Identification of quantitative trait loci responsible for rice grain protein content using chromosome segment substitution lines and fine mapping of qPC-1 in rice (Oryza sativa L.)

Protein content (PC) in rice endosperm plays an important role in determining rice grain quality. However, the genetic mechanism underlying grain PC remains unclear. In order to better understand the genetic basis of this trait, a chromosome segment substitution line (CSSL) population derived from the cross of Sasanishiki/Habataki was employed for genetic analysis and gene mapping. In three environments, seven quantitative trait loci in total were identified, of which only qPC-1 was repeatedly detected across three environments, and qPC-10 was identified in two environments; the other five QTLs were detected in one environment. In order to fine-map qPC-1, a CSSL with low PC, SL402, harboring qPC-1, was crossed with Sasanishiki to develop F-2 and F-3 segregation populations. qPC-1 was finally delimited to a 41-kb DNA region on chromosome 1. Storage protein component analysis indicated that the allele from Habataki on qPC-1 can significantly decrease the glutelin content, consequently leading to the decrease in PC. These results provide an important aid for map-based cloning of qPC-1, and the markers linked to qPC-1 could be applied to rice quality improvement.