Recent Advances in Molecular Genetics of Onion

Round 1

Reviewer 1 Report

This article summarizes recent advances in molecular genetics research on onions, focusing on bulb color, bulb quality, flowering, biotic stress and other related aspects. The summary is comprehensive and the work is appealing. However, there are still some shortcomings:

1. Whole genome sequencing plays a crucial role in onion genetics research, and there have been significant recent advancements in this area. However, the article does not provide a summary of this aspect.
2. The article outlines five major loci determining onion bulb color, including structural genes and regulatory genes. There have been new advancements regarding the interaction between these two types of genes, which are not provied in the article's description.
3. The flowering pathways in Arabidopsis and onion involve different regulatory mechanisms. It is unnecessary for the article to extensively describe Arabidopsis thaliana's flowering pathway.

It is better to modify the English language.

Author Response

Comment:

This article summarizes recent advances in molecular genetics research on onions, focusing on bulb color, bulb quality, flowering, biotic stress and other related aspects. The summary is comprehensive and the work is appealing.

Response:

There are reviews on onion breeding, flavonoid synthesis, and others but not a synthesized review of molecular genetics in onion. We attempted to compile molecular genetics research in this review. Thank you for finding the review “appealing.”

Comment:

However, there are still some shortcomings:

1. Whole genome sequencing plays a crucial role in onion genetics research, and there have been significant recent advancements in this area. However, the article does not provide a summary of this aspect.

Response:

We tried to focus on molecular genetics that would be relevant to breeders for marker assisted selection. We agree that draft genome assembly of onion is important to understand molecular genetics. In light of the comment from reviewer, we added a section on the draft genome assembly of onion.

Comment:

2. The article outlines five major loci determining onion bulb color, including structural genes and regulatory genes. There have been new advancements regarding the interaction between these two types of genes, which are not provied in the article's description.

Response:

We started the write up for review in 2023. Hence, we missed to include two recently published articles on bulb color. Thank you for pointing out. In the revised manuscript, we have included information from those two articles.

Comment:

3. The flowering pathways in Arabidopsis and onion involve different regulatory mechanisms. It is unnecessary for the article to extensively describe Arabidopsis thaliana's flowering pathway.

Response:

We think that the description of “the flowering pathway in Arabidopsis” would provide background information for readers. As onion flowering pathway is not completely understood, readers would able to relate those genes in the pathway.

Comments:

Comments on the Quality of English Language

It is better to modify the English language.

Response:

While writing the manuscript, we worked on the Quality of English Language. We also checked for grammar and English language on the final draft using subscription based Grammarly app.

Reviewer 2 Report

The paper titled "Recent Advances in Molecular Genetics of Onion" by Suman Sharma et al., focuses on the progress in onion molecular genetics for enhancing production quality and disease resistance. It covers the use of cutting-edge genomic technologies like genetic mapping, RNA sequencing, and various molecular markers to study genetic divergence, understand genes and pathways responsible for key traits like bulb color, bulbing, flowering, vernalization, and disease resistance. It also delves into quantitative trait loci associated with resistance to major diseases, the role of loci in male sterility, and hybrid development. The publication of the onion genome sequence is highlighted as a significant advance that will facilitate further gene identification and understanding of their roles in metabolic pathways.

The review is comprehensive, touching on the importance of onions in nutrition and food preparation, and the significance of understanding their genetic makeup for crop improvement. The exploration of molecular markers, their evolution from isozyme markers to SNP markers, and their application in studying genetic diversity and breeding is thoroughly discussed. The paper also addresses the challenges in onion breeding and the potential solutions offered by modern genomic tools, providing insights into the genetic basis of important onion traits and their regulation.

This critical review finds the paper to be a valuable resource for researchers in plant genetics and breeding, offering a detailed overview of the current state of onion molecular genetics research. It combines a review of recent advances with a discussion of the implications for future research and breeding programs, making it a significant contribution to the field.

Minor issues:

1. Generally, the review is mostly text based and visually reassembles publications from the past century. Even Figure 1 is black-white, despite several possibilities to improve general layout.

2. I would recommend doing some summarizing in tables (dieses vs markers and genes) or figures (like f.e. male sterility mechanism).

Author Response

Comments:

The paper titled "Recent Advances in Molecular Genetics of Onion" by Suman Sharma et al., focuses on the progress in onion molecular genetics for enhancing production quality and disease resistance. It covers the use of cutting-edge genomic technologies like genetic mapping, RNA sequencing, and various molecular markers to study genetic divergence, understand genes and pathways responsible for key traits like bulb color, bulbing, flowering, vernalization, and disease resistance. It also delves into quantitative trait loci associated with resistance to major diseases, the role of loci in male sterility, and hybrid development. The publication of the onion genome sequence is highlighted as a significant advance that will facilitate further gene identification and understanding of their roles in metabolic pathways.

The review is comprehensive, touching on the importance of onions in nutrition and food preparation, and the significance of understanding their genetic makeup for crop improvement. The exploration of molecular markers, their evolution from isozyme markers to SNP markers, and their application in studying genetic diversity and breeding is thoroughly discussed. The paper also addresses the challenges in onion breeding and the potential solutions offered by modern genomic tools, providing insights into the genetic basis of important onion traits and their regulation.

This critical review finds the paper to be a valuable resource for researchers in plant genetics and breeding, offering a detailed overview of the current state of onion molecular genetics research. It combines a review of recent advances with a discussion of the implications for future research and breeding programs, making it a significant contribution to the field.

Response:

Thank you for positive feedback.

Comment:

Minor issues:

Generally, the review is mostly text based and visually reassembles publications from the past century. Even Figure 1 is black-white, despite several possibilities to improve general layout.

I would recommend doing some summarizing in tables (dieses vs markers and genes) or figures (like f.e. male sterility mechanism).

Response:

In the revised manuscript, we added a table to improve the general layout.