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All comments of the reviewers were taken into account in the new version of the manuscript. I believe the manuscript is ready for publication.
[# PeerJ Staff Note - this decision was reviewed and approved by Jasmine Janes, a PeerJ Section Editor covering this Section #]
The citations for Pritchard and Evanno (under STRUCTURE analyses appear to be flipped. Pritchard should be the citation for the software; Evanno should be the citation for the evaluation of the optimal K. Also, PCoA is principal coordinates analysis, not principal component analysis - there is a bit of a difference. The PCoA is referred to correctly in the Methods but not in the Results. Regarding the use of STRUCTURE HARVESTER, Earl wrote the paper describing the use of this software. It implements the Evanno method (delta K) for determining the optimal K but Evanno did not make the software. As an aside, Evanno method consistently underestimates K-clusters; many papers have validated this pattern.
Authors should take into account all the numerous comments of reviewers when preparing the manuscript.
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The English language should be improved to facilitate the understanding of the text.
a. There is an excess of phrases in passive form or with a word ordering that results difficult to understand. Two examples could be found on lines 311-312 and 447-450.
b. I also think that the text could be lightened by avoiding the continuous repetitive use of both the symbol (A, B…) and the name of the population. For example, on lines 328-346, at least the second time populations are named it could be just by their symbol.
c. Some sentences need to be connected with their preceding ones. For example, sentence beginning at line 82.
Figures are all relevant and in general of high quality. Nevertheless, they could be improved in the following ways:
a. Figure 1. The red lettering of the two wild populations don’t stand out enough
b. Figure 3. Why are four accessions from the R population specifically indicated?
c. Figure 6. Bar labels are hard to read. Perhaps the figure could be divided into groups of 48 accessions (instead of 50), thereby increasing the size of the letters and also leaving entire populations in the same row.
I thank the authors for providing the raw data as images of the electrophoretic gels. However, I would also appreciate if they could indicate with a key which band corresponds to each one of those mentioned in Table_S3.
no comment
My main concern in this work is that the comparison of cultivated (T. fournieri) and wild populations (T. concolor) is between different species. Is it to be understood that the authors may have had problems obtaining samples from wild populations of T. fournieri due to their natural range? Otherwise this procedure would not be justified. In case of not being able to obtain the T. fournieri wild samples, I believe that the text should make two aspects clear: 1) justify why the comparison of cultivated and wild populations of these two species can be informative and 2) in the discussion indicate that when analyzing the results, it should be noted that two different species are being compared.
The manuscript by Guan, Song et al. “Genetic variation and population structure of wild and cultivated wishbone flower (Torenia fournieri Lind.) populations” analyses the genotype of 136 accession from 17 populations of Torenia using the retrotransposon based iPBS marker system. The 148 loci studied revealed that there is a clear genetic differentiation between populations whereas only one of the two wild populations showed high variability between individuals of the same population. The lowest variability within the commercial series should be due to breeding selection, and differences in variability between the two wild populations could be explained by differences in sampling method.
I think studies like this one that compare genetic variation between cultivated and wild populations are very interesting. They provide insight into the effect on genetic variation in a population experiencing a bottleneck in which strong phenotypic selection overlaps.
1. Nevertheless, as I said before, my main concern in this work is that the comparison of cultivated (T. fournieri) and wild populations (T. concolor) is between different species.
2. Another concern I have is the behavior of the wild population Q. On the one hand, although it is a wild population, it presents a very low variability that the manuscript indicates could be due to the sampling method. On the other hand, in the PCoA analysis, the Q population is located closer to the cultivated populations of the other species than to the other wild population of its own species and, in the tree in Figure 4, Q and R do not form a monophyletic group. Therefore, I wonder how it was determined to which species each individual belonged. Couldn't it be that the individuals in population Q belonged to T. fournieri?
3. L262-263. I don’t think that having a total of 148 scorable bands, necessarily indicates a high degree of genetic variability. I understand a scorable band as one that might be detected and that in some individuals is present and in others not. Nevertheless, with only this information, we cannot advance if there is variability within each population and or among populations. Maybe it should be better substitute “which indicated a…” to “and they revealed a…”
4. L 307 The variation between populations is including the variation between species because two of the 17 populations are T. concolor. AMOVA should also be performed only for the 15 populations of commercial T fornieri.
5. L442-446 I agree that the specific bands are highly interesting, but, in the results, there is no any information about them. Perhaps the authors are working on a new paper, but some information could be advanced on how many specific bands each population has, and which iPBS are responsible for them.
6. L. 365 Table 5. As the information in this table 5 can be easily extracted from figure 5 (therefore redundant), I think this table could be moved to the supplementary material.
Minor comments and typos:
L. 82-83. This phrase needs some connector with the preceding phrases. Maybe “Nevertheless” or “However”.
L.84. The first sentence “in relation to interspecific hybrids” sounds strange when obtaining tetraploid plants of T. fournier is explained bellow. These individuals are not interspecific hybrids.
