Improvements in Plant Morphology Facilitating Progressive Yield Increases of japonica Inbred Rice since the 1980s in East China
Round 1
Reviewer 1 Report
The article entitled " Improvements in plant morphology facilitating progressive yield increases of japonica inbred rice since the 1980s in east China" contributed by Meng et al. (agriculture-1337562) was reviewed.
This is an excellent manuscript dealing with the genetic alteration of the grain yield as well as the plant morphological traits of the recently released japonica rice inbred lines as the achievement of breeding from 1983 to 2013 in eastern China. Based on the two-year field experiment, the authors concluded that several morphological traits are closely associated with expanded sink size, such as the number of spikelets per panicle, increased leaf area by leaf width, optimized leaf photosynthetic capacity, and so on, would be contributing the yield improvement.
While not entirely novel, this manuscript is concise and well organized. This is an important result for facilitating the achievement of breeding for japonica rice inbred lines that need to be widely circulated. Thus, some points as indicated below need to be addressed by the authors to improve the quality of the article.
- The legend in Figure 1 has an insufficient legend and presentation. “Scheme 2. (c)” must be clear the trait authors address.
- The procedure of the ‘specific leaf weight’ was not specified in the manuscript (P10 L211). According to the authors’ claims, the specific leaf weight was one of the positively correlated morphological characters with the yield. Authors should add some description of the materials (timing of growth and replication) and the method.
- The conclusion is short and to the point but does not clearly show the importance and relevance of the manuscript findings. In particular, the last sentence of this section gives readers a weak and ambiguous impression of ‘future breeding’ to develop further high-yielding varieties in eastern China, for example. Is there any more space to improve plant morphology in addition to the latest plant type in japonica rice inbred lines? Or researchers and breeders should take steps to shift the phase to explore novel and/or finer tuning strategies to realize further high-yielding varieties development?
Author Response
Point 1: The legend in Figure 1 has an insufficient legend and presentation. “Scheme 2. (c)” must be clear the trait authors address.
Response 1: Good suggestion. We changed “Scheme 2. (c)” with “spikelets per m2 (c)” in the legend in Figure 1.
Point 2: The procedure of the ‘specific leaf weight’ was not specified in the manuscript (P10 L211). According to the authors’ claims, the specific leaf weight was one of the positively correlated morphological characters with the yield. Authors should add some description of the materials (timing of growth and replication) and the method.
Response 2: Good suggestion. We added the details about specific leaf weight, and such information was follows: “Plants of four hills were collected at full heading stage to measure specific leaf weight, and photosynthetic rate and SPAD values of flag leaves. Specific leaf weight was calculated as the ratio of leaf dry mass to leaf area. Leaf area was determined by a leaf area meter (LI-3100C, Li-Cor, Lincoln, NE, USA), then leaf dry mass was weighted after oven-drying at 75 °C for 80 h.”
Point 3: The conclusion is short and to the point but does not clearly show the importance and relevance of the manuscript findings. In particular, the last sentence of this section gives readers a weak and ambiguous impression of ‘future breeding’ to develop further high-yielding varieties in eastern China, for example. Is there any more space to improve plant morphology in addition to the latest plant type in japonica rice inbred lines? Or researchers and breeders should take steps to shift the phase to explore novel and/or finer tuning strategies to realize further high-yielding varieties development?
Response 3: Good suggestion. As suggested, we changed the Conclusion as follows: “The genetic improvement achieved a 63.3 kg ha-1 year-1 yield increase across two years of japonica inbred rice since the 1980s in east China. The morphological changes in japonica inbred rice have enlarged sink size through spikelets per panicle, increased leaf area by leaf width, optimized leaf orientation and light distribution within the canopy, improved plant height and leaf photo-synthetic capacity, and enhanced stem strength. These improved plant morphology contributed to yield improvement of japonica inbred rice since the 1980s. The declined filled-grain percentage in modern rice cultivars might be attributable to more attention for sink, while relatively less for source during the genetic improvement. Future breeding should focus more on source improvement on the basis of expanding sink to develop high-yielding cultivars.”
