Fruit Crop Improvement with Genome Editing, In Vitro and Transgenic Approaches
Round 1
Reviewer 1 Report
The authors reviewed and discussed the major breeding technology and approach in fruit crops to improve important traits like abiotic and biotic stress and fruit quality. I have some major and minor concerns listed as following:
Line 27-28. Figure 1 doesn't show an increase in production, it shows banana has a top production. Please clarify.
Figure 2 text is messed up, not sure if it happened in the original figure or because of the format conversion.
Figure 3. The authors presented 14 different colors, but only 7 were labeled. Please correct this. And in line 90-91, the authors stated that 39 fruit crops and 42 fruit trees have mutant cultivars. I am not clear on the definitions of fruit crops and fruit trees. For example, banana is a fruit crop but it is a tree as well, how do you divide the fruit species into these two categories?
The labels in figure 1 and figure 3 are all capitalized which is hard to read. Please revise them.
Line 20197-202. Myb as a TF regulated a lot of genes and is involved in flavonoid biosynthesis. The way the authors wrote makes me confused that the induced anthocyanin in the engineered apple reduced inflammation, but that is not true in the reference paper.
Line 232-235, the sentence is confusing, please revise.
I would ask the authors to revise entirely the session '4. Genomics insights into fruit quality'. For example, in 4.1 Gene duplication, the authors mainly talked about transposon and TE insertion, which do nothing to gene duplication. In 4.2 and 4.4, the authors talked about GWAS, however, GWAS is not really a sequencing method, it is a genomic analysis method, similar to QTL studies, but it doesn't need a breeding population.
In figure 2, the authors included transcriptomics and metabolomics, but neither of them is reviewed in the manuscript. Do the authors want to discuss them?
Author Response
Reviewer 1 The authors reviewed and discussed the major breeding technology and approach in fruit crops to improve important traits like abiotic and biotic stress and fruit quality. I have some major and minor concerns listed as following:
Line 27-28. Figure 1 doesn't show an increase in production, it shows banana has a top production. Please clarify.
Reply: Thanks for pointing out the error. With due apologies, the same is corrected.
Figure 2 text is messed up, not sure if it happened in the original figure or because of the format conversion.
Reply: Thanks. This happened during the pdf making. We have corrected and presented it without any mess.
Figure 3. The authors presented 14 different colors, but only 7 were labeled. Please correct this. And in line 90-91, the authors stated that 39 fruit crops and 42 fruit trees have mutant cultivars. I am not clear on the definitions of fruit crops and fruit trees. For example, banana is a fruit crop but it is a tree as well, how do you divide the fruit species into these two categories?
Reply: Thanks. The figure has been corrected with all the labels properly represented. The problem happened during the pasting the figure into the word document. The sentence is now changed with representation of total mutant varieties in fruit species. The FAO/IAEA mutant database had presented the information that 39 fruit crops and 42 fruit trees have mutant cultivars. Taking your suggestion and to avoid the confusion, we have used the term ‘fruit species’.
The labels in figure 1 and figure 3 are all capitalized which is hard to read. Please revise them.
Reply: Thanks. We have corrected and all the font has been modified as suggested.
Line 20197-202. Myb as a TF regulated a lot of genes and is involved in flavonoid biosynthesis. The way the authors wrote makes me confused that the induced anthocyanin in the engineered apple reduced inflammation, but that is not true in the reference paper.
Reply: Thanks for pointing out this. We may have over-simplified the writing but, corrected the sentences with more clarity and correctness. The authors of this paper mentioned that feeding of MYB10 engineered apples to mice showed altered expression of inflammatory genes and reduced inflammation in treated mice
Line 232-235, the sentence is confusing, please revise.
Reply: Thanks. We have modified as suggested.
I would ask the authors to revise entirely the session '4. Genomics insights into fruit quality'. For example, in 4.1 Gene duplication, the authors mainly talked about transposon and TE insertion, which do nothing to gene duplication. In 4.2 and 4.4, the authors talked about GWAS, however, GWAS is not really a sequencing method, it is a genomic analysis method, similar to QTL studies, but it doesn't need a breeding population.
Reply: Thanks for your critical view. We have corrected the portions in section 4, as suggested.
In figure 2, the authors included transcriptomics and metabolomics, but neither of them is reviewed in the manuscript. Do the authors want to discuss them?
Reply: Thanks. We have omitted both these as we have not covered; this is now corrected in Fig.2.
Reviewer 2 Report
This review focused on the development and production of genetically elite species using strategies ranging from conventional to mutagenesis, in vitro, molecular, transgenic and genomics breeding tools. In this article, we have presented an outlook on the aspects of fruit crop improvement using in vitro and molecular breeding approaches. The manuscript is well-structured and well-discussed. However, some points should be checked and corrected before it's accepted in this journal.
Therefore, according to my comments, I recommended the publication of the paper after minor revision.
[1] The abstract is not clear. Please add the aim and objective of the MS.
[2] The study's background should be clearly stated. Describe the introduction and review of the work (Please add more information).
[3] The MS English needs to be improved. The article's English must be carefully checked for grammatical errors.
Author Response
Reviewer 2
This review focused on the development and production of genetically elite species using strategies ranging from conventional to mutagenesis, in vitro, molecular, transgenic and genomics breeding tools. In this article, we have presented an outlook on the aspects of fruit crop improvement using in vitro and molecular breeding approaches. The manuscript is well-structured and well-discussed. However, some points should be checked and corrected before it's accepted in this journal.