Maybe it could be changed by something like “In relation to new (or artificial) variants”
L. 120 Use italics for the name of the locus "plena"
L.126. Check the spelling of the plant hormone. It should be “forchlorfenuron”
L. 139 Change “SSR” to “microsatellite” or “simple sequence repeat”. This name is not used more in the text and is not necessary the use of abbreviations that difficult the understanding.
L. 162. Eliminate “Lindl.” It has been already referred before in L 59.
L. 202 Change “examined manually” to “visually examined”
L. 205 The meaning of PIC should be explained.
L 222 – L 232. The whole paragraph is very confusing
• Line 222 change “accordingly” to “respectively”
• L 224-225 I don’t understand how there could be any gap or missing data. From Table 1, I know each individual should have data for 148 loci.
• It’s not clear to me which kind of tree the authors obtained: parsimony, UPGMA, MCL?
• L.232 Last sentence seems the explanation of part of a figure.
L. 266 Table 1 only presents data for the commercial series. It should also show the same data for the wild populations
L. 267 Change “and primer 2377” to “while primer 2377”.
L. 277-281. The list of the populations should be moved to the material and methods section. This change will allow understand better in the material and methods section why the wild populations received their names of Q and R.
Line 293 “PhiPT matric values” eliminate “matric”
Line 294 Change “population PhiPT” to “population PhiPT values”
L 295 Rewrite this sentence. The values don’t vary “from x and y” The reader expects “from x to y” and only two values.
L. 312 Change “coordinate” to “component”
L328-346. (and also, through the whole text in general). The correspondence between letters and population origin could be used to lighten the text, eliminating the full name of the population.
L. 447-450. Change the order in the sentence, and use italics for the variable symbols, as:
“From among the 17 Torenia populations tested, the lowest values of <i>Na</i> (number of different alleles), <i>Ne</i> (the number of effective alleles), <i>I</i> (Shannon’s information index), <i>He</i> (expected heterozygosity), and <i>uHe</i> (unbiased expected heterozygosity) were for population J (Kauai: White) and the highest for population R (wild: Xichou).”
L. 454-455. Use the statistic symbols instead of their full names. They have been described just two sentences before.
L.456 Please, clarify that the differences in the results correspond to the comparison with other genera. I was surprised to find no further discussion on this fact, and only realized why after checking all the references made at this point. Thus, I propose to change “are considerably less than that reported previously by” to “are considerably less than that reported previously in other genera of plants by”
The authors analyzed 136 accessions which were selected from 17 populations of two Torenia species with iPBS markers. These cultivated accessions were obtained from markets and the wilds from two different subtropical habitats in southern China.
The experiments were performed well and the results seem good. The authors tried to address every molecular aspect of the accessions based on iPBS markers.
The manuscript is well-written, but some minor corrections are needed in the text. See the attached PDF file.
The authors' literature review about Torenia is quite detailed. This literature is presented in the introduction section.
All references are correctly presented in the reference list.
All raw data about gel pictures and band scoring with iPBS studies were presented as supplementary files.
The results of the study were relevant to the authors' aim.
This study is the first to investigate the genetic structure of Torenia accession with iPBS markers. The accessions used in the study were obtained from two Torenia species.
Examination of genetic diversity intra- and interspecies with the data obtained from iPBS analysis in the study will make the results of the study more meaningful.
All analyzes were matched to evaluate a dominant DNA marker system.
The temperatures of the iPBS primers have been chosen quite differently from the original described publication, Kalendar et al. (2010).
iPBS primers with relatively short sequences with lowered annealing temperatures would result in a considerably increased probability of random linking outside of the specific region for which they were designed. This raises the suspicion that it is likely to cause the primers to act as if they were RAPD primers.
Please give the axis values in the figure related to the principal coordinate analysis.
The findings are listed quite clearly. Statistical analyzes were selected in accordance with the analysis.
When I examined the iPBS band profiles presented as supplementary agarose gel photos stated to belong to accessions 1-48, I could not say to see the grouping in the dendrogram, the principal coordinate analysis, and Bar plots. However, I know well that there are differences between eyes in gel scoring.
I can say that I enjoyed reviewing the article titled "Genetic variation and population structure of wild and cultivated wishbone flower (Torenia fournieri Lind.) Populations".
In this study, the authors use the iPBS transposon-based marker system to capture genetic diversity among 15 cultivated lines of Torrenia fournieri and two wild-collected populations of T. concolor. The motivating questions for collecting these data are not developed in the background or introduction sections of the manuscript and multiple conclusions drawn in the discussion are not well supported by the results.
In terms of basic reporting, I think the manuscript falls short in these three specific areas:
Self-contained with relevant results to hypotheses.
Research question well defined, relevant & meaningful. It is stated how research fills an identified knowledge gap.
