Pyramiding Submergence Tolerance and Three Bacterial Blight Resistance Genes in Popular Rice Variety Hasanta through Marker-Assisted Backcross Breeding

Round 1

Reviewer 1 Report

The manuscript by Das et al. reports pyramiding a submergence tolerance gene and three bacterial blight resistance genes in the rice variety Hasanta through marker-assisted backcross breeding and speed breeding. The authors could develop introgressed lines carrying Sub1+Xa21+xa13+xa5 that are tolerant to submergence and resistant to bacterial blight. Some physiological and chemical aspects regarding submergence tolerance mechanism were also provided. The authors claimed that the pyramided lines attained complete product profile of recurrent parent (Hasanta) and could contribute to sustainable rice production under the rainfed shallow-lowland (RSL) ecosystem.  The results of this study are of good quality and well presented. However, I still have some comments as listed below.

Comments

Line 51: citation of relevant references in the main text should start by [1]. 

Line 97: correct the word 'confer' to 'conferring'

Figure 1: please provide full description of each abbreviation, i.e., FS, BS. Please also use a consistent abbreviation format for month names.  

Line 133: please specify "robust phenotyping".

Line 134: please clarify "desirable phenome".

Line 140: please provide full description of DFF, PH, L/B, HRR and AC as there are first present here.

Table 2: mb should be written as Mb. I would suggest to provide Mb in the column header as Physical position (Mb), and remove "mb" in the corresponding rows. 

Lines 166-167: Table 2 was referred, but I cannot find the genetic distance (cM) in Table 2. Only physical distance in Mb was provided.

Lines 172: correct "chromosome 09, 11, 08, and 05" to "chromosomes 9, 11, 8, and 5".

Please check all subscripts throughout the manuscript.

Lines 187-191: how were lesion length and score associated?

Line 233: remove an "and" after Sub1.

Figure 3: sub Figure 3b, the number of lanes is not same as in a, c, and d. Please correct.

Line 263: there are two types of arrows. Do the authors mean vertical arrows? 

Figure 4: sub Figure 4c, the number of lanes is not same as in a, b, and d. Please correct.

Figure 5: the names of lines in the picture are different from those in the figure legend. Please correct.

Table 4: the names of Xoo races are confusing as they are somewhat similar to the BB resistant genes. Are they associated with the resistant genes?

Line 313: what are stressed and non-stressed environments?

Line 334: correct the word "delimted" to "delimited".

Line 337: correct the word "intervension" to "intervention".

Line 354: I am not sure whether the word "phenomics" can be used with this kind of data.

Line 498: remove "were" before "had".

Author Response

Response to the reviewer’ comments

Authors thank the Editor for arranging qualified Reviewers and providing us with the opportunity to revise our manuscript. As suggested, we have performed extensive language and grammar related corrections in the revised manuscript. The corrected portions (reviewer 4) are highlighted with red colour. We believe that the quality of the manuscript has now improved substantially. And, we hope that the revised version is acceptable for publication in the journal “Agriculture’.

Reviewer 1

Comments. Citation of relevant references in the main text should start by [1]. Line 51: citation of relevant references in the main text should start by [1]. Line 97: correct the word 'confer' to 'conferring' Figure 1: please provide full description of each abbreviation, i.e., FS, BS. Please also use a consistent abbreviation format for month names.  Line 133: please specify "robust phenotyping". Line 134: please clarify "desirable phenome". Line 140: please provide full description of DFF, PH, L/B, HRR and AC as there are first present here. Table 2: mb should be written as Mb. I would suggest to provide Mb in the column header as Physical position (Mb), and remove "mb" in the corresponding rows. Lines 166-167: Table 2 was referred, but I cannot find the genetic distance (cM) in Table 2. Only physical distance in Mb was provided. Lines 172: correct "chromosome 09, 11, 08, and 05" to "chromosomes 9, 11, 8, and 5". Please check all subscripts throughout the manuscript. Lines 187-191: how were lesion length and score associated? Line 233: remove an "and" after Sub1.Figure 3: sub Figure 3b, the number of lanes is not same as in a, c, and d. Please correct. Line 263: there are two types of arrows. Do the authors mean vertical arrows? Figure 4: sub Figure 4c, the number of lanes is not same as in a, b, and d. Please correct. Figure 5: the names of lines in the picture are different from those in the figure legend. Please correct. Table 4: the names of Xoo races are confusing as they are somewhat similar to the BB resistant genes. Are they associated with the resistant genes?Line 313: what are stressed and non-stressed environments? Line 334: correct the word "delimted" to "delimited". Line 337: correct the word "intervension" to "intervention". Line 354: I am not sure whether the word "phenomics" can be used with this kind of data. Line 498: remove "were" before "had".

