Resistant starch (RS) can help prevent diabetes and decrease calorie intake and that from plants are the main source of mankind consumption. Rice is many people’s staple food and that with higher RS will help health management. A significantly positive correlation exists between apparent amylose content (AAC) of rice and its RS content. In this study, 72 accessions with moderate or high AAC were selected to explore the regulatory mechanisms and physicochemical properties on different proceeding types of rice RS. RS in raw milled rice (RSm), hot cooked rice (RSc), and retrogradation rice (RSr) showed a wide variation and distinct controlling mechanisms. They were co-regulated by Waxy (Wx), soluble starch synthase (SS) IIb and SSI. Besides that, RSm was also regulated by SSIIa and SSIVb, RSc by granule-bound starch synthase (GBSS) II and RSr by GBSSII and Pullulanase (PUL). Moreover, Wx had significant interactions with SSIIa, SSI, SSIIb and SSIVb on RSm, but only the dominant interactions with SSIIb and SSI on RSc and RSr. Wx was the key factor for the formation of RS, especially the RSc and RSr. The genes had the highest expression at 17 days after flowering and were beneficial for RS formation. The longer the chain length of starch, the higher the RS3 content. RSc and RSr were likely to be contained in medium-size starch granules. The findings favor understanding the biosynthesis of different subtypes of RS.

Glutinous rice (Oryza sativa L.) quality includes thermal properties, retrogradation and pasting viscosity properties, and so on, which have little or no amylose. However, the genetic network regulation of different quality indices has not been systematically studied. The aim was to investigate the relationship between starch synthesis-related genes (SSRGs) and the physicochemical properties of glutinous rice by targeted-gene association analysis (TGAS). The genotypes of 17 SSRGs were analyzed using 46 gene-specific molecular markers in 63 glutinous rice accessions. TGAS and gene interactions analysis indicated that soluble starch synthase (SS) IIa, SSI, starch branching enzyme (BE) IIa, and pullulanase (PUL) had significant genetic effects on glutinous rice quality. SSI and SSIIa were the major genes that regulated thermal properties and retrogradation properties (RP). PUL was central in the regulation of gel consistency (GC), and it participated in the regulation of pasting viscosity parameters (PVP) except for the pasting time and the pasting temperature. BEIIb, ISA1, SSIVb, BEIIa, SSIVa, and their interactions with SSIIa regulated gelatinization temperature (GT) and PVP. The starch properties of glutinous rice are mainly controlled by SSIIa, SSI, PUL, and their interactions, but SSIIa is central among them. These findings indicate that starch properties in glutinous rice have a complex genetic system. It provides crucial information for promoting glutinous rice quality.

The morphology of rice grains represents one of the most vital agronomic characteristics, significantly impacting both grain productivity and the subsequent milling and nutritional quality of the crop. A comprehensive understanding of the genetic basis and molecular drivers of grain shape is vital for the targeted breeding of high-performance rice lines with consistent yield stability. To pinpoint the genomic regions influencing grain dimensions, we conducted a genome-wide association analysis across a panel of 231 distinct rice accessions, focusing on the discovery of loci associated with length and width. Our analysis revealed four consistent quantitative trait loci (QTLs) distributed across chromosomes 3, 4, and 11. Notably, grain length was associated with qGL3.1, qGL3.2, and qGL11. The first two were co-localized with GS3 and SMG3, respectively, whereas qGL11 likely constitutes a novel locus. One QTL, qGW4, which governs grain width, was found to co-localize with the gene OsOFP14. Haplotype analysis further revealed that the characteristic haplotypes of the candidate genes for qGL3.1, qGL3.2, and qGW4 were enriched in eight germplasm accessions (including Newbonnet, Skybonnet, and Lemont), all of which exhibit a slender-grain phenotype. This finding suggests that the specific combination of these characteristic haplotypes is a common genetic signature of slender-grain rice, serving as a potential gene combination for the targeted improvement of rice grain shape. Our results reveal valuable QTLs and candidate genes and highlight specific germplasm resources that can be readily applied in marker-assisted breeding to improve rice grain shape.