Using genomic screening methods to create high-quality rice breeding material

Rice, as a key model in the study of agroecosystem genomics, is the focus of research meant to address the challenges of producing sufficient food for the growing global population. In breeding programs developing new varieties, improving the physicochemical properties of the grain is crucial. Based on the analysis of national and international research, this article presents information on new molecular genetic methodologies and advances in the development of new valuable rice genotypes using genome sequencing data. Continuous enrichment of rice germplasm at global breeding centers is achieved through the use of highly effective approaches employing postgenomic and cellular technologies in combination with traditional phenotyping methods. This review examines the achievements of molecular genetic research in rice, focusing on valuable grain quality traits such as vitreousness (chalkiness) and shape (size). GWAS analysis is widely used in marker-assisted and genomic rice breeding programs. More recently, GBS analysis has been used to identify relationships between phenotype and genotype based on the analysis of bi-parental mapping populations and varietal accessions. The post-genomic research period, focused on the search for candidate genes for valuable quality traits, had started after the genomic reference sequences were obtained. As a result, hundreds of QTLs for the chalkiness trait were discovered across 12 chromosomes, few were accurately mapped or sequenced. By 2018, several major QTLs affecting grain size were sequenced and characterized. For example, the presence of the recessive GS3 allele and the dominant GW7TFA allele increases the grain length-to-width ratio. In 2023, it was shown that overexpression of OsFIF3 inhibits the expression of FLO2 and SUT1, thereby increasing chalkiness and reducing grain size. This breeding breakthrough is attributed, for example, to the use of non-digital markers for length, width, thickness, and the grain length-to-width ratio, GS3RGS1 and RM505, as selection markers. All research is an ongoing process aimed at achieving the highest possible level of high-quality rice products.