Fine Mapping and Candidate Gene Analysis of the Gv1 Locus Controlling Green-Peel Color in Eggplant (Solanum melongena L.)

Round 1

Reviewer 1 Report

Fine mapping and candidate gene analysis of Gv1 locus 1 controlling green-peel color in eggplant (Solanum melongena L.)

The manuscript by Lv et al., presents a robust study on the genetic control of peel colour in egg plant. However, the manuscript needs English language editing before it can be published. In addition, I also have the following concerns which also need to be addressed by the authors.

·         The tile needs to be revised slightly. The GV1 locus controls the inheritance of both peel colour in general – both white and green peel colour. So the tile should be revised to reflect this. This revision should be made throughout the manuscript.

·         Suggested title: Fine mapping and candidate gene analysis of Gv1 locus 1 controlling peel color in eggplant (Solanum melongena L.)

·         The objective of the study are not clear as they have not been stated anywhere

·         Many in-text citations are poorly done and need to be revised

·         There is need for consistency when referring to the Gv1 locus. In some cases, it is referred to as Gv1 gene and in other cases as Gv1 locus. In my view it would be better to refer to it as Gv1 locus as it is comprises many genes

·         Line 16 and 17: was – is (change “was” to “is”)

·         Line 17: control – controls

·         Line 18: this gene has – these genes have

·         Line 22: 7.66 Mb associated region - region spanning 7.66Mb on……

·         Line 27: might have three types - might have been three types

·         Line 28/29: and of them deletion mutation like 19141 - and of these, deletion mutation like that in in-bred line 19141

·         Line 33: Write MAS in full when mentioned the first time

·         Line 38: Please include a reference for this recommendation.

·         Line 39/40: Eggplant is a vegetable and therefore does not play any role in the production of vegetables. This sentence needs to be rephrased or the second part of the sentence deleted.

·         Line 39/40: should be solanaceae family

·         Line 40: Rich in what? Please add more information

·         Line 46: delete “for eggplant peel” as it is redundant

·         Line 51: Chlorophyll-deficit - Chlorophyll-deficient

·         Line 52: In text citations poorly done

·         Line 54: had – has

·         Line 56: Check format of citation

·         Line 60: delete “for eggplant peel” as it is redundant

·         Line 61: Change “occur the” to “have”

·         Line 66: It is not clear what germplasm innovation is

·         Line 70: inheritance of green peel color -  inheritance of peel color

·         Line 112: How did you determine this threshold? Is there a reference for this?

·         Line 130: Where is this reference genome published?

·         Line 150: 3.1 – revise to “Inheritance of peel colour in egg plant”

·         Line 154: Chlorophyll contents – chlorophyll content (this should be corrected throughout the manuscript

·         Line 159: were – had

·         Figure 1: The letters a, b and c are wrongly placed in the caption, thus making it difficult to understand what they refer to. They should be placed at the beginning of the respective description.

·         Line 177: results – resulted

·         Line 178: positioning – mapping

·         Line 178: What do you mean by clean reads?

·         Line 183/184: …..was close and the polymorphism difference was less…. – this is very subjective. On what basis did you determine that the genetic relationship was close and their differences in polymorphism was less? We need a reference for this and preferably the last part of the statement should be moved to the discussion section. I personally don’t think that with over 100,000 SNPs between them, the parents can be considered genetically close.

·         Line 187: proximately - approximately

·         Line 197-199: This sentence is not clear and needs to be revised

·         Line 225: Delete the word “therefore”

·         Line 257: was – were

·         Figure 9: Once gain the letters a, b and c are wrongly placed in the caption. They should be placed at the beginning of the respective description.

·         Line 396/399: Format of in-text citations needs to be checked. Do you need to include the publication year here? Are the numbers (1) and (2) really necessary?

·         Line 399: localiztion  - localization

·         Line 404: materials and methods – perhaps a better word would be methodology

·         Line 438: In present study – in the present study

·         Line 440: delete “in eggplant” as it is redundant

·         Line 441: as in 19141

·         Line 441: types of – type in

 

·         Line 468: In the present study

English language editing required

Author Response

Please see the attachment.

Author Response File: Author Response.docx

Reviewer 2 Report

Title: Fine mapping and candidate gene analysis of Gv1 locus controlling green-peel color in eggplant (Solanum melongena L.)

 

In this manuscript, the author focused on the appearance quality of eggplant, specifically the color of the peel. They aimed to map the Gv1 gene, which controls chlorophyll biosynthesis in eggplant peel. They used white-peel and green-peel inbred lines, along with their F2 progeny, to map the gene using whole-genome re-sequencing and bulked segregant analysis. The Gv1 gene was in a 7.66 Mb region on chromosome 8, which was narrowed down to a 173.2 kb interval using InDel and SNP markers. Within this region, 16 candidate genes were identified, with SmAPPR2-Like being the most promising candidate gene for Gv1 based on RNA-Seq data. Further analysis revealed three types of mutations (large deletion, frameshift variant, and premature stop codon) in white-peel accessions, with the deletion mutation being the most common. Molecular markers were developed to distinguish between white and green peel accessions in eggplant populations based on the sequence differences of SmAPPR2-Like. This study plays a key role in uncovering the molecular mechanisms of chlorophyll biosynthesis in eggplants. The experiment design is rigorous organized, which can explain the conclusion clearly. However, there are still some improvements need the author’ s attention:

1.     P5, Figure 1; the photos need to be aligned and figure legend needs to add more detail information in it, for example, how do the author conduct the significant analysis. In panel b, letter ‘b’ needs to locate at the top left corner. the panel c includes three figures; each one needs to be labeled as a panel and explain how to obtain the corresponding results.

2.     P5, Table 1; the font size in table 1 is too big and needs to be optimized. Similar with Figure 1, more detail information must be explained.

3.     P12, L322; Inconsistent line spacing.

4.     P13, Figure 8; the gel figure (panel c) is unpublishable, which is very weird. Please replace with a clear gel figure. For panel b and d, all the eggplants photo need to aligned and the photo size should be unified.

5.     There are a lot of small grammar mistakes. For example, "In present study" should be "In the present study."; "SmAPRR2 -Like" should be "SmAPRR2-Like" (remove the space); "was used to analyzed" should be "was used to analyze." ; "CDS length of SMEL4_08g005930.1 (SmAPRR2-Like) was 1137 bp" should be "The CDS length of SMEL4_08g005930.1 (SmAPRR2-Like) was 1137 bp."; "encoding 378 AA" should be "encoding 378 amino acids (AA)."; "had the highest coverage and homology with the reported tomato SlAPRR2-Like gene." should be "had the highest coverage and homology with the reported tomato gene SlAPRR2-Like."; L270, "when using cDNA and genomic DNA from19143" should be "when using cDNA and genomic DNA from 19143."; "with 4 SNPs (two of them were missense variants)" should be "with 4 SNPs, two of which were missense variants."; "9 SNP and 7 small InDel in intron region" should be "9 SNPs and 7 small InDels in the intron region.".

6.     P17, L518; The reference lines need to be aligned.

Finally, to further investigate the molecular mechanisms of chlorophyll biosynthesis in eggplant, the author should clone the gene SmAPPR2-Like and express it in transgenic eggplant to visualize the peel color. If the color indeed changed, it could prove the target gene SmAPPR2-Like is functional.  In all, the manuscript still needs a major revision.

It must be improved. 

Author Response

Please see the attachment.

Author Response File: Author Response.docx