Review Reports

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

This paper focuses on the germplasm resources of the Colombian national pepper (Capsicum spp.), performing phenotypic characterization in three locations under multiple environments. It also conducts a preliminary integrated exploration combining AMMI stability analysis and genome prediction (BayesA/B/C, BRR, BL, RKHS). Furthermore, it references previously collected GBS/pan-genome data from across China as background information. The topic has practical breeding value, and the data volume and analytical approach also have potential contributions.

The main questions are as follows:
1. The paper states, "32 genotypes, three locations, multiple environments; 7 plants were selected from the middle plot for fruit collection; 'three replicates, three fruits evaluated each time'." Please clarify: Does this "three replicates" refer to plot replicates (biological replicates) or fruit replicates (technical/subsample replicates)?

2. The paper states, "CIELab (L*, a*, b*, C, h) was measured using a digital refractometer." A refractometer is not used for color analysis.

3. The correspondence between phenotype and genomic data sample sets is unclear. The intersection of these three needs clarification: Which genotypes simultaneously possess both phenotype and genotype data? The N and list for training (La Selva) and extrapolation (Palmira/Cauca); the origin of N=19/22/25/27 in Table 5; handling of missing data. Furthermore, Tables 4/5 show extremely high test correlation (r_test ~0.94–0.98), but many traits have h² close to 0 or very low (e.g., "Luminosidad h²≈0.008"), indicating logical inconsistency.

4. The text uses "mg g⁻¹" and "mg kg⁻¹" interchangeably; the same trait (e.g., capsaicin) appears in two units. Consistency is recommended.

5. Color index: Please provide the exact formula or citation.

6. PSI/ASV index: Calculation formula and citation are recommended.

7. Genus and species names are italicized; the full name appears first, followed by abbreviations.

Author Response

Please see the attachment

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

Comments for Authors:

The abstract presents a well-structured and comprehensive study integrating phenotypic stability analysis with genomic prediction to advance multi-environment breeding in Capsicum spp. The work demonstrates methodological rigor by combining AMMI models with Bayesian genomic prediction (BayesC), which enhances its novelty and relevance for genomic-assisted selection. The focus on both physicochemical and biochemical traits, along with the integration of stability and prediction analyses, provides valuable insights for breeding programs targeting quality and stability across environments. The writing is mostly clear and technically sound, though a few areas could be further refined for clarity and flow.

Specific comments:    

1. The abstract is dense and information-rich, which is good scientifically but slightly challenging to read in one pass. Consider dividing long sentences (e.g., lines 31–35) into shorter ones to enhance readability and emphasize key results.
2. The shift from genetic diversity (Lines 59–78) to fruit composition and organoleptic quality (Lines 79–93) is somewhat abrupt. Consider adding a brief transitional sentence that links genetic diversity to phenotypic and biochemical diversity.
3. Several sentences (especially Lines 116–121) are quite long and conceptually dense. Splitting them into shorter, direct statements would enhance readability.
4. The final paragraph (Lines 125–132) effectively summarizes the four research aims. It might be stylistically improved by using concise bullets or semicolons instead of a long compound sentence to enhance readability.
5. Although the section mentions seven plants per plot and three replications per measurement, it remains slightly unclear whether the trials followed a randomized complete block design (RCBD) or completely randomized design (CRD) across locations. Suggestion;;;;;;; A randomized complete block design (RCBD) with three replications was used at each location.” This will help readers understand how environmental and genotypic effects were statistically partitioned (Materials section) (Lines 134–151).
6. Could the authors clarify whether any genotype-by-trait correlations (e.g., between firmness and antioxidant capacity) were examined to explore trait co-selection potential?
7. (Lines 595–812): The discussion reads as a series of well-written but somewhat independent parts. Consider inserting short transition sentences at the start or end of each subsection to improve flow and emphasize how each result supports the study’s central conclusion.
8. Some subsections (Lines 766–796) include several quantitative details. Condensing them and focusing on the most critical comparisons would enhance readability.
9. (Lines 635–652, 813–826): Strengthen the link between research outcomes and their use in breeding programs — e.g., how the identified stable or high-GBV accessions can be integrated into selection pipelines or hybrid development.
10. (Lines 683–699 and 694–711): The discussion repeats environmental effects on phenolics and carotenoids. Consolidate these paragraphs to avoid redundancy and maintain focus.
11. There are many grammatical and language mistakes that should be improved.
12. Please avoid symbols at the beginning of the sentences.
13. Please arrange all the references according to the Journal format.

Author Response

Please see the attachment

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

The author has made the required revisions. After checking the formatting, we can consider accepting the manuscript.