Studies on the Molecular Basis of Heterosis in Arabidopsis thaliana and Vegetable Crops
, Elizabeth S. Dennis 3,4, Ryo Fujimoto 1,* and Hasan Mehraj 1,*Round 1
Reviewer 1 Report
The paper entitled: "Heterosis studies in horticultural crops", submitted by Shiraki et al. is an interesting paper that discusses the state of art of current research on heterosis in vegetable crops. The paper fits perfectly into the scope of the section (of Horticulturae), Genetics, Genomics, Breeding, and Biotechnology (G2B2). Discussing heterosis in leafy and fruit vegetables is the main point of this paper. The overall of the manuscript is good, however, including the following comments and remarks, may improve the quality of the paper. Thus, I recommed considering the paper after minor revisions.
Specific comments:
* In the introduction section, the authors have mentioned that heterosis may occur under two classes of hypotheses, either the dominance hypotheses or the overdominance hypotheses, the authors must point that the two hypotheses are not mutually exclusive and that heterosis can be caused by the action of both types of genes.
* It is clever to mention epistasis (a phenomena in which the influence of one gene is altered by one or more other genes). It is desirable to explain epistasis as a genetic model for heterosis, as it differs from dominance, which is the interaction of alleles at the same gene locus.
* Dominance, overdominance, and epistatic are not the only genetic models of heteosis. It is mandatory to mention the fourth model, which is Pseudo-Overdominance Model (genrally explained as follows, F1 hybrid's improved performance is attributed to a narrow chromosomal area containing two or more loci). (see, https://doi.org/10.3390/genes12111688).
* The intensity of the heterotic effect, is another major concept that needs to be discussed in this review, as heterosis is generally subdivised into three groups based on the parental genetic distance, namely, intraspecific heterosis, inter-subspecific heterosis, and the wide-hybridation heterosis. (see, https://doi.org/10.1007/s10528-017-9837-2, https://doi.org/10.1007/BF00226083, and https://doi.org/10.1007/BF00226083)
* There is no mention of the transcriptomic, and the proteomic biomarkers, found to be linked to proteins and their expressions, and its utility to unveal the hybrid vigour at a very early stage of development in plants.
* Subsection (2.3. Epigenetics), In line 179, change "such as", with "namely", since DNA methylation occurs in three contexts: CG, CHG and CHH (where H is any base except G).
* The 4th section of the paper must be developed and must contain the conclusions of the work in its whole, future directions, and the significance of this paper in understanding heterosis in horticultural crops.
General comments:
-
Abbreviate the words at the start and then utilize them throughout the manuscript.
-
Use homogenous terms for the explanation, don’t use multiple terms for the same purpose.
-
Avoid formatting mistakes.
- Check accordingly the references' order (see line 151, a misplaced numbering, refresh your references list).
Author Response
The paper entitled: "Heterosis studies in horticultural crops", submitted by Shiraki et al. is an interesting paper that discusses the state of art of current research on heterosis in vegetable crops. The paper fits perfectly into the scope of the section (of Horticulturae), Genetics, Genomics, Breeding, and Biotechnology (G2B2). Discussing heterosis in leafy and fruit vegetables is the main point of this paper. The overall of the manuscript is good, however, including the following comments and remarks, may improve the quality of the paper. Thus, I recommed considering the paper after minor revisions.
Specific comments:
* In the introduction section, the authors have mentioned that heterosis may occur under two classes of hypotheses, either the dominance hypotheses or the overdominance hypotheses, the authors must point that the two hypotheses are not mutually exclusive and that heterosis can be caused by the action of both types of genes.
(Response)
We have revised following the reviewer’s suggestion as follows.
"The genetic mechanism of heterosis is complicated, especially in yield, as many loci are involved in heterosis, and cumulative effects of dominance, overdominance, pseudo-overdominance, and epistasis could be important for heterosis [17, 18]."
* It is clever to mention epistasis (a phenomena in which the influence of one gene is altered by one or more other genes). It is desirable to explain epistasis as a genetic model for heterosis, as it differs from dominance, which is the interaction of alleles at the same gene locus.
(Response)
We have described epistasis in the second paragraph of the introduction.
* Dominance, overdominance, and epistatic are not the only genetic models of heteosis. It is mandatory to mention the fourth model, which is Pseudo-Overdominance Model (genrally explained as follows, F1 hybrid's improved performance is attributed to a narrow chromosomal area containing two or more loci). (see, https://doi.org/10.3390/genes12111688).
(Response)
We added a sentence regarding the Pseudo-overdominance Model (L70-72).