With the changes in the Conclusion, information in the Discussion section was improved, which could clearly be seen in the revised manuscript.
Thank you for your professional comments and valuable time to improve this manuscript.
Author Response File: 
Author Response.docx
Reviewer 2 Report
Dear authors,
Per request of the editors, I reviewed your manuscript entitled "Improvements in plant morphology facilitating...".
The paper is rich in data and is well written. Nevertheless, I have some major and minor comments and suggestions.
Major comments (must be adressed):
1. The study mixes cultivars from different breeding institutions, which are not informed in the paper. This information must be included in Table 1. Although it is said that the cultivars were selected due to their popularity, there should be an objective criterium to select them. This is because, if the cultivars are handpicked, all the results of the study would be biased. Additionally, if different institutions work with different breeding pools, morphologycal traits in the cultivars might be merely a consequence of population structure. I think that not enough emphasis has been done on the selection of the material, to make clear that those 12 cultivars can indeed represent the history of japonica rice breeding in the target region and period of time.
2. Data analysis was inadequately described in M&Ms. If the focus of the study was to detect trends of change in morphologycal traits through time, a regression of phenotypes on year of release should be done. However, regression is not mentioned in the text, only in some tables. In the ANOVA, replicates are also a source of variation, not mentioned. In all figures, exclude the ANOVA table in the plots. In the regression analysis, re-number the years starting at 1 = 1983 and so on, such that, in the regression equations, the intercept will correspond to the value of the trait in 1982, which is useful information.
3. Throughout the paper, results are shown for each year of evaluation (2019 and 2020). There is no point in duplicating all the results, the two years were only to get a more precise point estimation of the phenotypes of each cultivar. The results of ANOVA (Table 2) show that YxC was non-significant for all traits, except for grain yield, reinforcing this point. The whole paper should be consolidated to the means between the two years of experiments, making it much more clean and readable. All the figures and tables will be affected (for better) by this change. All the text will have to be revised accordingly. By doing this, the size of the paper will be significantly reduced, without loss of information.
4. In the results section, some traits are shown in figures and others are shown in tables. I could not understand why it was done this way, since the type of information is identical. I think the authors should opt for figures for all traits, eliminating tables 3, 4, 5, 6.
Minor comments:
L 55: were studied in maize
L 72: (re)presentative japonica ...
L 102: avoid repeating the word 'spacing'.
L 106: describe the irrigation regime briefly.
L 109 - 111: unnecessary repetition of 'at heading and maturity'. The paper has several instances of repetition that could be cut out.
L 142: the interaction, not their
L 153: Scheme 2 ??
L 183: was increased
L 272: Clarify what you mean by "The determined parameters".
Table 7 would be more informative and complete if replaced by a correlation matrix.
L 285: Brazil, not Brazilian
L 305 - 306: Please clarify what is the contradiction quantity/quality.
L 324: light extinction
L 342 - 361: I was surprised with the fast increase in plant height. No lodging was observed in the plots? Please add that information.
In conclusion, it will take a complete revision of data analysis and a restructuring of the results section. Notwithstanding, the article will be much cleaner and efficient at delivering its message.
Author Response
Point 1: The study mixes cultivars from different breeding institutions, which are not informed in the paper. This information must be included in Table 1. Although it is said that the cultivars were selected due to their popularity, there should be an objective criterion to select them. This is because, if the cultivars are handpicked, all the results of the study would be biased. Additionally, if different institutions work with different breeding pools, morphological traits in the cultivars might be merely a consequence of population structure. I think that not enough emphasis has been done on the selection of the material, to make clear that those 12 cultivars can indeed represent the history of japonica rice breeding in the target region and period of time.
