*Article* **Genome-Wide Identification of QTLs for Grain Protein Content Based on Genotyping-by-Resequencing and Verification of** *qGPC1-1* **in Rice**

**Yi-Bo Wu 1,**†**, Guan Li 1,**†**, Yu-Jun Zhu 1, Yi-Chen Cheng 1, Jin-Yu Yang 1, Hui-Zhe Chen 1, Xian-Jun Song <sup>2</sup> and Jie-Zheng Ying 1,\***


Received: 22 November 2019; Accepted: 7 January 2020; Published: 9 January 2020

**Abstract:** To clarify the genetic mechanism underlying grain protein content (GPC) and to improve rice grain qualities, the mapping and cloning of quantitative trait loci (QTLs) controlling the natural variation of GPC are very important. Based on genotyping-by-resequencing, a total of 14 QTLs were detected with the Huanghuazhan/Jizi1560 (HHZ/JZ1560) recombinant inbred line (RIL) population in 2016 and 2017. Seven of the fourteen QTLs were repeatedly identified across two years. Using three residual heterozygote-derived populations, a stably inherited QTL named as *qGPC1-1* was validated and delimited to a ~862 kb marker interval JD1006–JD1075 on the short arm of chromosome 1. Comparing the GPC values of the RIL population determined by near infrared reflectance spectroscopy (NIRS) and Kjeldahl nitrogen determination (KND) methods, high correlation coefficients (0.966 and 0.983) were observed in 2016 and 2017. Furthermore, 12 of the 14 QTLs were identically identified with the GPC measured by the two methods. These results indicated that instead of the traditional KND method, the rapid and easy-to-operate NIRS was suitable for analyzing a massive number of samples in mapping and cloning QTLs for GPC. Using the gel-based low-density map consisted of 208 simple sequence repeat (SSR) and insert/deletion (InDel) markers, the same number of QTLs (fourteen) were identified in the same HHZ/JZ1560 RIL population, and three QTLs were repeatedly detected across two years. More stably expressed QTLs were identified based on the genome resequencing, which might be attributed to the high-density map, increasing the detection power of minor QTLs. Our results are helpful in dissecting the genetic basis of GPC and improving rice grain qualities through molecular assisted selection.

**Keywords:** quantitative trait locus; grain protein content; single nucleotide polymorphism; residual heterozygote; rice (*Oryza sativa*); specific length amplified fragment sequencing; Kjeldahl nitrogen determination; near infrared reflectance spectroscopy
