Rice (Oryza sativa L.) is one of the most important cereal crops in the world and is a dietary staple food for over half of the world’s population. An increase in grain yield is continuously required to ensure food security. In addition to yield, grain quality is also paid particular attention by rice consumers, food industries, farmers, and seed producers (Champagne et al. 1999; Fitzgerald et al. 2009). Grain size and quality essentially determining the market price of rice. The global improvement in living standards is enhancing consumer preference for high-quality grains in rice cultivars. Therefore, grain quality, including grain size, is a major target in rice breeding programs globally (Bao 2014).

Grain quality is a complex quantitative trait because it is determined by many characteristics, including physical appearance, milling quality, nutritional value (grain components), aroma, and cooking and eating quality (Fig. 1). It is known that a lot of genes are involved in controlling each grain-quality trait. Decoding whole-genome sequences of rice cultivars has accelerated the detection of genetic factors (QTLs) and isolation of genes for the grain-quality traits. For example, grain size shows high heritability, and studies conducted so far have isolated several responsible genes, such as GS3, GW2, GS5, and TGW6 (Li et al. 2018). In addition to these major genes, a lot of minor QTLs are associated with grain size (Nagata et al. 2015). Chalkiness grains have opaque spots in endosperm and reduce grain quality because of decreasing milled rice ratio, especially indica rice cultivars of slender grains. The high temperature at grain-filling stage increases chalkiness and decreases grain quality in japonica rice cultivars of shorter and wider grains. Therefore, there have been a lot of genetic studies to detect QTLs and genes for grain chalkiness, such as Chalk5, Flo2, and GIF2 (Li et al. 2022b). Novel grain length QTL of qGL11 was fine mapped within the 810-kbp interval region on chromosome 11. Gene x gene interaction (combination of gene alleles) creates novel grain quality that does not exist in natural variation of rice cultivars. Combinations of deficient alleles among starch biosynthesis genes GBSSI, SS2a, SS3a, SS4b, ISA1, and BE2b showed unique starch properties such as increasing resistant starch for improving human health benefits (Fujita et al. 2022; Miura et al. 2022). Information on genetic diversity and gene allelic variations are useful for applications of fundamental genetic studies to develop novel breeding lines. Near-isogenic lines (NILs) are good candidates for breeding new rice cultivars and for introducing specific gene alleles for improving grain quality and increasing grain yield. The deficient allele of PDIL1-1 gene increases grain chalkiness but improves rice flour qualities such as small particle size of rice flour and large loaf volume of rice bread. NILs introducing the deficient allele of PDIL1-1 gene showed phenotypic alterations between different genetic backgrounds of two rice cultivars (Hori et al. 2022). The deficient allele of the Dep1 gene makes dense and erect panicles in rice plants, and increases grain yield and nitrogen use efficiency. Chen et al. (2022) revealed that NILs introducing the erect type allele of the Dep1 gene showed additional positive effects on protein accumulation but adverse effects on eating quality. The recent rapid development of genome editing technology can easily create knockout and modification of target gene alleles. Several genome editing studies successfully improved the number of specific grain components such as amylose, amino acids, fatty acids, β-carotene, 2-Acetyl-1-pyrroline (for fragrance), and cadmium (elements) by enhancing biosynthetic pathways or suppressing catabolic pathways (Sukegawa et al. 2022). Genome editing technology would be a powerful tool for the development of novel rice cultivars.

Based on the critical scientific information conveyed in these articles, we realized that understanding the genetic basis is the prerequisite to improve grain-quality traits in rice. We hope that the topics in this special issue will enhance the efficiency of breeding selections for improving grain quality with other agronomic traits, including high grain yield and strong disease/insect resistance.