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.
Highlights
Rice grain quality, including appearance, milling, cooking and eating, as well as nutritional qualities, determines the market value, and is getting more and more concern from rice researchers, producers and consumers [1,2]
Using the gel-based low-density map consisted of 208 simple sequence repeat (SSR) and insert/deletion (InDel) markers, the same number of Quantitative trait locus (QTL) were identified in the same HHZ/JZ1560 recombinant inbred line (RIL) population, and three QTLs were repeatedly detected across two years
Based on genotyping-by-resequencing, a total of 14 QTLs controlling Grain protein content (GPC) were identified with an indica/japonica (HHZ/JZ1560) RIL population in 2016 and 2017
Summary
Rice grain quality, including appearance, milling, cooking and eating, as well as nutritional qualities, determines the market value, and is getting more and more concern from rice researchers, producers and consumers [1,2]. Grain protein content (GPC) is one key factor determining nutritional quality, but is closely associated with cooking and eating qualities [3,4]. The increase of GPC may lead to low eating quality. Compared to the protein content of other cereal crops such as wheat and barley, GPC in rice is relatively low, with a mean about 8.0% and a range of 4.9% to 19.3% in the indica subspecies and 5.9% to 16.5% in the japonica subspecies [5]. Illuminating the genetic basis of GPC makes a lot of sense in constructing a molecular marker-assisted selection system to improve rice grain quality [6,7]
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