Conclusions are well stated, linked to original research question & limited to supporting results.
Here are more specific points:
1. The authors need to provide clear framework (in abstract/background section) for why population structure/diversity is an important question among cultivated accessions of this group. This is not presented in the background section and in the lengthy introduction, only historical information about Torrenia is presented, but not clear set of questions that can be addressed by the data being collected. Here are some possible questions:
Do cultivated lines show a pattern of genetic similarity that correlates with flower color or other phenotypic characteristics? Do cultivated lines show a pattern of genetic similarity that informs on future breeding strategies? Is genetic diversity within cultivated lines similar to that found in natural populations from a closely related species? These are just some thoughts on how to unite the data with specific questions.
2. The authors should explain why the wild population are from a different species. How distantly related is T. concolor to T. fournieri? What is gained by including a separate species? Why were no wild populations of T. fournieri included which might have allowed the authors to address the specific origins of cultivated lines?
3. Starting at line 146: our objectives were to investigate the genetic pattern, population structure and genetic relationships among 136 Torenia accessions including 15 T. fournieri populations from 3 commercial series (Duchess, Kauai, Little Kiss) and two wild T. concolor populations sampled by different methods from two distant sites. Our overall aim was to estimate the selective pressure and provide a practical model for the genetic analysis of Torenia populations so as to better enable selective breeding in the future.
The data collected are not sufficient or appropriate for estimating selective pressures imposed during cultivation.
4. Starting at line 389: indicate that some morphological traits such as the population floral colors could be used as an associated genotypic identification, thereby potentially guiding breeding practices that target such traits.
Perhaps this is a guiding question of the study as well?
5. Starting at line 398: Specifically, the Phi-statistics analysis we used showed the correlation of some genes or loci within the subdivided populations. In particular, the genetic pattern and structure of the wild population Q (selected from one site) was similar to the 15 commercial populations, but was significantly different from the other wild population R (selected from multi sites in the region). This indicates the selective pressure during the breeding practices leading to these 15 commercial populations.
These data do not inform on selective pressures during cultivation. Most likely, these differences in genetic diversity result from bottleneck/drift effects with bringing a small number of individuals into cultivation. The loci sampled are not loci on which selection acted during cultivation, at least there is no data to suggest that they are cultivation loci.
6. Starting at line 160: 200 seedlings for each cultivar were germinated first, and eight plants were randomly selected to represent individual populations of the cultivar.
This is an issue throughout. Selecting 8 plants from a seed package is not standard population level sampling. I think the authors should not call these “populations” but instead call them “cultivated lines”.
7. Starting at line 409: In our study, correlations among populations via our PCoA analysis showed interesting patterns. For instance, there were more negative correlations among the populations that included Q (wild: Lipu Blue), R (wild: Xichou Blue), I (Kauai: Lemon Drop), K (Little Kiss: White), M (Little Kiss: Blue and White), N (Little Kiss: Rose Picotee), and P (Little Kiss: Blue).
PCA provides clustering information, not correlation. This discussion section needs to be re-worked. I think what the authors mean is that much of the variance in genotype among lines is due to differences between certain sets of lines (the lines that are most distant from one another on PCA 1. But they need to write their discussion using the proper terminology of PCA.
8. Starting at line 412: Since blue is the common wild type of floral color for T. fournieri and T. conclor, such negative correlations could be due to a high content of the wild genetic background within these populations.
Again, PCA is not a correlation analysis. Also, if each cultivated line has similar reduction in diversity/heterozygosity from a bottleneck event, each will retain a similar (but different from each other) content of the wild genetic diversity.
9. Starting at line 419: In relation to their specific floral color, it could be concluded that these populations have a more positive effect on determining the relevant genetic constituents. Consequently, these results from our population genetic analyses could be used to target the future selection of desired traits in Torenia breeding.
This statement requires more explanation.
10. Starting from line 428: Results from our study indicated that the wild population Q (Lipu: Blue) is more closely related to populations M (Little Kiss: Blue and White), N (Little Kiss: Rose Picotee), and P (Little Kiss: Blue) and they are likely therefore to have had a common ancestor.
Not true, according to your dendrogram, all cultivated varieties are equally related to Q. Perhaps you are referring to overall genetic similarity from the PCA analysis? Overall similarity is different from common ancestry.
11. Starting at line 458: Our lower values indicate significant inbreeding in the 15 Torenia series that have been released, and in the wild population Q (wild: Lipu Blue). This suggests either some kind of selective pressure or the effect of selection during breeding practices.
Your data as presented do not inform on inbreeding coefficients or selective pressures. Low genetic diversity/heterozygosity most likely points to bottleneck/drift effects.
12. Please define PIC – polymorphic informative content
As described above, the target of "Research question well defined, relevant & meaningful. It is stated how research fills an identified knowledge gap." has not been met.
As described above, the target of "Conclusions are well stated, linked to original research question & limited to supporting results." has not been met.
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