*4.13. Statistical Analysis*

Values are presented as mean ± standard deviation (SD). Means were tested by analysis of variance (ANOVA) followed by Tukey's or Duncan's multiple range test at *p* < 0.05 in SPSS software (SPSS Inc., Chicago, IL, USA).

**Supplementary Materials:** The following are available online at http://www.mdpi.com/1422-0067/20/10/2585/s1. Table S1: Cross-efficiency rate and advanced generation duration in biotron breeding system. Table S2: Annotation of SNPs and indels in BC3F<sup>2</sup> #31-2-4. Figure S1: Schematic representation of biotron speed-breeding system. Figure S2: Frameshift deletion in *Os09g0356200* affects days-to-heading of YNU31-2-4 plants. Figure S3: Agronomic trait assessment of "Kaijin", WT, and "YNU31-2-4" plants under control field condition. Figure S4: "YNU31-2-4" maintains higher relative water, chlorophyll, and proline contents at the seedling stage under salt stress. Figure S5: "YNU31-2-4" plants have an enlarged root system.

**Author Contributions:** M.M.R., T.T., M.B., K.K. and T.M. designed the experiments and analyzed the data; M.M.R. performed most of the experiments; T.T. performed the computational analysis of N.G.S. data; K.K., N.H., T.S. and T.O. contributed analytic tools; K.I., T.O., T.K. and H.T. jointly conceived the work; M.M.R., M.B. and T.M. wrote the article with contributions from all authors; and T.M. conceived the project and research plans and supervised the research.

**Funding:** This research was supported by KAKENHI Grants-in-Aid for Scientific Research (A) (15H02486) from Japan Society for the Promotion of Sciences, Strategic International Collaborative Research Program by the Japan Science and Technology Agency (JST SICORP), and Grant for Promotion of KAAB Projects (Niigata University) from the Ministry of Education, Culture, Sports, Science, and Technology, Japan.

**Acknowledgments:** Computations were performed on the NIG supercomputer at the ROIS National Institute of Genetics.

**Conflicts of Interest:** The authors declare no conflict of interest.