Response 1. Citations of relevant references are thoroughly rectified as per suggestion and instruction, suggested word are incorporated, full description of each abbrebriation are given when it appear first in the text. Desirable phenome means background traits of RP which is recovered as such in derivatives.  Justification for association of lesion length and disease score is given in the text as after 21 days of inoculation, the lines where lession length appeared <5 cm were considered as resistance, and accordingly other score were recorded as per SES of IRRI, 2010. Figure 3 and 4 is corrected as it was due to amplicon band lane selection mistake. Xoo races are not associated with resistance genes, these are the name of Xoo races given by the institute. Stressed is 14 days submergence and non-stressed is control condition. All corrections are highlighted in blue sky and yellow colours.

We hope that the revised version is acceptable for publication in the journal ‘Agriculture’.

 

See attachement

Author Response File: Author Response.pdf

Reviewer 2 Report

Manuscript entitled “Pyramiding submergence tolerance and three bacterial blight resistance genes in popular rice variety Hasanta through marker-assisted backcross breeding” by Goutam Das et al. address the study genetic improvement of the Hasanta rice variety by markers-assisted backcrossing.

The authors demonstrate the utility of marker-assisted back-crossing based introgression of the submergence tolerant (Sub1) and bacterial blight resistant genes (xa5+xa13+Xa21) into the background of Hasanta.

The work is very interesting but, in my opinion, the manuscript presents many issues mainly with the format, citing figures and tables, abbreviations and in the References, and other things, that need to be checked to make this work suitable for publication.

 

 

1. Main issues:

1.1. Regarding main text Formatting

Authors should check the Abbreviations. I must remind to the authors that abbreviations should be defined the first time that appear in the text. e.g. line 15, Flash flooding (FF); line 52, please correct “due to flash flooding (FF)” with “due to FF”; line 99, please correct “flash flooding” with “FF”; line 559, please correct “flash flooding” with “FF”.  Please check all abbreviations [e.g. Back cross (BC), MAS, MAB, ADH, RDL, BB, etc.]

Please remove the hyphen when citing Tables and Figures [e.g. line 117 change “Figure-1” with “Figure 1”, line 130 (Table-2), line 242 (Table-3), etc.].

Also, the name of genes and mutants should appear in italics [e.g. lines 146, 185, etc. (Xoo); lines 166 to 172, 226, 236, 352, 402, etc. (Sub1, Xa21, xa13, xa5); lines 519 and 520 (SUB1A1-1, etc.); etc.]

 

In the Instructions for Authors its indicated that “All Figures and Tables should be inserted into the main text close to their first citation and must be numbered following their number of appearance (Figure 1, Figure 2, Figure 3, etc.; Table 1, Table 2, etc.)”. And same rules apply for Supplemental Material. The authors have cited the figures as follows: Figure 1 (line 117), Figure 2 (line 198), Figure 8 (line 229). Therefore, Figure 8 should be Figure 3, and all the others will be misquoted. Please check all Figures, Supplementary Figures, Tables, and Supplementary Tables.

I must insist that these are only a few examples, please check the manuscript thoroughly.

