Provide references for the field management conditions/protocols;
Line 192 – I guess, ‘Oringe’ is a typo for ‘Orange’ or ‘Origin’ software. In any case, please, specify the details for the software, as you did for SPSS and Excel;
211-215 – Here, while describing the Fig.1, it would be good to say if the differences in the measured parameters (GE, GR, GI, etc.) are significantly differ between the various time-points of aging (at 24h, 36h, etc.). Therefore, please, visualize the results of the statistical test for the measured parameters in Fig. 1 (second and fourth columns of graphs);
383-385 – It would be good to provide gene names within the text, besides their ID code. Thus, it will be more easier for a reader to follow up the results outline;
406-408 – ‘a lot of 407 physiological and biochemical processes occurred’ briefly specify, which changes took place and/or support this statement with a reference;
414-417 – Again, support these findings with statistical analysis;
539-595 – Provide gene names instead of the gene IDs in wheat genome (find gene names for these genes or assign them). You can keep IDs in rounded brackets;
Also, a more general comment to the last section of discussion:
You have identified that the genes, related to the seed vigor are located in a cluster on chromosome 2A. Since T. aestivum is allohexaploid species, homologous loci might be expected to be found in chomosomes 2B and 2D. Gene homeologs from B and D subgenomes might still have effect on seed vigor regulation. It would be good to mention, if these genes remain functional (if they are not pseudogenised) and if the expression of such homeologs (from B and D) is lesser, than the expression of the identified candidate genes (from A subgenome). This may explain the higher regulatory importance of genes from 2A chromosome (if so). This could be easily investigated in such resources as: https://bar.utoronto.ca/eplant_wheat/ Or at least this question worth discussing.
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