Review Reports

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

Sugarcane is a strategic crop for global energy and food security. The focus on accelerating the breeding cycle through cutting-edge technologies, specifically omics and molecular breeding, is of significant relevance to the readership of Plants.

The manuscript provides an excellent state-of-the-art review, incorporating highly contemporary references (predominantly from 2024 and 2025), including the most recent genomic assemblies. The discussion regarding the first field trials of CRISPR-edited sugarcane represents a significant highlight. Overall, the manuscript is relevant and well-aligned with the scope of the journal, particularly within the plant biotechnology and genetics sections.

Comments

Abstract: The abstract should be more specific regarding the core conclusions of the "multi-omics integration" mentioned, rather than merely listing the technologies employed.

Main Strengths

- Integration of recently released reference genomes (2024–2025).

- Practical detailing of approved commercial varieties, such as "Cana Flex" and Bt varieties in Brazil and Pakistan, which bridges the gap between research and field application.

Main Weaknesses

- The manuscript describes the various omics layers in a "compartmentalized" manner. There is a lack of in-depth discussion regarding the computational tools and algorithms required to integrate data across different biological levels (transcriptomics, metabolomics…) for predictive modeling.

- The actual integration of these layers (systems biology approach) is treated superficially, focusing more on enumerating existing studies rather than explaining the underlying integration models.

Suggestions

- I suggest adding a subtopic or a figure detailing a "Systems Biology Framework for Sugarcane" illustrating how disparate data streams converge into cohesive multi-omics models.

- I suggest create a figure comparing "Speed Breeding" with “Conventional breeding”. This figure should emphasize how speed breeding, when empowered by multi-omics integration, could practically reduce breeding cycles from the traditional 15 years to approximately 6–7 years.

 

Author Response

Comments and Suggestions for Authors

Sugarcane is a strategic crop for global energy and food security. The focus on accelerating the breeding cycle through cutting-edge technologies, specifically omics and molecular breeding, is of significant relevance to the readership of Plants.

The manuscript provides an excellent state-of-the-art review, incorporating highly contemporary references (predominantly from 2024 and 2025), including the most recent genomic assemblies. The discussion regarding the first field trials of CRISPR-edited sugarcane represents a significant highlight. Overall, the manuscript is relevant and well-aligned with the scope of the journal, particularly within the plant biotechnology and genetics sections.

Comments

Abstract: The abstract should be more specific regarding the core conclusions of the "multi-omics integration" mentioned, rather than merely listing the technologies employed.

Answer: We have revised the abstract to emphasize the key conclusions of multi-omics integration, highlighting how linking genotype to phenotype improves predictive accuracy and provides deeper insights into the molecular mechanisms underlying complex traits.

Main Strengths

- Integration of recently released reference genomes (2024–2025).

- Practical detailing of approved commercial varieties, such as "Cana Flex" and Bt varieties in Brazil and Pakistan, which bridges the gap between research and field application.

Main Weaknesses

- The manuscript describes the various omics layers in a "compartmentalized" manner. There is a lack of in-depth discussion regarding the computational tools and algorithms required to integrate data across different biological levels (transcriptomics, metabolomics…) for predictive modeling.

- The actual integration of these layers (systems biology approach) is treated superficially, focusing more on enumerating existing studies rather than explaining the underlying integration models.

Suggestions

- I suggest adding a subtopic or a figure detailing a "Systems Biology Framework for Sugarcane" illustrating how disparate data streams converge into cohesive multi-omics models.

Answer: We have added a new Figure 1 in Section 4 illustrating: (A) integration of multi-omics technologies into sugarcane breeding programs using unified predictive models; (B) speed breeding empowered by multi-omics integration; and (C) conventional breeding.

- I suggest create a figure comparing "Speed Breeding" with “Conventional breeding”. This figure should emphasize how speed breeding, when empowered by multi-omics integration, could practically reduce breeding cycles from the traditional 15 years to approximately 6–7 years.

 

Answer: We have added a new Figure 1 in Section 4 illustrating: (A) integration of multi-omics technologies into sugarcane breeding programs using unified predictive models; (B) speed breeding empowered by multi-omics integration; and (C) conventional breeding.

 

Author Response File: Author Response.docx

Reviewer 2 Report

Comments and Suggestions for Authors

This review article discusses the current status of sugarcane breeding in terms of technologies being used for crop improvement. It is very comprehensive, but it is still missing important information, and the organization needs to be improved for the whole to make sense. It makes more sense to start with an overview of the breeding cycle, including information about how many sugarcane breeding programs exist (in public and private sectors), where they are located, and the most important breeding targets for the industry. If there are important germplasm resources in the public sector, those can be mentioned. Next, the section describing genomic resources can be introduced, followed by the other ‘omics resources. Then, GS and high-throughput phenotyping can be presented. Lastly, the various transformation and gene editing information can be presented.