 

 

 

 

 

 

1.2. Regarding References in the main text

I must point to the authors that, according to the Instructions for Authors “References must be numbered in order of appearance in the text (including table captions and figure legends) and listed individually at the end of the manuscript”

In the present version of the manuscript references do not follow a numeration according to their order of appearance, please correct it. Also, when citing multiple references, their numbers should appear separated only by commas.

Line 386. Is “(IRRI, 2014) a Reference?  If that is the case, should be appear in the properly format [number].

 

 

 

1.3. Regarding References section

The references list has numerous format mistakes. The most serious mistakes refer to:

-Reference list should be ordered according to their appearance in the text

-many titles include names of organisms that should be italicized (e.g. Oryza nivara in reference 14, Oryza sativa in reference 25, etc.).

-There is an extra space after the initial of the author (e.g. in reference 1 “M. K or D. K. D”, in reference 4 “M. R”, etc.).

-Almost all the words in the title begin with capital letters. Many of them should not be in that format. Please correct this (e.g. reference 8, 33, 38, etc.)

- I think that the hyphen separating the pages should be long (see recent publications of the journal).

- Please remove the DOI, Epub, PMID (e.g. reference 8, 10, 18, 95, etc.).

- Please revise general format of reference 33.

- The journal name should be abbreviated and in italics.

- The year should be in bold font

Again, I must insist that these are only a few examples, please check the manuscript thoroughly.

 

 

1.4. Regarding Figures.

Figure 1. Should be in the materials and methods section or in the results section, since it describes the crossing strategy to obtain the new lines.

Please standardize the years and months format (e.g. years with or without italics, “hyphen” or “to” between the months.

Figure 2. The letters of the panels should be lowercase. The size bar is missing

Line 200. Please correct “RGA (a)” with “rapid generation advance. (a)”

Line 201. Please correct “flowering (b)” with “flowering. (b)”

Line 201. Please correct “5cm” with “5 cm”.

Line 202. Please correct “flowering (c)” with “flowering. (c)”.

 

Figure 3. In panel “b” of figure 3 one lane is absent (there are only 10 lanes). Units should be separated from the number by a space (e.g. 300 pb).

Line 260. Please correct “Figure 3:” with “Figure 3.”

Line 260. Please correct “(a)” with “. (a)”

Line 261. Please correct “primer (b)” with “primer. (b)”. Please correct “primer (c)” with “primer. (c)”. Please correct “primer (d)” with “primer. (d)”.

Line 262. Please correct “Marker” with “marker”

Line 263. Please correct “Nos.1-8 represent” with “Lanes 4-11 represent”

Line 263. I am confused with the meaning of “ ‘+’ ve ”. Perhaps is “positive”? Please use correct English terminology (positive).

 

Figure 4. In panel 9 of figure 4 there are 11 lanes (Panels a, b and d =10 lanes). Units should be separated from the number by a space (e.g. 300 pb).

Line 266. Please correct “Figure 4:” with “Figure 4.”

Line 266. Please correct “(a)” with “. (a)”

Line 267. Please correct “primer (b)” with “primer. (b)”. Please correct “primer (c)” with “primer. (c)”.

Line 268. Please correct “primer (d)” with “primer. (d)”.

Line 268. Please correct “Marker” with “marker”

Line 269. Please correct “ Nos.1-7 represent” with “Lanes 4-10 represent”

Line 269. P2 is missing.

Line 270. Please correct “ ‘+’ ve ” with “positive”.

 

Figure 5. Units should be separated from the number by a space (e.g. 300 pb).

Line 274. Please correct “Figure 5:” with “Figure 5.”

Line 274. Please correct “(a)” with “. (a)”

 

Line 275. Please correct “primer (b)” with “primer. (b)”. Please correct “primer (c)” with “primer. (c)”. Please correct “primer (d)” with “primer. (d)”.

Line 276. Please correct “Marker” with “marker”

Line 276. Please correct “Nos.1-13 represent” with “Lanes 4-16 represent”

Line 276. P2 is missing.