Response 1: Good suggestion. First, we added the breeding institutes of rice cultivars applied in this study in Table 1. Second, we added information about the reason why we chose these rice cultivars in the Materials and Methods section. The related information was follows: “Twelve japonica inbred rice released from 1983 to 2013 were grown in this field experiment. These rice cultivars were selected because they were all released by local breeding institutes, and well-adapted to the agro-ecological conditions of the study area. The rice cultivars were very popular and widely adopted by local farmers during historical periods. For example, Wuyujing 3 was famous for its high and stable grain yield and was widely planted with a cumulative area of 6.1 Mha as of 2020. Nanjing 5055 and Nanjing 9108 were grown in a large area for their excellent grain quality in recent years [25]. Besides, these rice cultivars were generally considered representative during the breeding process of japonica inbred rice since the 1980s, and always chosen as the control (CK) in the crop variety regional trials conducted in Jiangsu, east China [23].”
Point 2: Data analysis was inadequately described in M&Ms. If the focus of the study was to detect trends of change in morphological traits through time, a regression of phenotypes on year of release should be done. However, regression is not mentioned in the text, only in some tables. In the ANOVA, replicates are also a source of variation, not mentioned. In all figures, exclude the ANOVA table in the plots. In the regression analysis, re-number the years starting at 1 = 1983 and so on, such that, in the regression equations, the intercept will correspond to the value of the trait in 1982, which is useful information.
Response 2: Good suggestion. As suggested, (1) regression equations of phenotypes against year of release were listed in Figures, and described in the revised manuscript; (2) we added df of source in the ANOVA in Table 2; (3) the ANOVA Table in the original Figures were all excluded in the revised manuscript; (4) year of release was re-numbered, and started at 1=1983 in the revised manuscript.
Point 3: Throughout the paper, results are shown for each year of evaluation (2019 and 2020). There is no point in duplicating all the results, the two years were only to get a more precise point estimation of the phenotypes of each cultivar. The results of ANOVA (Table 2) show that YxC was non-significant for all traits, except for grain yield, reinforcing this point. The whole paper should be consolidated to the means between the two years of experiments, making it much more clean and readable. All the figures and tables will be affected (for better) by this change. All the text will have to be revised accordingly. By doing this, the size of the paper will be significantly reduced, without loss of information.
Response 3: Good suggestion. As suggested, all data in the revised manuscript were averaged across two study years; the figures and tables were also revised accordingly.
Point 4: In the results section, some traits are shown in figures and others are shown in tables. I could not understand why it was done this way, since the type of information is identical. I think the authors should opt for figures for all traits, eliminating tables 3, 4, 5, 6.
Response 4: Good suggestion. As suggested, we opted for figures for all traits, and original Tables 3, 4, 5, 6 were excluded in the revised manuscript.
Point 5: L 55: were studied in maize
Response 5: Done. We changed “were studies in maize” with “were studied in maize” in the revised manuscript.
Point 6: L 72: (re)presentative japonica ...
Response 6: Good suggestion. We changed “presentative” with “representative” in the revised manuscript.
Point 7: L 102: avoid repeating the word 'spacing'.
Response 7: Good suggestion. We changed “The hill spacing was 30 cm row spacing and 12 cm plant spacing” with “The hill spacing was 30 cm row and 12 cm plant” in the revised manuscript.
Point 8: L 106: describe the irrigation regime briefly.
Response 8: Good suggestion. We added the information of irrigation regime applied in this study. Such information was follows: “The irrigation regime adopted in field experiment followed alternate wetting and drying method, which applied multiple flooding and drainage during the rice-growing cycle [26].”
Point 9: L 109 - 111: unnecessary repetition of 'at heading and maturity'. The paper has several instances of repetition that could be cut out.
Response 9: Good suggestion. We deleted the 'at heading and maturity' in Line 109-111 (original manuscript). Besides, such unnecessary repetition was deleted in the Result section in the revised manuscript.
Point 10: L 142: the interaction, not their
Response 10: Good suggestion. We changed “their interaction” with “the interaction” in the revised manuscript.
