PONE-D-20-34918

Allelic composition of carotenoid metabolic genes in 13 founders influences carotenoid composition in fruits among Japanese citrus breeding population

PLOS ONE

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Chunxian Chen, Ph.D.

Academic Editor

PLOS ONE

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"This work was partially supported by a grant from the Ministry of Agriculture,

Forestry, and Fisheries of Japan (Genomics-based Technology for Agricultural

Improvement, HOR-2003, DNA-marker breeding project), by a grant from the Project

of the Bio-oriented Technology Research Advancement Institution, NARO (the special

scheme project on advanced research and development for next-generation technology),

and by a Grant-in-Aid for Scientific Research of Japan Society for the Promotion of

Science (JSPS), Grant Number 23580055.".

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Additional Editor Comments (if provided):

The paper was to identify alleles of carotenoid biosynthetic genes using citrus breeding parents and populations using the SureSelect target enrichment method. The results are of great value for understanding the diversity of carotenoid gene expressions and compositions. The paper was well written. The authors need attentions to some editorial issues in the paper.

Introduction:

Some early relevant works on citrus carotenoid biosynthetic genes/alleles and the pigment compositions should be cited, for example, those from Ollitrault’s group (e.g., Fanciullino et al. 2007) and Dr. Gmitter’s group (e.g., Chen et al. 2010).

Abstract and main text:

Abbreviations are needed only when they are used afterwards (no need of abbreviations otherwise). This rule is also applied to the main text.

Figures and tables:

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Reviewers' comments:

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Comments to the Author

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Reviewer #1: Yes

Reviewer #2: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: I Don't Know

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

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Reviewer #1: “Carotenoids are C40 lipophilic isoprenoid pigments biosynthesized from 5-carbon isoprene units” should be “Carotenoids are mostly C40 lipophilic isoprenoid pigments biosynthesized from 5-carbon isoprene units”. There are C30 carotenoids in citrus.

Valencia orange (Citrus sinensis Osbeck) and Lisbon lemon (Citrus limon Burm. f.) should be Valencia orange (C. sinensis Osbeck) and Lisbon lemon (C. limon Burm. f.)。

For a better understanding, the procedures in “SureSelect target enrichment of carotenoid metabolic genes in 13 founders” are suggested to be present with a diagram.

The abbreviations in the text, such as “PHY, 400 nm for ZCA, 452 nm for t-VIO, c-VIO, LUT, BCR, ACA, and ZEA, and 453 nm for BCA”, make it difficult to read and understand, full terms are suggested to be present.

I guess the sentences below Figure titles are notes, but not the text, so please add “Notes” before them. However, the ‘Fig. 1. Carotenoid metabolic pathway in citrus fruits’ should be better put in the section of ‘Introduction’, not in the ‘Results’. And QTL and eQTL sites in Fig.1 should be mentioned as specially generated from juice sacs, but not from the flavedo, albedo and segment membrane, for carotenoids and carotenogenesis in the later fruit tissues are quite different.

Please specify those negative, positive and optimum alleles were based on previous Estimated effect size from Bayesian statistical analysis.

Please rephrase the sentence of ‘When the mean values of conditions 1 and 2 were compared with those of condition 3, it was clear that PSY-c and PSY-g had negative effects on reducing the carotenoid concentration.’

Reviewer #2: 1. According to introduction, the authors mentioned “eQTLs of PSY, HYb, and ZEP could be mapped on the loci of their corresponding genes, revealing that their transcription is regulated primarily by cis-elements in their promoter regions.” So what are the polymorphism in the promoter region of these genes?

2. Filtering parameters for the SNP should be added. In the text, the authors mentioned that ”The number of SNPs in PSY, HYb, ZEP, and NCED with more than readable SNP quality score (>150) according to manufacturer’s description were 107, 31, 54 and 19 respectively”, and “Based on the SNP information, 17 SNP markers for PSY, 15 for HYb, 31 for ZEP, 8 NCED, and 5 for TCL were developed for a SNP genotyping assay using the GoldenGate assay system (Illumina) and Fluidigm BioMark™ HD assay system (Fluidigm).” in page 17. What kind of SNPs used? Nonsynomous mutations in coding regions or others?

3. Figure 9, the normal distribution and variance should be assessed before the Welch's test and the Tukey's HSD test were used for significance analysis, and the information should be added.

4. A mistake in page 7 “PYS, HYb, ZEP, and TCL possessed 7, 11, 5, and 4 independent alleles in 13 founders”, PYS should be PSY.

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Reviewer #1: Yes: Dr. Juan Xu

Reviewer #2: No

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Allelic composition of carotenoid metabolic genes in 13 founders influences carotenoid composition in juice sac tissues of fruits among Japanese citrus breeding population

PONE-D-20-34918R1

Dear Dr. Shimada,

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,

Chunxian Chen, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

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