Apple Fruit Size QTLs on Chromosomes 8 and 16 Characterized in ‘Honeycrisp’-Derived Germplasm
Round 1
Reviewer 1 Report
In this paper, the authors report A pedigree-based QTL analysis approach to examine the genetic basis of fruit weight in 'Honeycrisp' derived germplasm. Historical fruit weight data and genome-wide single nucleotide polymorphism (SNP) data were exploited to map QTLs on chromosomes (Chrs) 8 and 16. The research work presented by the authors, remains original. The research topic is very significant for the field. The topic is interesting, and the methodology is appropriate for this category of research. The manuscript is written in a very clear and interesting way. It is well organized and structured. The results are clearly presented. References are cited as per the authors' instructions. Overall, I recommend publishing the manuscript after minor corrections. The title of the article could be modified to conform to the results obtained. It is also suggested that the authors provide a conclusion, which briefly summarizes the results obtained.
Author Response
1. In this paper, the authors report A pedigree-based QTL analysis approach to examine the genetic basis of fruit weight in 'Honeycrisp' derived germplasm. Historical fruit weight data and genome-wide single nucleotide polymorphism (SNP) data were exploited to map QTLs on chromosomes (Chrs) 8 and 16. The research work presented by the authors, remains original. The research topic is very significant for the field. The topic is interesting, and the methodology is appropriate for this category of research. The manuscript is written in a very clear and interesting way. It is well organized and structured. The results are clearly presented. References are cited as per the authors' instructions. Overall, I recommend publishing the manuscript after minor corrections.
Response. Thank you for taking the time to thoroughly review this manuscript. Your comments are greatly appreciated.
2. The title of the article could be modified to conform to the results obtained.
Response. We believe that the current title clearly communicates the main results of this manuscript. The chromosome (Chr) 8 and Chr 16 QTLs detected in a pedigree-connected germplasm set primarily derived from ‘Honeycrisp’ were the focus of this manuscript.
3. It is also suggested that the authors provide a conclusion, which briefly summarizes the results obtained.
Response. Thank you for the suggestion. We have added a conclusion paragraph that briefly summarizes the results and implications.
Updated text (lines 467-478)
“Results of this study supported the conclusion that fruit size is a quantitative trait controlled by multiple QTLs throughout the genome. In this study, two large-effect fruit weight QTLs on Chrs 8 and 16 were characterized in breeding derived from ‘Honeycrisp’, an important apple cultivar and breeding parent. Additionally, putative QTLs were detected on Chrs 2, 4, 6, 10, and 14. Results of this study further demonstrated the importance of considering the proximal end of Chr 16 when targeting fruit quality in apple as the fruit weight QTL colocalized with multiple Chr 16 trait loci. QTLs characterized in this study will enable more informed parent selection, development of trait-predictive DNA tests for use in apple breeding programs and/or development of genomewide prediction models that include large-effect QTLs as fixed effects. Future studies should aim to validate QTL allele effects and/or other putative QTLs in different germplasm sets and environments.”
Reviewer 2 Report
The manuscript "Apple fruit size QTLs on chromosomes 8 and 16 characterized in 'Honeycrisp-derived germplasm" was carefully read and analyzed. The work brings important and useful genetic information for targeting the use of fruit weight in apple breeding programs.
The manuscript is well written, reasoned, presents relevant results that were adequately discussed. In addition to presenting originality.
Author Response
The manuscript "Apple fruit size QTLs on chromosomes 8 and 16 characterized in 'Honeycrisp-derived germplasm" was carefully read and analyzed. The work brings important and useful genetic information for targeting the use of fruit weight in apple breeding programs. The manuscript is well written, reasoned, presents relevant results that were adequately discussed. In addition to presenting originality.
Response: Thank you for taking the time to thoroughly review this manuscript.
Reviewer 3 Report
The manuscript from Kostick and Luby is very well written, the language is clear, and the results are very organized and presented in a consistent fashion. I find the article suitable for publication after only minor editing:
- Further information on previous studies on fruit size x QTLs from other plant species would be appreciated.
- You state that “QTLs associated with fruit size traits have been mapped to almost every chromosome in the apple genome [8-13]. Fruit size QTL studies in apple have been limited to a few biparental families representing cultivars ….”. Which were the main conclusions?
- Please double-check the writing in lines 28-29, 54, and 65.
- Consider changing the colors of Figures 1 and 2 to improve their readability when printed in grayscale.
- The Discussion feels somewhat partitioned with so many subheadings, some of them consisting of a single paragraph. Consider merging some of the sub-headings to turn the Discussion more engaging.
