Characterization of a Major Quantitative Trait Locus for the Whiteness of Rice Grain Using Chromosome Segment Substitution Lines

The whiteness of rice grains (WRG) is a key indicator of appearance quality, directly impacting its commercial value. The trait is quantitative, influenced by multiple factors, and no specific genes have been cloned to date. In this study, we first examined the correlation between the whiteness of polished rice, cooked rice, and rice flour, finding that the whiteness of rice flour significantly correlated with both polished and cooked rice. Thus, the whiteness of rice flour was chosen as the indicator of WRG in our QTL analysis. Using a set of chromosome segment substitution lines (CSSL) with <i>japonica</i> rice Koshihikari as the recipient and <i>indica</i> rice Nona Bokra as the donor, we analyzed QTLs for WRG across two growth environments and identified six WRG QTLs. Notably, <i>qWRG9</i> on chromosome 9 displayed stable genetic effects in both environments. Through chromosomal segment overlapping mapping, <i>qWRG9</i> was narrowed to a 1.2 Mb region. Additionally, a BC₄F₂ segregating population confirmed that low WRG was a dominant trait governed by the major QTL <i>qWRG9</i>, with a segregation ratio of low to high WRG approximating 3:1, consistent with Mendelian inheritance. Further grain quality analysis on the BC₄F₂ population revealed that rice grains carrying the <i>Indica</i>-type <i>qWRG9</i> allele not only exhibited lower WRG but also had significantly higher protein content. These findings support the fine mapping of the candidate gene and provide an important QTL for improving rice grain quality through genetic improvement.