Characterization of Flowering Time in Genebank Accessions of Grain Amaranths and Their Wild Relatives Reveals Signatures of Domestication and Local Adaptation

Round 1

Reviewer 1 Report

Introduction:

• Justification is good but it is too long. It would be good if you can decrease.

Materials and Methods:

• Line 161: Why did you perform a field trial in a single location? It would be good if you have more than one location. Explain.
• Line 185: “Flowering time was recorded as number of days from sowing until pollen shedding” First day or 50% of population in each plot? Specify.

Results:

• Figure 3 is not clear. Please make this figure clearer.

Discussion

• Line 420 “Relationship between phenotypic traits and environmental variables” Add scientific paper to support your statement?
• Based on your results and materials, which accessions or species should be used as parental lines for breeding application? and why?

Author Response

Comment:

“Introduction:

Justification is good but it is too long. It would be good if you can decrease. “

Response: Thank you for your comment. We might have given more information than that is needed for justification purpose. As amaranth is a minor crop and most of the relevant information about it is unknown by the majority of the readers, we find it important to provide the readers with strong background information.

Comment: “Line 161: Why did you perform a field trial in a single location? It would be good if you have more than one location. Explain.”

Response: Thank you for pointing this out. The use of a higher number of locations would have been better to catch the environmental variation. However, the limited number of seeds did not allow us to use more replications and this is common in the early stage breeding programs, which we mentioned in line 167 with a citation.

Comment: “Line 185: “Flowering time was recorded as the number of days from sowing until pollen shedding” First day or 50% of population in each plot? Specify.”

Response: We agree with you and changed the statement.

“Flowering time was recorded as number of days from sowing until pollen shedding, and seed setting was recorded as binary trait at harvest time. Plant height and seed setting were recorded based on three randomly selected plants, whereas flowering time was recorded plot-wise when 50% of the plants in a plot flowered.”

Comment: “Figure 3 is not clear. Please make this figure clearer.”

Response: We agree with this comment and changed it. Now its size is bigger and the resolution is higher.

Comment: “Line 420 “Relationship between phenotypic traits and environmental variables” Add scientific paper to support your statement?”

Response: Thank you for pointing this out. In this section, we actually discussed the factors that might have affected our correlation analyses driven by the specific nature of our data i.e, validity and reliability of our results. On the other hand, we discussed the contributions of our results to the study objectives under the different sections of interest and supported our hypotheses with additional references. For example, the relationship between temperature (as a function of elevation) and flowering time was discussed under the “Selection of early flowering local adaptation” section (lines 484-496).

Comment: “Based on your results and materials, which accessions or species should be used as parental lines for breeding application? and why?”

Response: Thank you for your question. We answered this question under the “Future prospects” section in detail (Lines 553-561). We recommended specific species for different breeding objectives but not genotypes. The reason is we tested the genotypes with an unreplicated experimental setup and this is not sufficient to make a conclusion about individual genotypes. However, the species and latitudinal groups were represented with many genotypes and therefore can be generalized.

Reviewer 2 Report

The authors assessed flowering time in genebank accessions of
grain amaranths and their wild relatives, and further revealed signatures of
domestication and local adaptation. In general, this is a high-quality manuscript that warrants publication on Agronomy. It has made my day after reviewing this paper.

Here are some minor comments:

1) Figure 2 should indicate A-H in the figure legend.

2) I would like to suggest the authors to add a new Figure 1 with photos from different grain amaranth species.

3) Are there any flowering-related genes that associated with domestication and adaptation in this species clade? If possible, I would like to suggest to discuss some flowering time-related genes in the Discussion section.

Author Response

Comment: “Figure 2 should indicate A-H in the figure legend.”

Response: Thank you for your pointing this out. We changed the figure legend as follows (line 291-292);

Figure 2. Box and bar plots of four phenotypic traits grouped by species and latitudinal groups (A-H), in each box and bar plot the respective groups were compared using a least significant difference (LSD) test and the groups with the different letters are significantly different at alpha=0.05. No letters if there is no significant difference among the compared groups. Black asterisk indicate the mean values of each group in the box plots. Species are cau, A. caudatus; cru, A. cruentus; hdus, A. hybridus; hyb, the ‘hybrid’ group; hypo, A. hypochondriacus and quit, A. quitensis.

Comment: “I would like to suggest the authors to add a new Figure 1 with photos from different grain amaranth species.”

Response: Thank you for your comment. We especially preferred not to do that because high morphological variation and phenotypic plasticity existing in this genus can be likely misleading in the visual separation of the species.

Comment: “Are there any flowering-related genes that associated with domestication and adaptation in this species clade? If possible, I would like to suggest to discuss some flowering time-related genes in the Discussion section.”

Response: This is an important question that needs to be answered. However, there is not such a study in the current literature, according to our knowledge.