Specific comments:

Very basic information is missing from the introduction section. The first paragraph gives the range of ploidy of S. officinarum and S. spontaneum species from which sugarcane is derived, but the base chromosome numbers and ploidy of these species is not given. The latin names of the hybrid species  and the direction of the crosses made to produce hybrids are also not mentioned. The authors do not even spell out the genus name where it should be shown, in the first sentence after the first word (Saccharum spp.).  They also fail to mention the genome size range in megabases (Mb) or gigabases (Gb).

In section 2.1, the second paragraph (“Sugarcane biotechnology has advanced rapidly…”) would be better placed as the first paragraph.

Line 544-545: “Traditional phenotyping methods are subjective…” That is simply false. Measurements such as plant height and yield may vary in accuracy depending on the method, but are certainly not made up by the observer.

Author Response

Comments：

This review article discusses the current status of sugarcane breeding in terms of technologies being used for crop improvement. It is very comprehensive, but it is still missing important information, and the organization needs to be improved for the whole to make sense. It makes more sense to start with an overview of the breeding cycle, including information about how many sugarcane breeding programs exist (in public and private sectors), where they are located, and the most important breeding targets for the industry. If there are important germplasm resources in the public sector, those can be mentioned. Next, the section describing genomic resources can be introduced, followed by the other ‘omics resources. Then, GS and high-throughput phenotyping can be presented. Lastly, the various transformation and gene editing information can be presented.

Comments1：the organization needs to be improved for the whole to make sense

Answer: We have reorganized the manuscript into seven sections as follows:

1. Introduction
2. Overview of Global Sugarcane Breeding Program (new adding)
3. Sugarcane Genome
4. Multi-Omics technology；4.1. Transcriptomics，4.2. Proteomics，4.3 Metabolomics，4.4 Phenomics

5. Genomic selection (GS)
6. Sugarcane genetic engineering
7. Discussion and Future Directions
   
   Comments2：an overview of the breeding cycle, including information about how many sugarcane breeding programs exist (in public and private sectors), where they are located, and the most important breeding targets for the industry

Answer: we added Global breeding programs in the Section2: Overview of Global Sugarcane Breeding program

Specific comments: Very basic information is missing from the introduction section. The first paragraph gives the range of ploidy of S. officinarum and S. spontaneum species from which sugarcane is derived, but the base chromosome numbers and ploidy of these species is not given. The latin names of the hybrid species  and the direction of the crosses made to produce hybrids are also not mentioned. The authors do not even spell out the genus name where it should be shown, in the first sentence after the first word (Saccharum spp.).  They also fail to mention the genome size range in megabases (Mb) or gigabases (Gb).

Answer: We have revised the Introduction to include comprehensive information on the genus Saccharum, including base chromosome numbers (2n = 40-128, x = 8 for S. spontaneum; 2n = 80, x = 10 for S. officinarum), ploidy levels (2n = 100-130), genome sizes (10-12 Gb), and the interspecific hybridization process that produced modern sugarcane cultivars (Line 53-62).

In section 2.1, the second paragraph (“Sugarcane biotechnology has advanced rapidly…”) would be better placed as the first paragraph.

Answer: Section 2.1 has been reorganized and moved to Section 6.1. We moved the paragraph as placed in first paragraph. The revised text now in Line 521-525

Line 544-545: “Traditional phenotyping methods are subjective…” That is simply false. Measurements such as plant height and yield may vary in accuracy depending on the method, but are certainly not made up by the observer.

Answer: We have corrected this statement. The revised text now reads (Line 405-407): "Traditional phenotyping methods can be labor-intensive and may vary in precision depending on the measurement technique, though they remain valuable for assessing key agronomic traits".

 

Author Response File: Author Response.docx

Reviewer 3 Report

Comments and Suggestions for Authors

This is an interesting review on the current state of the tools used in sugarcane breeding. In addition to the technical tools employed, -which have been correctly described- I suggest adding two main paragraphs. At the beginning, it would be helpful to indicate the main problems affecting sugarcane cultivation, including biotic and abiotic stress, productivity constraints, low genetic diversity, etc.

On the other hand, in the “Future challenges and directions” section, beyond describing the technical tools, the paper should address the true challenges faced by the crop; for example, the emergence of new pests and diseases, for which cultivars with polygenic resistance would be highly desirable. It should also consider producers’ needs, such as tolerance to additional herbicides, reduced flowering, and improved agronomic traits for ethanol production, for example. These could include higher yield and improved industrial quality, earlier maturation, and lower levels of phenolic compounds and other contaminants that hinder clarification/crystallization. Regarding plant architecture, mechanized agriculture requires more uniform stalks, reduced lodging, and resistance to pests, with special emphasis on borers. As for abiotic stress, drought, extreme heat, high irradiation, salinity, marginal soils, waterlogging, improved nitrogen use efficiency, and greater ratoon longevity are also key targets.

