Screening Tolerance to Phosphorus Deficiency and Validation of Phosphorus Uptake 1 (Pup1) Gene-Linked Markers in Thai Indigenous Upland Rice Germplasm

Round  1

Reviewer 1 Report

This manuscript dealt with the variation in Thai indigenous upland rice germplasm for the tolerance against P-deficiency, in solution culture. The objective is sound and important, but the content of the manuscript involved many ambiguous parts to be collected, and some additional data may be required. I concluded that the manuscript should be re-reviewed after major revision. This does not mean the revised manuscript will be certainly accepted. One of the major problems is why the authors could select 12 accessions as tolerant materials against P-deficiency. The authors should show clearly this very important results. How about the differences between these 12 accessions and other accessions? Another is the ambiguity for using the term “gene” in this manuscript. Please use “allele” or “locus” instead of “gene”, as far as possible. I think the authors themselves might be confusing for these terms. Other problems to be revised, including the above, are follows.

L2: Pup1

L19: Pup1

L24: nine markers linked to Pup1 locus

L25: The presence or absence of the tolerant allele at Pup1 locus

“gene” is very an ambiguous term. Use “locus” or “allele” instead of “gene” in academic articles.

L49: .. Assam, India, has been …

L55: high P-uptake allele

L56: foreground => forward (?)

L57: Show the accession number of the sequence of Pup1.

L57: What about the relationship between Pup1 and OsPupK46-2? Identical? Linked?

L59: What is the “Pup1 gene family”? I cannot understand #family”.

L76: I think “+P” and “-P” are better instead of “P+” and “P-“. Because readers may confuse that “-“ means “dash”.

L98: “Pup1” should be in italic.

L135: 0.536

L141: Table 1  What are the values in the columns under P+ and P-? F or MS for genotpes? State clearly in the Table’s title.

L170: I think it is better to make a new paragraph at “The genotypes in our study can be …”

L172: Show the evidence or reasons clearly why the accessions should be grouped into group 1 to 3, instead of 6 categories of IRRI.

L182 (Figure 1) Index Y1 and Index Y2 should be Season 1 (2016) and Season 2 (2017).

L188 “accurate” should be “comprehensive” or appropriate terms.

L194: Why and how the authors could select 12 cultivars from Figure 3 and Table 3? State briefly. In addition, readers cannot discriminate which are the selected cultivars in Figure3. Also, there was no description about the relationship between SC and PDTI shown in Figure 3.

L203: Pup1 linked markers

L204: Pup1 linked markers

L204: Readers cannot understand if an allele at a marker which is linked to the tolerant allele at Pup1 means always the presence (1) of PCR product or not. It is possible that the absent of the PCR product can have an allele linked to the tolerant allele at Pup1. This was very ambiguous. Also, the authors should evaluate not only the case of high-tolerant accessions, but also the case of low-tolerant accessions for their marker genotypes.

L214 (Table 3): What is “Sum allele” or “summation of the alleles tested”?

L223: Why these 12 accessions can be selected clearly from the present data?

L226: The authors should state here that the tolerance in this study was not associate the tolerant allele at Pup1.

Author Response

Dear reviewer:

Thank you for all suggestions of reviewer. Reviewer’s comment is very much appropriate. The necessary correction has been done in the revised manuscript.

Sincerely,

Sompong Chankaew, Ph.D

Author Response File: Author Response.pdf

Reviewer 2 Report

The present manuscript report the screenong of 160 rice varieties to P deficiency and analysis with markers linked to  the QTL responsible of  phosphorous uptake. There are some revisions required which i list below:

1) The name of the QTL should be Pup1 not Pub1 as in the title. Moreover check through the text how it is named: Pup1 (withouth space, i.e. L24), Pup 1 (with space i.e. L27, L68) or Pup1 (no italics L98, L260). Correct!

2) Check the terminology of Pup1, QTL (L50), gene (l19, L24) and gene family (L59) are different things. It seems from literature that Pup1 is a QTL, refer to this in the text

3) L26 UlR183 must be UL183

4) L119-122, the authors debate about  the environmental conditions that influenced the severity simptoms. The experiment have been carried out in greenhouse, therefore,  humidity, temperature and ligh intensity fluctuation should minimized across years respect open field. Did they monitored the internal conditions? In my opinion is important to have these information to give strenght to the statement and to the GxY analysis

5) check degree (°C) with space (L168) or without space (L170)

6) Is it possible in figure 3 to color the line belonging to different groups (according to figure 2), it could give a better readability

7) L205 what means 0 to 9, the scoring is 0/1

8) About the paragraph 3.2 i found the discussion very poor the author should expand this part giving  more details, as example discussing the combination of molecular and phenotypic data (i.e to which group belong each line) as well as provide more statistic on the markers (i.e PIC value)

In general i recommend a native speaker revision in order to make some sentences more fluid and correct typos through the text

Author Response

Dear reviewer:

Thank you for all suggestions of reviewer. Reviewer’s comment is very much appropriate. The necessary correction has been done in the revised manuscript.

Sincerely,

Sompong Chankaew, Ph.D

Author Response File: Author Response.pdf

Round  2

Reviewer 1 Report

The revised manuscript was well improved. I understand how to select the tolerant accessions from the materials. I cannot agree with the authors about the criterion of the classification of tolerant accessions, because the distribution of PDTI was continuous in both years (Why the tolerant accessions cannot be more than 12, or less than 12?). Readers may have the same question. However, this cannot be a reason that this manuscript cannot be accepted, I think.

Other problem for PCR products were still ambiguous. Please state clearly the relationship between the presence(1)/absence(0) of the PCR products and the presence/absence of the alleles at marker loci linked to the tolerant allele at Pup1. In general, it is possible that the tolerant allele at Pup1 exists when PCR product from linked marker locus is absent. For example, “When PCR product for one of the nine linked markers are present (“1” in Table 3) in an accession, it is possible that this accession possesses the tolerant allele at Pup1 (italic) (related references).” (Is it correct?)  Please insert this kind of sentences into somewhere at line 220 or others. I concluded that this manuscript will be accepted after minor revision. I think that the editor, not reviewer, will judge if the revisions are well-done or not. Other minor problems to be corrected are as follows. 

Line 64: “,” => “.”

Line 71: Pup1 linked

Line 101: Pup1 linked markers

Author Response

Dear reviewer,

Thank you for the comments and suggestions, we corrected the manuscript accordingly.

1.       We selected the top 12 accessions based on the value of combined PDTI higher than 7 and SC lower than 3 [line 208].

2.       We added the sentences of “When PCR product for one of the nine linked markers are present (“1” in Table 3) in an accession, it is possible that this accession possesses the tolerant allele at Pup1” as your suggestion [lines 220-222].

3.       All mistake were corrected though out the manuscript.

Best regards

Sompong Chankaew

Reviewer 2 Report

The manuscript has been improved

Author Response

Dear reviewer,

Thank you for your review the revise (R1) manuscript.

Best regards

Sompong Chankaew