Although great progress has been made in the development of hybrid rice with increased yield, challenges for the improvement of grain quality still remain. In this study, the textural properties of cooked rice and physicochemical characteristics of starch were investigated for 29 new hybrid rice derived from 5 sterile and 11 restorer rice lines. Except for one sterile line Te A (P1) with high apparent amylose content (AAC) (26.9%), all other parents exhibited a low AAC. Gui 263 demonstrated the highest AAC (20.6%) among the restorer lines, so the Te A/Gui 263 hybrid displayed the highest AAC (23.1%) among all the hybrid rice. The mean AAC was similar between sterile, restorer lines and hybrid rice. However, the mean hardness of cooked rice and gels of sterile lines were significantly higher than that of restorer lines and hybrid rice (p < 0.05). Pasting temperature and gelatinization temperatures were significantly higher in the hybrids than in the restorer lines (p < 0.05). Cluster analysis based on the physicochemical properties divided the parents and hybrid rice into two major groups. One group included P1 (Te A), P12 and P14 and three hybrid rice derived from P1, while the other group, including 39 rice varieties, could be further divided into three subgroups. AAC showed significant correlation with many parameters, including peak viscosity, hot peak viscosity, cold peak viscosity, breakdown, setback, onset temperature, peak temperature, conclusion temperature, enthalpy of gelatinization, gel hardness and cooked rice hardness (p < 0.05). Principal component analysis revealed that the first component, comprised of the AAC, peak viscosity, breakdown, setback, onset temperature, peak temperature, conclusion temperature and gel hardness, explained 44.1% of variance, suggesting AAC is the most important factor affecting the grain quality of hybrid rice. Overall, this study enables targeted improvements to key rice grain quality attributes, particularly AAC and textural properties, that will help to develop superior rice varieties.

The Shanlan landrace rice in Hainan Province, China, is a unique upland rice germplasm that holds significant value as a genetic resource for rice breeding. However, its genetic diversity and its usefulness in rice breeding have not been fully explored. In this study, a total of eighty-four Shanlan rice, three typical japonica rice cultivars, and three typical indica rice cultivars were subjected to resequencing of their genomes. As a result, 11.2 million high-quality single nucleotide polymorphisms (SNPs) and 1.6 million insertion/deletions (InDels) were detected. Population structure analysis showed all the rice accessions could be divided into three main groups, i.e., Geng/japonica 1 (GJ1), GJ2, and Xian/indica (XI). However, the GJ1 group only had seven accessions including three typical japonica cultivars, indicating that most Shanlan landrace rice are different from the modern japonica rice. Principal component analysis (PCA) showed that the first three principal components explained 60.7% of the genetic variation. Wide genetic diversity in starch physicochemical parameters, such as apparent amylose content (AAC), pasting viscosity, texture properties, thermal properties, and retrogradation representing the cooking and eating quality was also revealed among all accessions. The genome-wide association study (GWAS) for these traits was conducted and identified 32 marker trait associations in the entire population. Notably, the well-known gene Waxy (Wx) was identified for AAC, breakdown viscosity, and gumminess of the gel texture, and SSIIa was identified for percentage of retrogradation and peak gelatinization temperature. Upon further analysis of nucleotide diversity in Wx, six different alleles, wx, Wx^a, Wx^b, Wxⁱⁿ, Wx^la/mw, and Wx^lv in Shanlan landrace rice were identified, indicating rich gene resources in Shanlan rice for quality rice breeding. These findings are expected to contribute to the development of new rice with premium quality.