Genetic Architecture of Grain Chalk in Rice and Interactions with a Low Phytic Acid Locus.

Grain quality characteristics have a major impact on the value of the harvested rice crop. In addition to grain dimensions which determine market classes, translucency is also required for the highest grain quality. Over the last several years, the USA rice industry has been concerned about the increasing prevalence of chalky rice which is resulting in a loss of some markets. This study was conducted to identify genetic markers associated with grain chalk that could be used by breeders to select for translucency. A mapping population developed from KBNT-1-1, a translucent, low phytic acid (LPA) long grain from USA was crossed with Zhe733, a chalky, long grain variety developed in China. The 185 F12 progeny were evaluated in trials conducted across two years and two planting dates that differed by one month. Grain was harvested at maturity and brown or milled rice were used to determine grain length, width, and percent chalk using an image analysis system. QTL analysis was performed using 160 genome-wide SSRs and 2 SNP markers. The delayed planting date resulted in exposure of the progeny to higher nighttime temperatures during grainfill. The RILs differed for grain length, width, chalkiness, and days to heading. Significant RIL interactions with planting date and year were determined. Even though the progeny were derived from two long grain varieties, a significant correlation was observed between chalk and grain width (r=0.32).  Surprisingly, a large effect QTL was co-located with the LPA gene with the KBNT-1-1 allele associated with increased chalk.    A SNP marker was developed directly within the LPA gene and genotyping using this SNP confirmed the previous result.  Additional QTL were detected with the KBNT-1-1 allele associated with reduced chalk.  Findings from this population will be verified in other mapping populations.