Identification of QTL for Plant Architecture and Flowering Performance Traits in a Multi-Environment Evaluation of a Petunia axillaris × P. exserta Recombinant Inbred Line Population

Round 1

Reviewer 1 Report

The article is devoted to the construction of a genetic linkage map for the population of the recombinant inbred line (RIL) Petunia axillaris × P. exserta F7 (AE) based on the identification of quantitative trait loci (QTL) for a number of important traits associated with production, including plant height at flowering, number of flower buds, time to bloom, flower size and lateral branching. The construction of such a map and the identification of markers of certain traits, according to the authors, can help reduce the resistance to linkage of loci associated with some undesirable traits along with useful ones.
The goals of the current study were to understand the relationship of traits for the AE RIL petunia population under a variety of growing conditions and to determine the QTL for the main phenotypic plant traits. The results of this work may facilitate marker-assisted breeding strategies and help identify the genes that underlie the control of these traits.
The authors achieved their goals by identifying QTLs useful for breeding improved petunia field productivity and determining the location on the chromosomes of candidate genes that underlie important traits.
The work is written in a clear language, it uses the most modern methods of molecular biology used in obtaining new genotypes of ornamental and agricultural plants. Its results can be used by many researchers working in the same branch of science.
All tables and graphs are well designed and serve as an accurate evidence base for the studies conducted by the authors of the article.
I have no comments on the text, design and used literature.
The article may be published in the journal without revision.

Author Response

We thank the reviewer for their comments.

Reviewer 2 Report

This paper investigates the genetic architecture of several performance related traits of advanced generation interspecific Petunia hybrids of interest to the horticultural breeding industry. The study investigates these traits under field conditions at four locations to ensure that any quantitative trait loci are robust.

This study develops earlier studies of this mapping family but the authors explain how the traits examined here are distinct. There is interest in confirming glasshouse expressed traits in the field as these are ultimately the horticultural breeding targets. Clear aims are posed at the end of the introduction. The methods are concise but complete, referencing related earlier studies as necessary. Several of the traits are based on qualitative scales that could be interpreted differently by different researchers at different sites. There should probably be some acknowledgement of this limitation in the discussion. Were any steps taken to limit scoring variation? (e.g. a clear list of criteria for each score, a photo guide, etc.) The data analysis section should include mention of tests of trait correlations. The discussion does well to interpret findings in a horticultural context and considers findings from previous studies to help evaluate the robustness of the identified QTLs. Overall, the paper is well written and the results seem robust and of value to the petunia breeding community.

 

Specific comments

L95-99 It would be interesting to know how similar are the climates of these field sites to the climate of origin of the founding parents.

L154 Briefly explain transgressive segregation here. Were mapping populations transgressive in each parental direction? Perhaps this could be shown by marking the parent mean values in the supplementary figures.

L177-178 Give the flow effect size units here.

L182-183 Mention the parental allele and effect size of the vigor rQTL.

Table 2 What is being compared by the t-test? Mention in the methods and results also. 

L204-208 These results for Height seem contradictory. 

L211-213 Give units of MaxWid effect size. 

L219-221 You could state numbers of beneficial alleles contributed by each parent here.

L244-246 Develop why transgressive segregation indicates polygenic inheritance. 

L275 Name the parent here.

Author Response

We appreciate the reviewer's comments and provide a line-by-line response below.

 

Were any steps taken to limit scoring variation? (e.g. a clear list of criteria for each score, a photo guide, etc.)

Response: We have revised the methods (lines 118-120) to clarify that the same individuals traveled to each trial site for data collection to minimize variation.

Specific comments

L95-99 It would be interesting to know how similar are the climates of these field sites to the climate of origin of the founding parents.

Response: We have added this information (lines 100-101).

 

L154 Briefly explain transgressive segregation here. Were mapping populations transgressive in each parental direction? Perhaps this could be shown by marking the parent mean values in the supplementary figures.