- I find that the conclusion is too brief; the authors should address if their original hypothesis presented in the Introduction was corroborated or not and explore a little further the agronomical implications and applications of the results.
Author Response
1. The manuscript from Kostick and Luby is very well written, the language is clear, and the results are very organized and presented in a consistent fashion. I find the article suitable for publication after only minor editing.
Response. We are grateful to you for taking the time to thoroughly review this manuscript.
2. Further information on previous studies on fruit size x QTLs from other plant species would be appreciated.
Response. We have added a statement regarding mapping of fruit size QTLs in other crops. Updated text (lines 42-44)
Updated text: “Fruit size traits have been investigated in QTL mapping studies in various crops such as peach (Prunus persica L. Batsch) [13], sweet cherry (Prunus avium L.) [14, 15], and tomato (Solanum lycopersicum L.) [16, 17].”
3. You state that “QTLs associated with fruit size traits have been mapped to almost every chromosome in the apple genome [8-13]. Fruit size QTL studies in apple have been limited to a few biparental families representing cultivars ….”. Which were the main conclusions?
Response. In these sentences we were trying to convey that multiple fruit size QTLs have previously been detected throughout the apple genome. The importance or location have been dependent on the germplasm studied. These studies have mostly been limited to QTL detection and have not characterized these QTLs for their allele effects. In addition, the germplasm that has been examined has been relatively limited. We have updated the text to provide an example of the type of results these studies have reported.
Updated text (lines 44-47)
Original text: “QTLs associated with fruit size traits have been mapped to almost every chromosome in the apple genome [8-13]. Fruit size QTL studies in apple have been limited to a few biparental families representing cultivars such as Braeburn, Co-op 17, Co-op 16, Discovery, Fiesta, Golden Delicious, Granny Smith, Jonathan, Prima, Royal Gala, Starkrimson, and Telamon [8-13].”
Updated text: “In apple, multiple QTLs associated with fruit size traits have been mapped to almost every chromosome (Chr) in the genome [8-12, 18]. For example, Liebhard et al. [18], detected several fruit weight QTLs on Chrs 1, 3, 6, 8, 10, 12, 16, and 16 in a biparental family (n = 251 offspring) derived from ‘Fiesta’ × ‘Discovery’. Fruit size QTL studies in apple have been limited to a few biparental families representing cultivars such as Braeburn, Co-op 17, Co-op 16, Discovery, Fiesta, Golden Delicious, Granny Smith, Jonathan, Prima, Royal Gala, Starkrimson, and Telamon [8-12, 18].”
4. Please double-check the writing in lines 28-29, 54, and 65.
Response. We checked the writing as suggested and did not find any errors.
5. Consider changing the colors of Figures 1 and 2 to improve their readability when printed in grayscale.
Response. Thank you for the suggestion. The color scheme was carefully chosen to ensure that it was accessible to color blind readers. Due to the multiple groups in Figure 2, use of a grayscale would make differentiation among groups challenging.
6. The Discussion feels somewhat partitioned with so many subheadings, some of them consisting of a single paragraph. Consider merging some of the sub-headings to turn the Discussion more engaging.
Response. Thank you for the suggestion. We considered this suggestion but believe the sub-headings enable the reader to understand the main findings and observations of this study more clearly.
7. I find that the conclusion is too brief; the authors should address if their original hypothesis presented in the Introduction was corroborated or not and explore a little further the agronomical implications and applications of the results.
Response. Thank you for the suggestion. We have added a conclusion paragraph that addresses if our original hypothesis was supported by our results and briefly discusses the implications of this work.
Updated text (lines 467-478)
“Results of this study supported the conclusion that fruit size is a quantitative trait controlled by multiple QTLs throughout the genome. In this study, two large-effect fruit weight QTLs on Chrs 8 and 16 were characterized in germplasm derived from ‘Honeycrisp’, an important apple cultivar and breeding parent. Additionally, putative QTLs were detected on Chrs 2, 4, 6, 10, and 14. Results of this study further demonstrated the importance of considering the proximal end of Chr 16 when targeting fruit quality in apple as the fruit weight QTL colocalized with multiple Chr 16 trait loci. QTLs characterized in this study will enable more informed parent selection, development of trait-predictive DNA tests for use in apple breeding programs and/or development of genomewide prediction models that include large-effect QTLs as fixed effects. Future studies should aim to validate QTL allele effects and/or other putative QTLs in different germplasm sets and environments.”