Line 279. Please correct “ ‘+’ ve ” with “positive”.

 

Figure 7. Image resolution is not good enough. Words and numbers cannot be read properly. Also, the green box is not defined in the figure, and the bottom of the image appears cropped. Finally, please correct “Swarna-Sub1” with Swarna Sub1”

Line 351. Sub1 should be in italics

Line 352. Xa5, xa13, Sub1, Xa21 should be in italics

 

 

Figure 8. the title of the Y axis should appear out of the figure. Also, Please correct “Swarna Sub-1” with Swarna Sub1”

 

 

Figure 9. Please correct “%Survival” with “% Survival”. Please correct “Swarna Sub-1” with Swarna Sub1”

 

Figures 10, 11, 12 and 13. Please correct “Swarna Sub-1” with Swarna Sub1”

Figure 11. the units of “Total soluble sugar” are missing.

Figures 12 and 13. The blue box that corresponds to “21 days” is missing.

 

Supplementary Figure 3. The names of the NILs are cut. The legend is not mentioned

Supplementary Figure 4. The legend is not mentioned

Supplementary Figure 5. The size bar is missing

Supplementary Figure 6. The size bar is missing. Please correct “Sub-1” with “Sub1”. Please correct “; (a)” with “. (a)”. Please correct “derivatives (b)” with “derivatives. (b)”.

 

1.5. Regarding Tables.

Table 1.

Please correct “yieldingwith” with “yielding with”, “and Bacterial leaf” with “and bacterial leaf”, “HRR, Tolerant” with “HRR, tolerant”, and “(135 days), Semi dwarf (95-100cm)” with “(135 days), semi dwarf (95-100 cm)”. Please standardize semi-dwarf (semi-dwarf or semi dwarf). What does MS mean?

 

Table 2. Units should be separated from the number by a space (e.g. 1.0mb, etc.). Please remove from bottom “FS, foreground…………selection.”

 

Table 3. please correct “S. Sub1and” with “S. Sub1 and”, “BS, Phenomics” with “BS, phenomics”, “68.43- 80.08” with “68.43-80.08”, “79.65- 89.40” with “79.65-89.40”, “91.35- 95.19” with “91.35-95.19”. Please remove the zero from the numbers: 08, 07, 06, and 07.

 

Table 4. Genes should be in italics. Please correct “Swarna-Sub1” with “Swarna Sub1”. The format of the last row should be like the rest of the rows.

 

Table 5. What does NS and S mean?

 

Table 6. Please correct “Swarna Sub1” with “Swarna Sub1”.

Supplementary Table 1. Please correct “Sub1” with “Sub1”.

Supplementary Table 3. Please correct “Swarna Sub1” with “Swarna Sub1”. some rows and columns do not have the same format.

Supplementary Table 4. Genes should be in italics. What does sl mean?

Supplementary Table 6. Please correct “Sub-1” with “Sub1”.

Supplementary Table 7. Please correct “Sub-1” with “Sub1”.

Supplementary Table 8. Please correct “Sub-1” with “Sub1”, “regimes (a)” with “regimes. (a)”, “(b)” with “. (b)”, “(c)” with “. (c)”

 

1.6. Regarding units and values of the magnitudes.

Please the units should appear separated from the numbers, with the exception of ºC, and %.

Please standardize the way how values are represented [e.g. file 37 (2.68± 0.26), file 38 (1.29±0.12), file 241 (11.82 ± 0.460)]. Please put or remove the spaces. Revise all the manuscript.

 

Units appear in different formats [e.g. Line 114 (t/ha), Line 399 (1.40 mg g-1), File 429 (minute per gm fr. wt.)]. What does gm mean? Please standardize them in all text.

 

 

 

 

 

1.7. Regarding Materials and methods

 

 

Section 2.2. PCR and marker analysis. Line 158. The primer table is missing

 

Please describes the methods to obtain the supplemental table 1 and 2, and supplemental figure 1 and 2

 

2. Additional comments

There are errors in the manuscript. Some of them are:

Lines 5, 6 and 7.  The numbers (1, 2 and 3) should be in superscript.

