The Genetic Architecture of the Root System during Seedling Emergence in Populus euphratica under Salt Stress and Control Environments

Round 1

Reviewer 1 Report

I congratulate the authors for their excellent work and suggest some small corrections:

Article

The Genetic Architecture of the Root System During Seedling Emergence in Populus Euphratica under Salt Stress and Control Environments

General comments

The approach used in the study to evaluate genetic architecture in Populus euphratica root system under salt conditions is solid and well-documented. Results and discussion are clear and well documented. Graphs and tables are comprehensive. Item needs minor specification and revision.

Suggestions for Authors

-You wrote : “We used the published experimental data of Populus euphratica as a mapping population for our study” but give more information on the P. euphratica.

-In materials and methods which rooting medium did you use? Did you use rooted microshoots (plantlets) to develop experiments?

-Some considerations resulted from previous research by other Chinese authors not reported in this work (see references below as a suggestion).

Ye Z-Q, Wang J-M, Wang W-J, Zhang T-H, Li J-W. 2019. Effects of root phenotypic changes on the deep rooting of Populus euphratica seedlings under drought stresses. PeerJ 7:e6513 DOI 10.7717/peerj.6513

-Put the doi number in all references.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

The authors have modeled the effect of salinity, an environmental factor important for plant growth, on a full-sib population of P. euphratica using an environmental differential interaction equation (EDIE). Then, systems mapping is used to map the EDIE to multiple quantitative trait loci (QTL). The results of this modeling approach are then discussed. The authors discuss a few notable findings in the QTL mapping.

While the study is interesting, there are several issues that need to be addressed in order to publish this material, including proper citation of prior work. It is also not clear why the choice of the full

My detailed comments are as follows:

Text of manuscript:

L78-83: In figure labels are needed to explain what is being illustrated.

L93-99: 0.1 % sodium chloride seems low. Furthermore, it is difficult to put in context as the composition of the root medium is not provided.

L105-109: Reference genome should be provided to enable extraction of sequence.

L118: Number of parameters (10?) should be mentioned

L125-126 and Eq. 3: Definition of alpha and beta are not clear

L189: In Figure 2 a and b, please explain negative measurements after accounting for kernel density estimate. Were there lots of zero values? Can statistics be computed on non-zero values and zero values separately? Was number of zeros statistically different between control and salt treated samples?

L219-224: Fig 2 c-f do not clearly explain what is being modeled. What is average growth? Why not fit across the entire set of observations?

L263: FDR control method needs to be mentioned

L386-407: This paragraph is vague and disconnected from the rest of the paper. Recommend elimination or replacement with a much more specific discussion of caveats.

Supplementary material:

1. In Figure S1a, consider making TRL the ordinate

2. In Table S1: suggest not showing alignment hits with E-values > 0.001. Alignment methods need to be provided in the methods section

References:

L34: Ref 8 seems inappropriate

L37-38: Ref 10 and 11 do not support the assertions

L40: Ref 13 does not support the assertion

L41: Ref 14 cites Lovelli (2012). Suggest citing the latter, original work

L113-116: Ref 29-30 seem inappropriate

L159: Did the authors mean Ref 39.

L200: Ref 46 seems inappropriate

L238: Ref 28 seems inappropriate

L244: Ref 53 does not support the statement

L247: Ref 54 seems inappropriate. Perhaps the authors meant Ref 55?

L402: Ref 65 needs to be provided

Recommend that the authors avail of professional writers to correct language semantics and grammar. Spellings are fine.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 3 Report

In this work, it is proposed in a novel way how, through a mathematical model, the physiology of “Populus euphratica” redirects the flow of energy-biomass towards the roots depending on the environmental conditions. To this end, a very well-founded and referenced introduction is articulated that allows us to understand the approach to the problem and the experimental strategy from a perspective that links genetics with an adaptive perspective.

To do this, they focus on QTLs, which makes sense since the adaptive phenomenon that is intended to be explained is based on a redistribution of biomass, which morphologically adjusts to stressful environmental conditions. As these are very general phenomena in genomic networks and therefore affect many genetic circuits, the approach towards expression regulation seems the most appropriate.