* The intensity of the heterotic effect, is another major concept that needs to be discussed in this review, as heterosis is generally subdivised into three groups based on the parental genetic distance, namely, intraspecific heterosis, inter-subspecific heterosis, and the wide-hybridation heterosis. (see, https://doi.org/10.1007/s10528-017-9837-2, https://doi.org/10.1007/BF00226083, and https://doi.org/10.1007/BF00226083)
(Response)
We have added sentences about this point in Perspective (L513-520).
* There is no mention of the transcriptomic, and the proteomic biomarkers, found to be linked to proteins and their expressions, and its utility to unveal the hybrid vigour at a very early stage of development in plants.
(Response)
We have added a sentence about this point in Perspective (L528-L536).
* Subsection (2.3. Epigenetics), In line 179, change "such as", with "namely", since DNA methylation occurs in three contexts: CG, CHG and CHH (where H is any base except G).
(Response)
We have revised.
* The 4th section of the paper must be developed and must contain the conclusions of the work in its whole, future directions, and the significance of this paper in understanding heterosis in horticultural crops.
(Response)
We have revised the 4th section to show our thoughts and future direction of heterosis research in horticultural crops.
General comments:
Abbreviate the words at the start and then utilize them throughout the manuscript.
Use homogenous terms for the explanation, don’t use multiple terms for the same purpose.
Avoid formatting mistakes.
Check accordingly the references' order (see line 151, a misplaced numbering, refresh your references list).
(Response)
We have revised noting these comments.
Reviewer 2 Report
In this paper, the authors try to review the new genetic and epigenetic studies on heterosis in horticultural crops. The transcriptome, noncoding RNAs, quantitative trait locus and DNA methylation was concluded. Some major issues were listed as follows.
1) A. thaliana is a model plant species rather than a horticultural crop, so I suggest remove the ‘Heterosis research findings in A. thaliana’ section.
2) The authors focused on the advance of heterosis research in only leafy and fruit vegetables. However, I miss the useful information on some other kinds of vegetable crops such as root vegetables and flower vegetables. The authors should add several corresponding sections associated with heterosis in these vegetable crops.
3) In the ‘Perspective’ section, the main questions concerning the heterosis formation in horticultural crops should be well concluded, and the authors need to provide some constructive suggestions for future investigation.
4) Some sentences in this paper are not well organized. The language should be comprehensively polished by a native English speaker.
Author Response
In this paper, the authors try to review the new genetic and epigenetic studies on heterosis in horticultural crops. The transcriptome, noncoding RNAs, quantitative trait locus and DNA methylation was concluded. Some major issues were listed as follows.
1)A. thaliana is a model plant species rather than a horticultural crop, so I suggest remove the ‘Heterosis research findings in A. thaliana’ section.
(Response)
One of the points of our review is analyzing findings on heterosis in Arabidopsis thaliana, a model plant of dicots, because this information can be useful for the study of heterosis in horticultural vegetables. Since there is no recommendation to remove this section from the other reviewer or editor, we would like to keep this section if it is not absolutely necessary to exclude it. Your understanding is requested.
2) The authors focused on the advance of heterosis research in only leafy and fruit vegetables. However, I miss the useful information on some other kinds of vegetable crops such as root vegetables and flower vegetables. The authors should add several corresponding sections associated with heterosis in these vegetable crops.
(Response)
Not many studies of heterosis in root vegetables have been reported, but one paragraph was added in the last paragraph of 3rd section.
3) In the ‘Perspective’ section, the main questions concerning the heterosis formation in horticultural crops should be well concluded, and the authors need to provide some constructive suggestions for future investigation.
(Response)
We have revised the 4th section to show our thoughts and future direction of heterosis research in horticultural crops.
4) Some sentences in this paper are not well organized. The language should be comprehensively polished by a native English speaker.
(Response)
Editing by a native speaker with a proven research record was done prior to submission, but was also done on the revise manuscript.
Round 2
Reviewer 2 Report
The authors have comprehensively improved this manuscript in this revised version. Before it's suitable for publication, one remaining major issue is that considerding the authors prefer to remain the '2. Heterosis research findings in A. thaliana' section, the title of this review should be changed into 'Heterosis studies in Arabidopsis and vegetable crops'.
Author Response
The authors have comprehensively improved this manuscript in this revised version. Before it's suitable for publication, one remaining major issue is that considerding the authors prefer to remain the '2. Heterosis research findings in A. thaliana' section, the title of this review should be changed into 'Heterosis studies in Arabidopsis and vegetable crops'.
(Response)
I have changed the title following reviewer's comment.