Line 22, 24, 125, etc. I kindly urge to the authors to standardize the nomenclature of the “xa5+xa13+Xa21”, “Xa21+xa13+Xa7+xa5+Xa4”, “Xa21, xa13, Xa7, xa5, Xa4”. With commas or with +

Lines 45 and 46. Please correct “Marker-assisted backcross breeding, biotechnology, molecular breeding, submergence tolerance, bacterial blight resistance; Yield and Quality, speed breeding, Flash flooding” with “marker-assisted backcross breeding; biotechnology; molecular breeding; submergence tolerance; bacterial blight resistance; yield and quality; speed breeding; flash flooding”.

Line 88. Please correct “Furthermore, bacterial blight (BB) (caused by Xanthomonas oryzae pv. Oryzae) disease” with “Furthermore, BB disease (caused by Xanthomonas oryzae pv. Oryzae; Xoo)”

Line 89. Please correct “20%-100%” with “20-100%”.

Line 89. Please check the format of “ºC”, since it is not similar to the format of other “ºC” (see lines 160 to 161).

Line 172. Please correct “09, 11, 08, 05” with “9, 11, 8, 5”

Line 190. Please correct “(MR),10” with “(MR), 10”

Line 235. Please correct “cM)c” with “cM)”

Line 236. Is 0.4 cm or 0.4 cM?

Line 403. Please correct “411-391-809-1recorded” with “411-391-809-1 recorded”

In the all text revise the word “supplementry”. Please correct with supplementary.

 

Lines 571 to 572, 580 to 583, and 590. Please correct “:” with “.”.

Line 573. Please correct “ Figure S-4” with “ Supplementary Figure 4”

Lines 590 and 591. Please correct “regimes (a)” with ““regimes. (a)”, “(b)” with “. (b)”, “g (b)” with “. (g. b)”

Lines 594 to 600. Please put only the initials of the names and surnames.

I must insist that these are only a few examples, please check the manuscript thoroughly.

Author Response

Response to the reviewer’ comments

Authors thank the Editor for arranging qualified Reviewers and providing us with the opportunity to revise our manuscript. As suggested, we have performed extensive language and grammar related corrections in the revised manuscript. The corrected portions (reviewer 4) are highlighted with red colour. We believe that the quality of the manuscript has now improved substantially. And, we hope that the revised version is acceptable for publication in the journal “Agriculture’.

Reviewer-2:

Comment -1.1: Regarding main text Formatting

Response 1.1: As per instruction guidelines and suggestions, article is thoroughly checked and formatted. We have also performed extensive language and grammar related corrections in the revised manuscript. The corrected portions are highlighted with sky blue and yellow colour.

Comment -1.2. Regarding References in the main text

Response 1.2. As per instructions and suggestions, references are numbered in order of appearance in the text. Hope this is now presentable as per format of the journal.

Comment -1.3. Regarding References section

Response 1.3. as per instruction and suggestions, all references are thoroughly checked and formatted in reference section.

Comment 1.4. Regarding Figures.

Response 1.4. All figures and supplementary figures are rearranged and legends are corrected as per suggestions which are highlighted in sky blue colour. Figure 1 is kept in materials and methods section.

Comments 1.5. Regarding Tables.

Response 1.5. as per instructions and suggestion all tables are rearranged, other minor corrections are incorporated in table 1-6 and supplementary table 1-8 and highlighted in sky blue. The meaning of NS and S are mentioned in the text and highlighted too with sky blue colour.

 Comments 1.6. Regarding units and values of the magnitudes.

Response 1.6. As per suggestions all units, word space is rectified and highlighted in sky blue.

 

Comment 1.7.  Regarding Materials and methods

Response 1.7. Table 2 in the main text is primers table, chromosome wise primer distribution is given in supplementary table 2. Methods to obtain supplemental table 1 and 2, and supplemental figure 1 and 2 are described in methods and material section. Rest suggestions are also incorporated in the main text and supplementary file and highlighted in sky blue colour.

