Genetic Variation and Association Analysis of Phenolic Compounds in Rapeseed (Brassica napus L.) Mutant Lines Using Genotyping-by-Sequencing (GBS)
, Jaihyunk Ryu 1,†, Baul Yang 1,2, Ye-Jin Lee 1,2, Jae Hoon Kim 1, Juyoung Kim 1, Woon Ji Kim 1, Sang Hoon Kim 1, Soon-Jae Kwon 1, Jin-Baek Kim 1, Si-Yong Kang 3, Jae Il Lyu 4, Chang-Hyu Bae 2 and Joon-Woo Ahn 1,*
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsComments on manuscript #2613264
The manuscript titled “Genetic Variation and Association Study of Phenolic Compounds in Rapeseed (Brassica napus L.) Mutant Lines Using Genotyping‐by‐Sequencing (GBS)” describes an association analysis of a rapeseed mutation population by gamma radiation. Since rapeseed is an amphidiploid species, the presence of both allelic and homeologus SNPs is expected. However, there is no description of any effort to distinguish allelic SNPs from homeologus SNPs in the manuscript. Fail to do so will lead to a large number of false SNPs and jeopardize the conclusion of this manuscript. The claim of SNP markers associated with GAMA mutant lines can be used for breeding programs is troublesome unless the mutant lines become available to other breeding programs. There is no indication that the authors will deposit their mutant lines for public access. In addition, the manuscript has a very low quality in writing due with numerous grammatic and spelling errors. It is not suitable for publication.
Line 31 change to ‘with TPC. They were selected as….’
Line 41 change to ‘There is a limited utility of rapeseed extracts for animal feed because of “
Line 46 change to ‘current rapeseed production cannot meet Korea’s demand; therefore, it is important to improve seed yield and nutritional value through molecular breeding’
Line 64 change to ‘synthesized’
Line 67-68 need rephrase. The meaning of the sentence is unclear.
Line 90-92 need rephrase. The meaning of the sentence is unclear.
Line 267 change to ‘difference’
Line 268 change to ‘among mutant lines.’
Figure 2 legend is not readable
Line 287 change to ‘difference’
Comments on the Quality of English Language
The quality of English is very poor. It needs substantial improvement
Author Response
"Please see the attachment"
Author Response File: 
Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for AuthorsGeneral comment
The manuscript ''Genetic Variation and Association Study of Phenolic Compounds in Rapeseed (Brassica napus L.) Mutant Lines Using Genotyping‐by‐Sequencing (GBS)'' described the single nucleotide polymorphisms identified by genotyping-by-sequencing were investigated in 95 Brassica napus mutant lines derived from gamma rays and their original cultivar. Also, the phenolic content was investigated in the same mutant lines and their original cultivar. Among seven identified phenolic compounds, sinapine was the major compound in all genotypes and it content ranged from 91.2 to 99.2%. It was identified 241 single nucleotide polymorphisms which are significantly associated with seven phenolic compounds and total phenolic content.
In general, article is well done and I have only minor comments.
Minor comments
Abstract
Line 27: explain abbreviations ''TSC''
1. Introduction
Line 37: add '', family Brassicaceae'' after ''napus L.''
2. Materials and Methods
Line 102: write cultivar names on botanical correct way, that is change ‘Youngsan’ into Brassica napus 'Youngsan'
Line 102: change ‘Tammi’ into B. napus 'Tammi'
Line 116: omit dot before 51
Line 117: change letter ''x'' into ''symbol ''×''
Line 169: change style for bracket from Italic to Normal
Line 177: change cultivar into cultivars; add space before was
Line 184: change were into was?
Line 210: remove underline in https://genemania.org/
3. Results
Lines 252, 253: the same (like in line 210)
Lines 283, 284: add semi-quotes for cultivar names
4. Discussion:
Lines 374: add semi-quote after Tammi
Line 381: omit space before symbol for percent
References
In general, authors should check the journal style for references and make some corrections. Some mkistakes are given below.
Line 549: omit and before Prod.
Line 553: abbreviation for Phytochemistry is Phytochem.
Line 562: abbreviation for Nutraceuticals is Nutrac.
Ref. 21 and 22: article titles were not write on the same way
Author Response
"Please see the attachment"
Author Response File: Author Response.pdf
Reviewer 3 Report
Comments and Suggestions for AuthorsThe paper is interesting. However, some corrections should be made.
Line 50-51 needs a short explanation of why sinapine contents are not desired. Now it is not clear
Sinapine, a major phenolic compound in rapeseed seeds, is known for its antioxidative effects and is the most important natural source of cancer-preventive agents [6,7].
Lines 356-358 transfer into the introduction and will be clear why sinapine is not desirable
Lines 51-81. I recommend writing in the chemical structures of glucosinolates and sinapine in order to better accept the paper during reading.
Line 198-199. Please, provide this calibration curve (equation).
Chapter 3.3 . I recommend presenting the main structures.
Dihexose is a phenolic substance&
Lines 45-451correction should be
Comments for author File: Comments.pdf
good. Some corrections must be. In general. the language is readable.
Author Response
"Please see the attachment"
Author Response File: Author Response.pdf
Round 2
Reviewer 1 Report
Comments and Suggestions for AuthorsThe authors failed to address the question if they made any effort in curating allelic SNPs instead of false positive SNPs existing as homeologous SNPs in the allotetraploid species. The two quoted papers were from the same research group of this manuscript. Therefore, I don’t feel confident that this paper is presenting valid results for the scientific community.
The authors may refer to the following publication for explanation on false SNP discover for polyploids.
Clevenger, Josh, Carolina Chavarro, Stephanie A. Pearl, Peggy Ozias-Akins, and Scott A. Jackson. "Single nucleotide polymorphism identification in polyploids: a review, example, and recommendations." Molecular plant 8, no. 6 (2015): 831-846.
The revised manuscript improved in writing quality, however, there are still some obvious grammatic errors exist. For instance, Line 19-20 and Line 31-33 need revision.
Comments on the Quality of English LanguageThe revised manuscript improved in writing quality, however, there are still some obvious grammatic errors exist. For instance, Line 19-20 and Line 31-33 need revision.
Author Response
"Please see the attachment."
Author Response File: Author Response.pdf
