Multi-Year QTL Mapping and RNA-seq Reveal Candidate Genes for Early Floret-Opening Time in Japonica Rice
Round 1
Reviewer 1 Report
In this manuscript, the authors identified and validated a stable QTL underlying the variation in floret opening time between two japonica rice cultivars, G23 and NG9108, using F2, F4, and F6 mapping populations. The authors also conducted RNAseq experiments using lodicule tissues of the two parental cultivars collected at different time-points and identified an interesting set of genes that are relevant to floret opening. Overall, the results are presented well with appropriate figures and tables. The introduction & discussion sections include recent publications in the relevant field as well. I have two major points that should be addressed before considering the manuscript for publication in Agriculture.
1) I think the authors must provide heading date information of the two parental cultivars (G23 and NG9108) and the plants used for QTL mapping in F2, F4, and F6 populations. What is the heading date difference between G23 and NG9108 plants in Figure 1? Also, it seems the heading date range of the F2 population is over one month (Jul 15 – Aug 18) as described in line 224-225. What was the extent of daily FOT variation within that time period? How much correlation are there between FOT and heading date? I think it is important to clarify the answers to these questions to ensure how the phenological variation among different plants were controlled.
2) While the manuscript is well written with logical presentations and flows, there are many English language errors in terms of grammar and sentence structure across the whole manuscript. I think using a professional English editing service with the help of a native English speaker would greatly improve the quality of the manuscript.
Author Response
Please see the attachment.
Author Response File: 
Author Response.docx
Reviewer 2 Report
Flowering traits are difficult to phenotype, particularly since they are profoundly influenced by environment. Given the precautions taken by the authors to avoid such interactions and multiple populations/generations studied at different points of time to achieve the same result, this reviewer is not worried about the veracity of the results. This is a nice story to be published and hope that hybrid rice breeders are able to capitalize on the resource this group has developed and reported. A few comments:
1. RNA-seq could have used near-isogenic lines i.e., F4:5, if the authors were able to retrieve a heterozygous line in F4 and selfed it. Perhaps better than using the parents?
2. There need to be a discussion about how this study can eventually lead to the identification of the underlying gene with significant major effect. Also, need to discuss how the problem of missing heritability can be solved.
Suggested corrections are CAPITALIZED.
Author list:
Where is the 5th affiliation?
Abstract:
Line 12: “from the florets opening to CLOSING”
Line 14: “Here, we REPORT genetic mapping”
Lines 17-18: Please revisit the sentence “Integrated RNA-seq analysis….”. Sentence structure error.
Line19: “thus PROVIDING invaluable”
Keywords:
Words in the title should not be repeated as keywords. The objective of this section is to provide additional words/phrases for indexing.
Introduction:
Lines 37-39: The sentence “Rising global temperature……….” HAS LED TO or WILL LEAD TO. Similarly, HAS THREATENED or WILL THREATEN
Lines 40-42: If these events have been reported, please report as such. Do not suggest “might”. HAVE BEEN REPORTED or the usage of word like EVIDENTLY.
Line 42: not “Bring forward...” maybe, “BRINGING FORWARD (?)
Lines 50-53: “The FOT asynchromy HAS BECOME” (?)
Line 54: “DURING EARLY 1990s” (?)
Line 56: “FOR both the BFOR and PFOT traits”
Line 58: “GENETICALLY dissected”
Line 68: “we REPORT”
Line 72: we further REVEAL”
Materials and Methods
Line 100: “PHYSICAL INSPECTION”
Line 136: fastq is perhaps not a tool for adapter trimming. ‘FASTP’ perhaps?
Line 175: “To FIND THE candidate genes” perhaps (?)
Line 401: “THE”
Author Response
Please see the attachment.
Author Response File: Author Response.docx
Round 2
Reviewer 1 Report
The authors have provided sufficient explanations to the concerns regarding the potential effect of heading date variation on FOT, and revised the manuscript accordingly. English language-wise, I still see many minor grammatical errors. For example, just in the first page, I have encountered the following mistakes.
Line 29: "most florets open" or "most florets are opening", instead of "most florets opening"
Line 32: "floret closing time" instead of "floret closed time"
Line 42: "leads to in inhibition" instead of "lead to inhibition"
I cannot list all the minor errors throughout the manuscript, so please check carefully with the help of a language editing service or a native English speaker.
Another minor thing: Please check with the editor if it is acceptable to put Table 1 as a figure panel shown in Fig. 2B.
Author Response
Please see the attachment
Author Response File: Author Response.docx
