More than half of the world's population uses rice as a source of carbon intake every day. Improving grain quality is thus essential to rice consumers. The three main properties that determine rice eating and cooking quality-amylose content, gel consistency, and gelatinization temperature-correlate with one another, but the underlying mechanism of these properties remains unclear. Through an association analysis approach, we found that genes related to starch synthesis cooperate with each other to form a fine regulating network that controls the eating and cooking quality and defines the correlation among these three properties. Genetic transformation results verified the association findings and also suggested the possibility of developing elite cultivars through modification with selected major and/or minor starch synthesisrelated genes.association analysis ͉ grain quality ͉ starch synthesis R ice (Oryza sativa L.) is a pivotal cereal crop that provides the staple food for more than half of the world's population.

Starch paste viscosity plays an important role in estimating the cooking, eating, and processing quality of rice. The inheritance of starch paste viscosity in glutinous rice remains undefined. In the present study, 118 glutinous rice accessions were collected, and the genotypes of 17 starch synthesis-related genes (SSRG) were analyzed by using 43 gene-specific molecular markers. Association analysis indicated that 10 of 17 SSRGs were involved in controlling the rapid visco analyzer (RVA) profile parameters. Among these, the PUL gene was identified to play an important role in control of peak viscosity (PKV), hot paste viscosity (HPV), cool paste viscosity (CPV), breakdown viscosity (BDV), peak time (PeT), and paste temperature (PaT) in glutinous rice. Other SSRGs involved only a few RVA profile parameters. Furthermore, interactions between SSRGs were found being responsible for PeT, PaT, and BDV. Some of the RVA parameters, including PKV, HPV, CPV, CSV, and PaT, were mainly governed by single SSRG, whereas other parameters, such as BDV, SBV, and PeT, were controlled by a few SSRGs, functioning cooperatively. Further, three near-isogenic lines (NIL) of a japonica glutinous cv. Suyunuo as genetic background, with PUL, SSIII-1, and SSIII-2 alleles replaced with those of indica cv. Guichao 2, were employed to verify the genetic effects of the various genes, and the results were consistent with those obtained from the association analysis. These findings indicated that starch paste viscosity in glutinous rice had a complex genetic system, and the PUL gene played an important role in determining the RVA profile parameters in glutinous rice. These results provide important information for potentially improving the quality of glutinous rice.

Grain protein content (GPC) affects rice nutrition quality. Here, we identify two stable quantitative trait loci (QTLs), qGPC-1 and qGPC-10 , controlling GPC in a mapping population derived from indica and japonica cultivars crossing. Map-based cloning reveals that OsGluA2 , encoding a glutelin type-A2 precursor, is the candidate gene underlying qGPC-10 . It functions as a positive regulator of GPC and has a pleiotropic effect on rice grain quality. One SNP located in OsGluA2 promoter region is associated with its transcript expression level and GPC diversity. Polymorphisms of this nucleotide can divide all haplotypes into low ( OsGluA2 LET ) and high ( OsGluA2 HET ) expression types. Population genetic and evolutionary analyses reveal that OsGluA2 LET , mainly present in japonica accessions, originates from wild rice. However, OsGluA2 HET , the dominant type in indica , is acquired through mutation of OsGluA2 LET . Our results shed light on the understanding of natural variations of GPC between indica and japonica subspecies.

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