This way, readers would benefit not only from learning about the techniques and the plants obtained, but also from understanding the problems that still need to be solved and remain unresolved to date. Thank you for your attention.

Comments for author File: Comments.pdf

Author Response

Comments and Suggestions for Authors

This is an interesting review on the current state of the tools used in sugarcane breeding. In addition to the technical tools employed, -which have been correctly described- I suggest adding two main paragraphs. At the beginning, it would be helpful to indicate the main problems affecting sugarcane cultivation, including biotic and abiotic stress, productivity constraints, low genetic diversity, etc.

Comment 1：Adding two main paragraphs the main problems affecting sugarcane cultivation

Answer: We have added an overview of the major challenges affecting sugarcane cultivation in Section 1 (Introduction, lines 63–90), including biotic and abiotic stresses, narrow genetic diversity, and long breeding cycles.

On the other hand, in the “Future challenges and directions” section, beyond describing the technical tools, the paper should address the true challenges faced by the crop; for example, the emergence of new pests and diseases, for which cultivars with polygenic resistance would be highly desirable. It should also consider producers’ needs, such as tolerance to additional herbicides, reduced flowering, and improved agronomic traits for ethanol production, for example. These could include higher yield and improved industrial quality, earlier maturation, and lower levels of phenolic compounds and other contaminants that hinder clarification/crystallization. Regarding plant architecture, mechanized agriculture requires more uniform stalks, reduced lodging, and resistance to pests, with special emphasis on borers. As for abiotic stress, drought, extreme heat, high irradiation, salinity, marginal soils, waterlogging, improved nitrogen use efficiency, and greater ratoon longevity are also key targets.

This way, readers would benefit not only from learning about the techniques and the plants obtained, but also from understanding the problems that still need to be solved and remain unresolved to date. Thank you for your attention.

Comment 2：Address unresolved challenges in sugarcane cultivation

Answer: We have substantially expanded the Discussion and Future Directions section (Section7) in sub-topic; 7.2 Challenges and Future Directions (lines 768–805) to address:

-Polygenic resistance to emerging pests and diseases

-Weed management

- Industrial perspective challages

- Abiotic stress perspective

 

 

Author Response File: Author Response.docx

Reviewer 4 Report

Comments and Suggestions for Authors

Review of the manuscript titled: Strategies and Technologies to Accelerate Sugarcane Breeding.

The review is devoted to an important topic of sugarcane breeding and application of modern tools. The review is well justified considering increasing results and publications on the subject. It is well structured and covers all important technologies as well as breeding traits. The review is well written in good scientific language. It employs 160 references. Positive review feature is mention of the practical application of the modern tools. It certainly deserves publication and there are no major challenges to be addressed. Few suggestions which may improve the review are below.

1. It would be desirable to mention major sugar cane producing countries with data on area and, perhaps, yields.
2. Figure 2 has great potential for improvement: the plant may be removed as some lines towards different plant sections may be misunderstood; the references for each stage are needed; perhaps a table will be better to present it.
3. Title suggests that the review main focus is in speeding up the breeding while it is much broader.
4. The authors may like to add the application of modern tools in the main sugar cane breeding programs globally.

Author Response

Comments and Suggestions for Authors

Review of the manuscript titled: Strategies and Technologies to Accelerate Sugarcane Breeding.

The review is devoted to an important topic of sugarcane breeding and application of modern tools. The review is well justified considering increasing results and publications on the subject. It is well structured and covers all important technologies as well as breeding traits. The review is well written in good scientific language. It employs 160 references. Positive review feature is mention of the practical application of the modern tools. It certainly deserves publication and there are no major challenges to be addressed. Few suggestions which may improve the review are below.

Comment1：It would be desirable to mention major sugar cane producing countries with data on area and, perhaps, yields.

Answer: We have added major sugarcane production in Section 1 (Introduction, lines 44–51),  including cultivation area, production volume, and average yields for top five producing countries; Brazil, India, China, Thailand, Pakistan.

Comment2：Figure 2 has great potential for improvement: the plant may be removed as some lines towards different plant sections may be misunderstood; the references for each stage are needed; perhaps a table will be better to present it.

Answer: We have converted the information into a table format with added references in Table 2 , Section3: Sugarcane Genome

Comment3：Title suggests that the review main focus is in speeding up the breeding while it is much broader.

Answer: We have revised the title to better reflect the comprehensive scope of the review: Sugarcane Breeding in the Genomic Era: Integrative Strategies and Emerging Technologies.

Comment4：The authors may like to add the application of modern tools in the main sugar cane breeding programs globally.

Answer: We have substantially expanded in Section7: Discussion and Future Directions section. In sub-topic: Application of Molecular Breeding Tools in Sugarcane Programs  (lines 736–765)

 

Author Response File: Author Response.docx