We hope that the revised version is acceptable for publication in the journal ‘Agriculture’.

Author Response File: Author Response.pdf

Reviewer 3 Report

1. In the figure 2 PCR amplification of tolerance/resistance gene(s) of BC1F1, the band pattern of amplicons of two parents in the Xa21 using pTA248 primer is different from other figures. Please explain.

2. If it is the “Pyramiding submergence tolerance and three bacterial 2 blight resistance genes’, please present one figure showing that these genes or at least Sub1bc2, pTA248, xal3, and RM122 have been multiplexed (pyramided) in the NILs.

3. Present the regression results of genotypes (Sub1bc2, pTA248, xal3, and RM122, respectively) and phenotypes and their interaction.

Author Response

Response to the reviewer’ comments

Authors thank the Editor for arranging qualified Reviewers and providing us with the opportunity to revise our manuscript. As suggested, we have performed extensive language and grammar related corrections in the revised manuscript. The corrected portions (reviewer 4) are highlighted with red colour. We believe that the quality of the manuscript has now improved substantially. And, we hope that the revised version is acceptable for publication in the journal “Agriculture’.

Reviewer-3:

Comment -1: In the figure 2 (it is figure 3) PCR amplification of tolerance/resistance gene(s) of BC1F1, the band pattern of amplicons of two parents in the Xa21 using pTA248 primer is different from other figures. Please explain.

Response 1: PCR amplification of tolerance/resistance gene(s) in BC₁F₁ is presented in Figure three where 14 representative lanes of amplicons are kept. In figure 3b, by mistake only 13 gel lanes were selected and presented that is why band pattern of amplicon was appearing different. Now it is rectified.

Comment 2: If it is the “Pyramiding submergence tolerance and three bacterial 2 blight resistance genes’, please present one figure showing that these genes or at least Sub1bc2, pTA248, xal3, and RM122 have been multiplexed (pyramided) in the NILs.

Response 2: Multiplexing of markers/primers with different annealing temperature is tedious, even post PCR multiplexing with gradient electrophoresis is also giving very clumsy results. Here, Sub1 and BB resistance primers has different annealing temperature, amplicon size of Sub1bc2 and RM122 are also same, so, we tried but could not get clear gel picture. Though, figure 5 depicting full picture of the study so, I think multiplex figure is mandatory.

 Comment 3. Present the regression results of genotypes (Sub1bc2, pTA248, xal3, and RM122, respectively) and phenotypes and their interaction.

Response 3: The objective of this work is to improve sustainability of rice variety Hasanta under submergence and bacterial blight disease pressure which is well reflected with the results presented in this article (Table 4 & 5, supplementary table 3, 5, 6 & 7). The impact of genes introgressed and markers/primers utilised are already validated as successfully utilised in several trait introgression studies. So, regression analysis of genotypes (Sub1bc2, pTA248, xal3, and RM122, respectively) and phenotypes and their interaction are not needed.

We hope that the revised version is acceptable for publication in the journal ‘Agriculture’.

 

Author Response File: Author Response.pdf

Reviewer 4 Report

There is a “Title:” in your title. Please corrected.

Author Response

Response to the reviewer’ comments

Authors thank the Editor for arranging qualified Reviewers and providing us with the opportunity to revise our manuscript. As suggested, we have performed extensive language and grammar related corrections in the revised manuscript. The corrected portions (reviewer 4) are highlighted with red colour. We believe that the quality of the manuscript has now improved substantially. And, we hope that the revised version is acceptable for publication in the journal “Agriculture’.

Reviewer-4:

Comment -1: There is a “Title:” in your title. Please corrected.

Response: As suggested, we have corrected title and other minor mistakes. The corrected portions are highlighted with sky blue colour. We believe that the quality of the manuscript has now improved substantially. We hope that the revised version is acceptable for publication in the journal ‘Agriculture’.

