PONE-D-20-22147

A genome-wide association study in Indian wild rice accessions for resistance to the root-knot nematode Meloidogyne graminicola

PLOS ONE

Dear Dr. Uma Rao,

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Ji-Zhong Wan

Academic Editor

PLOS ONE

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Reviewer #1: Partly

Reviewer #2: Yes

Reviewer #3: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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Reviewer #1: No

Reviewer #2: Yes

Reviewer #3: No

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Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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5. Review Comments to the Author

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Reviewer #1: General comments: The paper is interesting and provides novel valuable information regarding new sources of genetic resistance in rice. My main concern regards the RT-qPCR experiments. It is not clear at all how the authors calculated the relative expression values of the selected genes. In papers reporting rigorous RT-qPCR experiments is not accepted to use only one reference gene, but at least three reference genes have to be included. I can understand that is often hard to find three or more stable reference gene, thus, in the case the authors decide to use only one reference gene, they have to demonstrate that this gene is stable under the experimental conditions. In this case the authors have to show the reaction efficiency and R2 and Cq values of the reference genes under the different experimental conditions. Moreover, the relative expression values are calculated by normalizing the Cq value of one gene to the Cq value of the reference gene and the Cq values of the mock control (and the relative expression values of the gene is calculated as follows: relative exp value= 2-ΔΔCq). In this manuscript it seems that the authors normalized the Cq values of the selected gene only to the Cq value of the reference genes, thus it is not clear at all how they calculated the relative expression value. I suggest to carefully read this paper: Bustin et al. 2009 “The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments”, Clinical Chemistry 55:4 611-622.

Please also the check the quality of your figures, some graphs are not clear, difficult to read.

Please change qRT-PCR into RT-qPCR

Line 219 “RNA quantity and quality were assessed in Nanodrop ND-1000 spectrophotometer”. To check the RNA quality is essential to run an agarose gel to verify if the extracted RNA was degraded or not. The quantification by using the Nanodrop does not provide information about the integrity of the RNA. Please, provide the gel of RNA as supplementary materials

Line 220 Please specify the starting amount of RNA used to synthetized the cDNA

Reviewer #2: Dear colleagues,

I found that the manuscript provided important novel results for the identification of QTL associated with rice resistance to root-knot nematode M. graminicola. The authors used a genetically diverse collection of wild rice, performed appropriate phenotyping and genotyping scores, and identified candidate genes for the resistance. The authors identified 40 accessions resistant to RNM, and 17 novel MTA for phenotypic traits of RNM. The provided original data is fully available. The statistical methods were applied properly. The manuscript is written using standard English, and the text is easy to read. Therefore, I am recommending to accept the manuscript for publication in PLOS ONE.

Reviewer #3: This manuscript describes variations in the responses to rice root-knot nematode (RRKN) among wild rice accessions and dissection of genetic factors conferring RRKN resistance. The authors identified 40 resistant accessions from a diversity panel of wild rice accessions using a sophisticated screening method. Using high-density SNPs data across the genome, 17 novel marker-trait associations related to RRNK resistance were detected by genome-wide association study. Furthermore, expression analysis revealed that nine genes around significant SNPs were upregulated in RRKN-infected plants indicating candidate genes related to RRKN resistance. The study is well designed, and the paper is well organized. However, it should be described the relationships between 40 resistant accessions and genotypes of significant SNPs detected. Therefore, I recommend the authors to add genotype data of the accessions and to discuss about the contribution of detected QTLs to RRKN resistant accessions. Additionally, I found some points that needed to revise or confirm. I recommend the authors to check these points carefully.

1) Relationship between resistant accessions and genotypes of significant SNPs should be described.

2) p.8, l. 226. “Table S4” should be changed to “Table S2”.

3) p.11, l. 311-312. According to the Fig. 3, the r values in the text seem to represent r square values. It should be changed to the values of correlation coefficients.

4) p.12, l. 337-338. I am confusing because you mentioned that population I and III are designated as “Pro-Aus” and “Pro-Indica”, respectively. And population II was designated as “Mid-Gangetic”. However, in the subsequent sentences, percentages of admixture types do not match with Fig. 4b. I wonder that population I, II and III are designated as “Pro-Aus”, “Pro-Indica” and “Mid-Gangetic”, respectively.

5) p.14, l. 394. “Table S2” should be changed to “Table S1”.

6) p.17, l. 431. “Os11g34450” should be changed to “Os11g34460”.

7) p.18, l. 443. “12 candidate genes” should be changed to “14 candidate genes”.

8) p.20, l. 523-525. I don’t understand the meaning of the sentence. I recommend you to rewrite it.

9) p.22, l. 557. “Rac protein; [70]; Moeder et al. [71]” should be changed to “Rac protein; [70, 71]”.

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

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A genome-wide association study in Indian wild rice accessions for resistance to the root-knot nematode Meloidogyne graminicola

PONE-D-20-22147R1

Dear Dr. Uma Rao,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

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Kind regards,

Ji-Zhong Wan

Academic Editor

PLOS ONE

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