Therefore, according to my comments, I recommended the publication of the paper after minor revision.
[1] The abstract is not clear. Please add the aim and objective of the MS.
Reply: Thanks for your critical view. We have corrected the portions in section 4, as suggested.
[2] The study's background should be clearly stated. Describe the introduction and review of the work (Please add more information).
Reply: Thanks for your critical view. We have corrected the portions, as suggested.
[3] The MS English needs to be improved. The article's English must be carefully checked for grammatical errors.
Reply: Thanks for your critical view. We have corrected the text as suggested.
Reviewer 3 Report
Dear editor and colleagues,
I have read the submitted manuscript “Fruit tree improvement with genome editing, in vitro and transgenic approaches” with interest.
It is a literature review that deals with the progress of plant breeding in significant crop plants (for horticulture) in the 'new genetic era'.
As a manuscript per se, is it well organized, robust, clearly focused, it includes recent and adequate bibliography and correlates to the aim and scopes of the Horticulturae-mdpi journal.
The grammar, syntax and quality of writing are also of high standards. Hence, the work has merit for publication.
I have however some suggestions that the authors could take into consideration in order to provide 'up to date' information for the readers and to distinguish their work for many other similar reviews already available in the literature.
· I am missing information on several works regarding transcriptome sequencing and comparative transcriptomics used across tissues and genotypes that help elucidating candidate genes in several metabolic pathways of fruit crops
· A comparison across the length of breeding cycles/generation time in conventional breeding, transgenic technology and genome editing technologies in fruit tree crops (maybe as a figure) could also add value to the manuscript.
· Progress regarding modification of plant and fruit architecture and/or shape is not adequately discussed
· The authors could additionally focus on the technical challenges for the application of genome editing and add a future perspectives paragraph
· Information regarding ploidy/ aneuploidy manipulation (a vital part in breeding) is missing
· Figure 2 needs text size enhancement
Based on the above my recommendation is acceptance after major revision
Author Response
Reviewer 3 I have read the submitted manuscript “Fruit tree improvement with genome editing, in vitro and transgenic approaches” with interest. It is a literature review that deals with the progress of plant breeding in significant crop plants (for horticulture) in the 'new genetic era'. As a manuscript per se, is it well organized, robust, clearly focused, it includes recent and adequate bibliography and correlates to the aim and scopes of the Horticulturae-mdpi journal. The grammar, syntax and quality of writing are also of high standards. Hence, the work has merit for publication.
Reply: Thanks for your encouraging comments. We appreciate your interest to go through our manuscript.
I have however some suggestions that the authors could take into consideration in order to provide 'up to date' information for the readers and to distinguish their work for many other similar reviews already available in the literature.
I am missing information on several works regarding transcriptome sequencing and comparative transcriptomics used across tissues and genotypes that help elucidating candidate genes in several metabolic pathways of fruit crops
Reply: Thanks for your critical view. We agree with the expert reviewer about the works on transcriptome sequencing which have contributed to great deal of knowledge on genes and metabolic pathways in fruit crops. There has been a great deal of research in this area. In the article, our intent has been to focus on improvement of fruit plant species using genome editing, in vitro and transgenic approaches, and hence did not cover the suggested topic.
- A comparison across the length of breeding cycles/generation time in conventional breeding, transgenic technology and genome editing technologies in fruit tree crops (maybe as a figure) could also add value to the manuscript.
Reply: Thanks for your comments. We have added a new figure to depict the comparison of the length of breeding cycles/generation time in conventional breeding, transgenic technology and genome editing technologies.
- Progress regarding modification of plant and fruit architecture and/or shape is not adequately discussed
Reply: Thanks for your comment. Since there have been several excellent reviews/papers (Ramirez-Torres et al. (2021). Transgenic research, 30(4), 499–528; Grumet et al. Eur Jou Plant Pathol. 2013; Li et al. 2022, Plants, 2128. https://doi.org/10.3390/ plants11162128; Mathiazhagan et al. 2021, Genes12, 1881. https://doi.org/10.3390/genes12121881) highlighting the progress on modification of plant and fruit architecture and/or shape, it was difficult to cover it extensively.
- The authors could additionally focus on the technical challenges for the application of genome editing and add a future perspectives paragraph
Reply: Thanks for your comment. We have added information the above aspects.
- Information regarding ploidy/ aneuploidy manipulation (a vital part in breeding) is missing
Reply: Thanks for your comment. We have added information the above aspects.
- Figure 2 needs text size enhancement
Reply: Thanks. We have corrected the text size in Fig.2.
Based on the above my recommendation is acceptance after major revision
Round 2
Reviewer 1 Report
The revised figures are improved and much clear than before. I have one minor issue in the genomic insights section.
Lines 237-249, Some explanations are needed to connect gene duplications and transposons. This paragraph reviewed the gene duplications first and stated transposon had a likewise effect? The logic doesn't make sense here.
Author Response
Authors thank reviewer for his remarks and suggestion. The text has now been modified.
Reviewer 3 Report
dear editor and colleagues
the authors have adressed most of my comments and i feel that the manuscript can be accepted
Author Response
Authors thank reviewer for his remarks and suggestion.
