QTL Analysis and Heterosis Loci of Effective Tiller Using Three Genetic Populations Derived from Indica-Japonica Crosses in Rice

Round 1

Reviewer 1 Report

Review of the mauscript: QTL analysis and heterosis loci of effective tiller using three genetic populations derived from Indica-Japonica crosses in rice submitted under the ID agronomy-1897248.

 

The research related to the detection of genome regions of breeding crops, bring significant knowledge in the field of genotype selection with the best combination of gene alleles determining important agronomic traits. In the genome mapping process, it is of particular importance to construct a mapping population that will allow for the determination of segregation of these alleles and showing the distribution of traits in descendants. The populations used in the presented research meet these requirements. The authors applied possible techniques for assessing population properties to characterize and identify the QTL regions regulating the studied PN and TN traits.

The results obtained as part of the research indicate a detailed, extensive knowledge by the authors of not only the subject but also the dependencies resulting from their interpretation.

The presented manuscript meets the requirements of the original scientific publication and can be published after minor changes.

1. In my opinion in the results, paragraph 3.3 in the description of figure 3 diagram b there is additional data for  gene OsCDC30 only for father. Nothing is said about this gene in the results. If this is a reference maybe it would be god to add this information (just one sentence – author decision).

2. If I may suggest the part from line 199 to the end of paragraph could be rewritten. Maybe it should be in the discussion since there is an autocitation or maybe it would be good to add, that in the previous analysis published, the same gene was located in the qtl for grain shape….. (for authors reflection).

3.  In addition and in my opinion the final part of the discussion is focused on the sequence analysis for MOC1 gene but maybe it would be good to extend the reason for this. Especially that the data are added in supplement, if those are some new results they should be in result paragraph (authors decision)

3. Some editorial correction are needed:

- line 61 replace However into Moreover, few…….

- line 84 add was after Luohui9.

- line 94 F11 change into F11

- line 117 – in this paragraph I would prefer to add the sentence “Recommended by authors Patrick and Nathan 2013). I think it should be added to the references.

- line 153 “…, which was just ….” – change into - ,”….with the size of….”

- line 163 should be independent

- line 182 add formula (Figure 3), this will direct the reader to your results,

- line 196 change “Besides……” into “In addition….”

- line 197 – after OsETR2 add words…. Mapped on chromosome 2…….

- line 227 after the sentence add (Table 1)

- line 239 - start the paragraph with….. “ In the next step of analysis we have detected……’ instead of - We further detected…”

- line 275 – after HN162 add word environment.

- line 293 – remove repeated word 'moreover' and change into …and - in addition…..

- line 304 - Replace the word ‘In this study ….” Into “We have observed that:……..”

Author Response

Please see the attachment

Author Response File: Author Response.docx

Reviewer 2 Report

The authors present a study that detects quantitative trait loci (QTL) and heterosis-related loci for TN or PN in rice, using a high generation recombinant inbred line (RIL) population and two hybrid populations. Using crosses of two elite cultivars, Luohui9 and RPY geng, and two testcross hybrid populations derived from the crosses of RILs and two cytoplasmic male sterile lines offers a good perspective on potential use of results in applied breeding programs. Identification of new candidate genes for PN is of interest for the scientific community.

Overall, the work seems to have been carried out competently and properly. However, I would recommend that the authors pay particular attention to some sections. In general, the manuscript is quite clear. I would propose to include in the manuscript a better description of plant material and statistical tools used and more focus on environmental stable QTL and co-localizing regions. I have some comments about this work:

Line 45: remove ‘Meta-QTL was abbreviated as MQTL in the rest of manuscript’, as MQTL abbreviation was already explained before: Meta-QTL (MQTL)

Lines 71-75: please try to rephrase this sentence and correct the English. ‘was typical’ is not the most appropriate description. “to identified” and “explored” are not correct.

Lines 83-84: similar to the comment above. Ex: “Luohio9 was used …” not only “used”.  

Line 99. RCBD for ‘two testcross population’ refers to the hybrid populations? Please clarify.

Line 104-105: PN for each inbred line use only 5 plants for all environments of 5 plant per environment (so 3 env. x 5 plants – 15 plants/genotype)? However, PN for RILs seem to have been tested in 4 environments: HB181, HB171, HN162 and HB191. Was any environmental adjusted means approach used? Please clarify this pharagraph.

Line 109:  Include a detailed description of the QTL/MQTL analysis in the M&M. Was only PN QTL analysed? What about TN? Was QTL done on each environment or using an adjMean approach, as for MQTL?

Add to M&M a section were the markers data is described. Raw data in Supplementary files. Genetic and physical positions? In cM and bp? What reference genome was used for physical positions?

Lines 135-145: similar to the comment above, it seems that the environment has a strong influence on the measured traits. From Fig 1, HN162 has lower values, on average, that the rest. This should be adjusted using mixed linear models.

Line 164: Figure 2 add description of Y-axis. Similar in Figure 5

Lines 228: please add in Table 1 the positions of QTL/genes on chromosome in bp.

Lines 260: ‘so,’ replace with ‘therefore’

Lines 294-287: Very long paragraph. Try splitting it into separate sentences.

Lines 305-309: This is interesting but a bit complicated to follow. The protein sequence is identical, but the nucleotide sequence had a 4bp deletion in noncoding region. In addition, a higher expression level of the MOC1 was observed in previous studies. Please try to clarify this paragraph.

Lines 315-117: Please modify/clarify this section. Different expression levels dose not necessary result in heterosis.

In discussions, please try to include a section were you discuss the genes present in the newly detected QTL. In addition, other potential candidate genes without functions ‘related’ to PN, TN. Overall, please focus more on environmental stable QTL and new candidate genes.

Author Response

Please see the attachment

Author Response File: Author Response.docx