**5. Conclusions**

Based on genotyping-by-resequencing, a total of 14 QTLs controlling GPC were identified with an *indica*/*japonica* (HHZ/JZ1560) RIL population in 2016 and 2017. Of the 14 QTLs, 13 QTLs showed similar chromosome regions with the QTLs for GPC documented in previous studies. The *qGPC10* with a minor effect was newly detected in this study. Seven of the fourteen QTLs were repeatedly identified across two years. The stably inherited *qGPC1-1* with a relatively large effect was validated and delimited to a ~862 kb region flanked by JD1006 and JD1075 on the short arm of chromosome 1, which is helpful for the construction of a marker-assisted selection system to improve rice grain qualities and further map-based cloning of this QTL. Our results indicated that instead of the KND method with lengthy operation, the NIRS with rapid and easy operation was a feasible strategy for measuring a massive collection of samples in the mapping and map-based cloning of GPC QTL. More stably expressed QTLs identified in the genetic map based on genotyping-by-resequencing suggested that high-density map enhanced the detection power of minor QTLs.

**Supplementary Materials:** Supplementary materials can be found at http://www.mdpi.com/1422-0067/21/2/408/s1.

**Author Contributions:** Conceptualization, X.-J.S.; Data curation, Y.-B.W., G.L. and Y.-C.C.; Formal analysis, Y.-J.Z.; Investigation, J.-Y.Y.; Methodology, H.-Z.C. and J.-Z.Y.; Supervision, J.-Z.Y.; Writing—original draft, Y.-B.W.; Writing—review & editing, G.L. All authors have read and agreed to the published version of the manuscript.

**Funding:** This research was funded by Chinese High-yielding Transgenic Program (Grant No. 2016ZX08001-004).

**Acknowledgments:** We thank L. Xie at China National Rice Research Institute for the measurements of grain protein content through near infrared reflectance spectroscopy.

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