Susong Zhu

Background: The differing floret opening times between subsp. indica and subsp. japonica in rice limit the potential for increased hybrid seed production. Objectives: To elucidate the physiological basis underlying the differences in floret opening time between indica and japonica rice. Materials: A comparative analysis involved nine indica and ten japonica rice varieties. Methods: Using paraffin sectioning, transcriptome sequencing, RT-PCR, and endogenous substance quantification, we investigated the structural variations in floral organs, the differences in the initiation timing of floret opening regulatory pathways, and endogenous regulators. Results: The results indicated insignificant differences in lemma thickness, lodicule thickness, lodicule area, and the coupling-lodicule length between indica and japonica rice. However, japonica rice exhibited larger lodicule-lemma gaps and more vascular bundles compared to indica rice. Within the 9:00 a.m. to 10:00 a.m. interval, the expression of OsAOS1 in α-linolenic acid metabolism and OsISA3 in starch and sucrose metabolism notably increased in indica rice, with no significant change in japonica rice. Additionally, the endogenous JA and α-amylase surged more significantly in indica rice than in japonica rice. The increase in soluble carbohydrate in indica rice is greater than in japonica rice, but the difference is not significant. Conclusions: These findings suggest that in the process of the floret opening, the α-linolenic acid metabolism and starch and sucrose metabolism are initiated earlier in indica rice, accompanied by a more pronounced elevation in endogenous JA and α-amylase. Furthermore, the smaller lodicule-lemma gap in indica rice contributes to earlier floret opening compared to japonica rice.

Given the notable ecological and breeding disparities between southern and northern rice regions, delving into the genetic diversity and divergence between southern and northern japonica rice contributes to enhancing the genetic pool for japonica rice breeding. In this study, we analyzed 90 southern and 51 northern japonica rice varieties, focusing on nucleotide diversity (Pi), agronomic trait variations, population structure, genetic divergence, and a neutral test. For genetic diversity, the results demonstrated higher Pi in northern japonica rice varieties (NJRVs) on Chr2, Chr5, Chr6, Chr8, and Chr10, whereas in southern japonica rice varieties (SJRVs) on Chr7 and Chr9. In addition, SJRVs exhibited higher grain width and thickness, whereas NJRVs featured a higher grain aspect ratio, filled grain number, and grain number per panicle. Regarding genetic divergence, geographic differentiation existed between NJRVs and SJRVs, with Chr5 exhibiting numerous higher genetic differentiation windows, including cloned grain shape-controlling genes RGA1 and SFD5, stemming from intensified selection pressure on SJRVs. In summary, SJRVs and NJRVs exhibited diversity differences and genetic differentiation. Hence, it was suggested to conduct genetic introgression between NJRVs and SJRVs to broaden the genetic basis of the local japonica rice germplasm. By exploiting their heterotic advantage, new japonica rice cultivars with superior comprehensive traits could be developed.