Response: We have added arrows indicating parental values to the supplemental figure. Additionally, we have expanded the text to state: “The P. axillaris × P. exserta RIL population exhibited a wide range of variation at all locations, with all traits displaying transgressive segregation in both directions at each location with the exception of Comp at NC, where P. axillaris was equal to the population minimum value (Table 2; Supplemental Fig. S1 – S4).”

 

L177-178 Give the flow effect size units here.

Response: Revised as requested.

 

L182-183 Mention the parental allele and effect size of the vigor rQTL.

Response: Revised as requested.

 

Table 2 What is being compared by the t-test? Mention in the methods and results also. 

Response: We have added information to the methods (lines 125-6). The results of these comparisons are described in the results lines 156-160.

 

L204-208 These results for Height seem contradictory. 

Response: Petunia exserta has a very strong upright growth habit, while P. axillaris is more freely branching. Thus, we do not believe it is contradictory for P. exserta to provide positive additivity for height and for P. axillaris to provide additivity for width.

 

L211-213 Give units of MaxWid effect size

Response: We have revised as requested.

 

L219-221 You could state numbers of beneficial alleles contributed by each parent here.

Response: Revised as requested.

 

L244-246 Develop why transgressive segregation indicates polygenic inheritance. 

Response: This sentence was edited incorrectly. We did not intend to suggest that transgressive segregation inherently implies polygenic inheritance. We have revised the sentence to read: “The P. axillaris × P. exserta RIL population exhibited transgressive segregation for all traits at most locations (Table 2; Supplemental Fig. S1-S4). Additionally, population distributions were generally normal, suggesting that multiple genes are involved in the control of these traits.”

 

L275 Name the parent here.

Response: We have revised to include information on which parent provided positive additivity at each of these two loci.

Reviewer 3 Report

This manuscript provides basic knowledge that can contribute to the breeding of petunia cultivars. However, there are some issues that should be addressed as described below.

1. In the breeding of petunia, it is desirable to specifically describe in the introduction what kind of traits new cultivars are desired to develop.

2. In the discussion section, it is preferable to describe the future prospects, such as what kind of cultivars can be bred by this research.

3. The word, petunia is written in scientific name (line 138, 277) or common name (line 239, 243, 252, 287, 296). It would be better to unify to common name.

4. The scientific name of Petunia (line 47, 55, 155, 179, 184, 290) is appropriate to abbreviate to “P.”.

5. The sentence, “vigorous plants did not promote vegetative growth at the expense of flowering performance” (line 262) needs rewriting.

Overall, this manuscript has provided useful basic knowledge for the breeding of petunia cultivars. I think that this manuscript is suitable for publication in horticulturae if the above issues are adequately addressed.

Author Response

We appreciate the reviewer's comments and provide a line-by-line response below.

 

This manuscript provides basic knowledge that can contribute to the breeding of petunia cultivars. However, there are some issues that should be addressed as described below.

1. In the breeding of petunia, it is desirable to specifically describe in the introduction what kind of traits new cultivars are desired to develop.

Response: We have added a sentence to the first paragraph describing some critical traits for new cultivars.

 

2. In the discussion section, it is preferable to describe the future prospects, such as what kind of cultivars can be bred by this research.

Response: We have edited a concluding paragraph to address this comment.

 

3. The word, petunia is written in scientific name (line 138, 277) or common name (line 239, 243, 252, 287, 296). It would be better to unify to common name.

Response: We have revised lines 138 and 277 to use the common name.

 

4. The scientific name of Petunia(line 47, 55, 155, 179, 184, 290) is appropriate to abbreviate to “P.”.

Response: We have revised lines 47, 55, and 290 to the abbreviation “P.”. However, we have left lines 155, 179, and 184 as originally written as sentences should generally not begin with an abbreviation.

 

5. The sentence, “vigorous plants did not promote vegetative growth at the expense of flowering performance” (line 262) needs rewriting.

Response: We have revised this sentence to:”… robust vegetative growth did not reduce flowering performance.