Point 11: L 153: Scheme 2 ??
Response 11: Good suggestion. We changed “Scheme 2. (c)” with “spikelets per m2 (c)” in the legend in Figure 1.
Point 12: L 183: was increased
Response 12: Good suggestion. We changed “were increased” as “was increased” in the revised manuscript.
Point 13: L 272: Clarify what you mean by "The determined parameters".
Response 13: Good suggestion. “The determined parameters” was indeed not so clear. We changed the title of original Table 7 (new Table 3) with “Correlation matrix between grain yield and plant morphological traits of rice cultivars.”
Point 14: Table 7 would be more informative and complete if replaced by a correlation matrix.
Response 14: Good suggestion. As suggested, the correlation analysis was listed through a correlation matrix, and seen in new Table 3 in the revised manuscript.
Point 15: L 285: Brazil, not Brazilian
Response 15: Done. We changed “Brazilian” with “Brazil” in the revised manuscript.
Point 16: L 305 - 306: Please clarify what is the contradiction quantity/quality.
Response 16: Good suggestion. We added the information about contradiction between the quantity and quality of crop population in the 2nd paragraph in the revised manuscript. Such information was follows: “Such a breeding strategy could balance the contradiction between the quantity and quality of crop population, as more quantity was always associated with poor quality during the process of crop population formation [30].”
Point 17: L 324: light extinction
Response 17: Good suggestion. We changed “leaf extinction” with “light extinction” in the revised manuscript.
Point 18: L 342 - 361: I was surprised with the fast increase in plant height. No lodging was observed in the plots? Please add that information.
Response 18: Good suggestion. In fact, no lodging was observed in each plot at two years. Such information was added in the Materials and Methods section, and shown as follows: “In the two-year field experiment, no lodging phenomenon was observed in each plot.”
Point 19: In conclusion, it will take a complete revision of data analysis and a restructuring of the results section. Notwithstanding, the article will be much cleaner and efficient at delivering its message.
Response 19: This manuscript was revised following the comments of Reviewers 1&2. Thank you for your professional comments and valuable time to improve this manuscript.
Author Response File: Author Response.docx
Round 2
Reviewer 2 Report
Dear authors,
Thank you for accepting most of my suggestions to your manuscript. I believe it is cleaner and more readable in the current form.
Nevertheless, I think figures still need a critical improvement. In the first review, I suggested you renumber the years such that the first year would be 1 and so on, such that the regression equations have the intercept at the first year of the series minus 1. In the x-axis of the plots, however, you must display the year tag, not what you called renumbered year of release. There is loss of information if you do like you did in the last format. To be more clear, for regression purposes, the series of years is 1,2,3,... but in the plots you should show 1980, 1985, 1990, and so on. Also, avoid the wide empty space at the right side of the plotting area. You could also considered drawing the regression line on the plots, although I do not consider it critical.
Author Response
Point 1: Nevertheless, I think figures still need a critical improvement. In the first review, I suggested you renumber the years such that the first year would be 1 and so on, such that the regression equations have the intercept at the first year of the series minus 1. In the x-axis of the plots, however, you must display the year tag, not what you called renumbered year of release. There is loss of information if you do like you did in the last format. To be more clear, for regression purposes, the series of years is 1,2,3,... but in the plots you should show 1980, 1985, 1990, and so on. Also, avoid the wide empty space at the right side of the plotting area. You could also considered drawing the regression line on the plots, although I do not consider it critical.
Response 1: Good suggestion. As suggested, (1) Figures in the revised manuscript were all improved following the method of the Reviewer. X-axis of the plots were shown as year of release (1980, 1985, 1990, and so on), and the x in the linear regression was reassigned as years after 1983; for example, x was valued as 1 in 1983 and so on; (2) we improved x-axis setting to avoid the wide empty space in the Figures; (3) Regression lines were added in the Figures.
Thank you for your professional comments and valuable time to improve this manuscript.
