Milling and appearance quality are important contributors to rice grain quality.  Abundant genetic diversity and a suitable environment are crucial for rice improvement.  In this study, we investigated the milling and appearance quality-related traits in a panel of 200 japonica rice cultivars selected from Liaoning, Jilin and Heilongjiang provinces in Northeast China.  Pedigree assessment and genetic diversity analysis indicated that cultivars from Jilin harbored the highest genetic diversity among the three geographic regions.  An evaluation of grain quality indicated that cultivars from Liaoning showed superior milling quality, whereas cultivars from Heilongjiang tended to exhibit superior appearance quality.  Single- and multi-locus genome-wide association studies (GWAS) were conducted to identify loci associated with milling and appearance quality-related traits.  Ninety-nine significant single-nucleotide polymorphisms (SNPs) were detected.  Three common SNPs were detected using the mixed linear model (MLM), mrMLM, and FASTmrMLM methods.  Linkage disequilibrium decay was estimated and indicated three candidate regions (qBRR-1, qBRR-9 and qDEC-3) for further candidate gene analysis.  More than 300 genes were located in these candidate regions.  Gene Ontology (GO) analysis was performed to discover the potential candidate genes.  Genetic diversity analysis of the candidate regions revealed that qBRR-9 may have been subject to strong selection during breeding.  These results provide information that will be valuable for the improvement of grain quality in rice breeding.

A total of 408 inbred rice cultivars bred in the last decade were analyzed for 24 SSR markers. The results showed the genetic diversity of indica cultivars was higher than that of japonica cultivars, and the genetic diversity of new cultivars raised in recent years was lower. Among the six rice cropping regions (RCRs) in China, genetic diversity was the highest in the central rice region (RCR-II) and the southwest rice region (RCR-III). Genetic differences among subpopulations of japonica were more complex than those in indica. Differentiation among seasonal ecotypes and RCRs in indica populations was unclear, but differentiation between RCR-II and northeast rice region (RCR-V) was more distinct for japonica cultivars. Considering the North rice region (RCR-IV) has very low genetic diversity among the tested cultivars, it is important to broaden the genetic background for future cultivars in rice breeding programs.