One of the elements that might need to be explained by the authors refers to the methodology that was used to select the SNPs. In my opinion, it is relevant to incorporate this information, since these specific differences propagate in the genomic network under a certain environmental context, affecting other genetic circuits through, for example, specific differences in the three-dimensional structure of proteins. This perspective has recently been published in biosystem

Marcos López-Pérez, Félix Aguirre-Garrido, Leonardo Herrera-Zúñiga, Francisco J. Fernández, Gene as a dynamical notion: An extensive and integrative vision. Redefining the gene concept, from traditional to genic-interaction, as a new dynamical version, Biosystems, Volume 234, 2023

In equation (1), the units that should be used to measure the impact of the environment (e₀) are not well understood. I understand that the plant can perceive stressful ecosystem conditions through various systems, and subsequently once this environmental context is characterized, the response is reflected in more defined phenotypic values. I think it is important to explain this point well since it acts as an important correction factor with respect to the proposed model.

En el texto se dice “For any QTL 𝑘 as a response, there are (𝐾 − 1) predictors, each of which contributes to the dependent epistatic effect of this response QTL through unknown nonpara- metric dependent parameters (𝛩𝑘|1, ⋯ , 𝛩𝑘|𝑘−1, 𝛩𝑘|𝑘+1, ⋯ , 𝛩𝑘|𝐾). However, the number of entities linked with a particular entity in a network is limited, depending on the network size [41].

In this sense, it is pertinent to question the authors in the following sense: why do they assume that networks are limited? This question is based on the fact that the response variable that they are managing in their model and mathematical analysis has the distribution of biomass as its fundamental basis. In this sense, it must be assumed that the entire gene regulatory network (GRN) must be reconfigured, so to a greater or lesser extent the entire GRN is conditioned and therefore is not consistent with working with limited networks. I agree that there are more contingent or “self-contained” genetic circuits, in the sense that they may be more peripheral circuits in the GRN, but when it comes to the flows of biomass and therefore energy in the plant, (related with primary respiratory metabolism, photosynthetic function (that regulates the energy input to the system), protein synthesis, regulation by phytohormones of systemic distribution in the plant), in fact it is cited later in the document (“he genes where these nodes are located may be functionally associated with plant signal transduction, nucleic acid metabolism, glucose metabolism, and DNA binding") then general mechanisms in the GRN must be considered, which in my opinion casts doubt on whether they are limited networks.

Later in the document it is cited “PPR proteins serve numerous essential functions across the life cycle”, which contradicts to a certain extent that its approach should be limited to limited networks. In my opinion, the model or parameters must refer to a reconfiguration of the entire GRN.

The document quotes “Despite the significantly lower number of QTLs in the salt stress networks compared to the control group, the complexity of the network is higher”, in the context of this phrase, I believe it is convenient to include an explanation of the term complexity. I understand that the term must refer to the number of interactions and interactors that act on the network, but in any case a comment should be added in this regard.

Elsewhere in the document it says “Suppose the adverse inhibitory effects are effectively silenced in genetic breeding. In that case, Q7816 could enhance root growth and development. This enhancement would enable Populus euphratica to withstand adverse conditions, ensuring survival and growth.”, I understand that it is valid to make this type of assertion based on the results of the study. However, it would be appropriate to include a comment clarifying that genetic improvement could have collateral or adjuvant effects on GRN since many interactions still act cryptic, and the final effect on the general physiology of the plant cannot be determined.

Finally, I consider that it is a novel work that provides an integrative vision to anticipate genetic improvement processes in plants through the proposal of mathematical models with data from genomic networks.

Author Response

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Author Response File: Author Response.pdf

Round 2

Reviewer 2 Report

Most of the issues raised in iteration 1 of review have been addressed. However, the authors have not disclosed the details of QTL mapping reference genome. This will help increase the interpretability of the results obtained by the authors and perhaps expand the discussion. This is the sole reason for recommending a major revision. Otherwise the article is fit to be published.

No significant issues apart from minor spelling and grammar checks and formatting of tracked changes.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf