Natural variation in salt-induced changes in root:shoot ratio reveals SR3G as a negative regulator of root suberization and salt resilience in Arabidopsis

Reviewer #1 (Public Review):

Summary:

The authors aim to assess the effect of salt stress on root:shoot ratio, identify the underlying genetic mechanisms, and evaluate their contribution to salt tolerance. To this end, the authors systematically quantified natural variations in salt-induced changes in root:shoot ratio. This innovative approach considers the coordination of root and shoot growth rather than exploring biomass and the development of each organ separately. Using this approach, the authors identified a gene cluster encoding eight paralog genes with a domain-of-unknown-function 247 (DUF247), with the majority of SNPs clustering into SR3G (At3g50160). In the manuscript, the authors utilized an integrative approach that includes genomic, genetic, evolutionary, histological, and physiological assays to functionally assess the contribution of their genes of interest to salt tolerance and root development.

Strengths:

The holistic approach and integrative methodologies presented in the manuscript are essential for gaining a mechanistic understanding of a complex trait such as salt tolerance. The authors focused on At3g50160 but included in their analyses additional DUF247 paralogs, which further contributes to the strength of their approach. In addition, the authors considered the developmental stage (young seedlings, early or late vegetative stages) and growth conditions of the plants (agar plates or soil) when investigating the role of SR3G in salt tolerance and root or shoot development.

Weaknesses:

The authors' claims and interpretation of the results are not fully supported by the data and analyses. In several cases, the authors report differences that are not statistically significant (e.g., Figures 4A, 7C, 8B, S14, S16B, S17C), use inappropriate statistical tests (e.g., t-test instead of Dunnett Test/ANOVA as in Figures 10B-C, S19-23), present standard errors that do not seem to be consistent with the post-hoc Tukey HSD Test (e.g., Figures 4, 9B-C, S16B), or lack controls (e.g., Figure 5C-E, staining of the truncated versions with FM4-64 is missing).

In other cases, traits of root system architecture and expression patterns are inconsistent between different assays despite similar growth conditions (e.g., Figures S17A-B vs. 10A-C vs. 6A, and Figures S16B vs. 4A/9B), or T-DNA insertion alleles of WRKY75 that are claimed to be loss-of-function show comparable expression of WRKY75 as WT plants. Additionally, several supplemental figures are mislabeled (Figures S6-9), and some figure panels are missing (e.g., Figures S16C and S17E).

Consequently, the authors' decisions regarding subsequent functional assays, as well as major conclusions about gene function, including SR3G function in root system architecture, involvement in root suberization, and regulation of cellular damage are incomplete.

Reviewer #2 (Public Review):

Salt stress is a significant and growing concern for agriculture in some parts of the world. While the effects of sodium excess have been studied in Arabidopsis and (many) crop species, most studies have focused on Na uptake, toxicity, and overall effects on yield, rather than on developmental responses to excess Na, per se. The work by Ishka and colleagues aims to fill this gap.

Working from an existing dataset that exposed a diverse panel of A. thaliana accessions to control, moderate, and severe salt stress, the authors identify candidate loci associated with altering the root:shoot ratio under salt stress. Following a series of molecular assays, they characterize a DUF247 protein which they dub SR3G, which appears to be a negative regulator of root growth under salt stress.

Overall, this is a well-executed study that demonstrates the functional role played by a single gene in plant response to salt stress in Arabidopsis.

The abstract and beginning of the Discussion section highlight the "new tool" developed here for measuring biomass accumulation. I feel that this distracts from the central aims of the study, which is really about the role of a specific gene in root development under salt stress. I would suggest moving the tool description to less prominent parts of the manuscript.