Author Response File: Author Response.pdf

Round 2

Reviewer 2 Report

The authors have resolved some of the limitations detected in the first version and have considerably improved the manuscript, but there are still aspects that need to be improved.

 

1. Main issues:

1.1. Regarding Materials and methods

Table 2. The sequence of the forward and reverse primers are missing

 

1.2. Regarding Figures and tables.

Figures numbers should be follow an order according to their citation in the main text: first figure 1, second figure 2........., As an example, but figure 2 is cited before the first figure, and figure 9 is cited before figures 6, 7 and 8. In the same way, the figures must appear in order. Some tables are also numbered incorrectly. Please check all figures and tables.

 

Why are the data represented in Figures 11 and 12 are different from those presented in the first version?

 

Figure 12 now has three color bars and the previous version had four.

Supplementary Figure 3. The legend of A, B and H is missing

Supplementary Figure 4. The legend of A, B and H is missing

 

 

2. Additional comments

2.1 Regarding References.

According to the “Instructions for Authors” the journal name should be abbreviated and in italics (Journal Articles: Author 1, A.B.; Author 2, C.D. Title of the article. Abbreviated Journal Name Year, Volume, page range.). Please revise all references

Almost all the words in the title begin with capital letters. Many of them should not be in that format. Please correct this (e.g. reference 3, 8, 9, etc.)

References 39 is a book chapter. Remove the DOI. Please format according to the Instructions for Authors (Books and Book Chapters: Author 1, A.; Author 2, B. Title of the chapter. In Book Title, 2nd ed.; Editor 1, A., Editor 2, B., Eds.; Publisher: Publisher Location, Country, Year; Volume 3, pp. XXX–XXX.)

In reference 94 Oryza sativa should be italicized.

 

2.2 Others

Line 95. Please check the “-“ in “-42]”. I think that is “41-42”

Line 98. Please check “47, , 48,]”

Line 106. Please check “, 5344]”

Line 119. Please correct “(Xa21+ xa13+ Xa7+ xa5+ Xa4)” with “(Xa21+xa13+Xa7+xa5+Xa4)”

Line 150. Please correct “Table 2” with “Table 2”

Line 227. Please correct “(Xa21+xa13+Xa7+xa5+ Xa4)” with “(Xa21+xa13+Xa7+xa5+Xa4)”

Line 231. Please check the size of “74”

Line 227. Please correct “Sub1+ Xa21+xa13+xa5” with “Sub1+Xa21+xa13+xa5”

Figure 3. Please correct “primer (d)” with “primer. (d)”.

Line 271. Please correct “Bc” with “BC”

Line 294. Please correct “Figures 8” with “Figure 8”

Line 368. Please correct “asdonor” with “as donor”

Line 369. Please correct “asheterozygosity” with “as heterozygosity”

Line 419. Please correct “Figure 10” with “Figure 10”

Line 431. Please correct “Figure 11” with “Figure 11”

Line 441. Please correct “Figure 12” with “Figure 12”

Line 442. 21 days in not represented in the Figure 12.

Line 513. Please correct “Tables 5” with “Table 5”

Line 574. Please correct “(Xa21+xa13 + xa5)” with “(Xa21+xa13+xa5)

Lines 600 to 602. Please correct “regimes (a)” with ““regimes. (a)”, “(b)” with “. (b)”, “g (b)” with “. (g. b)”

 

Figure 1. Please standardize the years and months format (e.g. years with or without italics, “hyphen” or “to” between the months, months abbreviated or not).

Figure 6. Please correct “Swarna Sub-1” with “Swarna Sub1”

Figure 7. Please correct “Swasrna Sub1” with “Swarna Sub1”

Figure 9. Please correct “Swarna-Sub1” with “Swarna Sub1”

Figures 10, 11, 12 and 13. Please correct “Swarna Sub-1” with Swarna Sub1”

Table 4. The format of the last row should be like the rest of the rows.

Author Response

Response to the reviewer’ comments

Authors thank the Editor for arranging qualified Reviewers and providing us with the opportunity to re-revise our manuscript. As suggested, we have performed extensive language and grammar related corrections in the revised manuscript. The corrected portions (reviewer2) are highlighted with sky blue colour. We believe that the quality of the manuscript has now improved substantially. And, we hope that the revised version is acceptable for publication in the journal “Agriculture’.

Reviewer-2:

Comment -1.1: 1.1. Regarding Materials and Methods-Table 2. The sequence of the forward and reverse primers are missing.

Response 1.1: As per suggestion, primer sequences are added to the Table 2. The corrected portions are highlighted with sky blue colour.

Comment -1.2. Regarding Figures and tables.

Figures numbers should be follow an order according to their citation in the main text: first figure 1, second figure 2........., As an example, but figure 2 is cited before the first figure, and figure 9 is cited before figures 6, 7 and 8. In the same way, the figures must appear in order. Some tables are also numbered incorrectly. Please check all figures and tables.

Response 1.2. As per instructions and suggestions, all figures and table are rearranged, in the main text, table 1, 2, 3, 4, 5 and 6 are mentioned first in line no. 121, 124, 167, 231, 256, and 400 respectively. Likewise, supplementary table 1, 2, 3, 4, 5, 6 and 7 are mentioned first in the main text in line no. 122, 127, 244, 250, 297 and 465 respectively.

Besides, figures are also rearranged in main and supplementary text, figure 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 are occurring first in line no. 121, 196, 242, 244, 248, 259, 323, 326, 345, 399, 415, 426, 431respectively. Supplementary figures 1, 2, 3, 4, 5, 6 are also rearranged, first appearing in line number 122, 255, 331, 334, 352, 352 respectively.  Hope this is now presentable as per format of the journal.

1.2.1 Why are the data represented in Figures 11 and 12 are different from those presented in the first version?

Response 1.2.1. Data which was presented in previous version for table 11 and 12 were mistakenly taken, where figure-10 was pasted for figures 11, 12 and 13. It was due to editing of these figures in word file where in excel data was selected directly in word file and wrong table was edited in excel which created disparity. Data in Supplementary Table 6 supports all figure in revised version.

1.2.2. Figure 12 now has three color bars and the previous version had four.

Response 1.2.2. As per guidelines, ADH data was taken in only three water regimes, 0, 7 and 14 days of submergence, thus only three colour bars are appeared representing three regimes.

1.2.3. Supplementary Figure 3. The legend of A, B and H is missing

Response 1.2.3. In Supplementary Figure 3, legends A, B and H are given in bottom side of the figure, it is software generated only.

1.2.4. Supplementary Figure 4. The legend of A, B and H is missing

Response 1.2.4. In Supplementary Figure 4, legends A, B and H are given on right side of the figure, it is also software generated only.

Comment 2.1. Regarding References.

Response 2.1. All references are modified as per authors instruction and suggestions received. Modified things are highlighted in sky blue colour.

Comment - 2.2 Others

Response 2.2. All suggestions are incorporated throughout the article, only Sub1 in figures 6, 7, 9, 10 could not be made italic as software not supported. Though, it is not big issue as Swarna Sub1 is product, not genes/QTLs, it could be like as presented.

We hope that the revised version is acceptable for publication in the journal ‘Agriculture’.

Author Response File: Author Response.pdf

Reviewer 3 Report

It should be okay to be sent for proofreading this time. 

Author Response

Response to the reviewer-3’ comments

Authors thank the Editor for arranging qualified Reviewers and providing us with the opportunity to revise our manuscript. As suggested, we have performed extensive language and grammar related corrections in the revised manuscript. The corrected portions are highlighted with red, sky blue colour. We believe that the quality of the manuscript has now improved substantially. And, we hope that the revised version is acceptable for publication in the journal “Agriculture’.

Author Response File: Author Response.pdf