Vacuolar invertase is involved in sugar metabolism and plays a crucial role in plant growth and development, thus regulating seed size. However, information linking vacuolar invertase and seed size in rice is limited. Here we characterized a small grain mutant sg2 (grain size on chromosome 2) that showed a reduced in grain size and 1000-grain weight compared to the wild type. Map-based cloning and genetic complementation showed that OsINV3 is responsible for the observed phenotype. Loss-of-function of OsINV3 resulted in grains of smaller size when compared to the wild type, while overexpression showed increased grain size. We also obtained a T-DNA insertion mutant of OsINV2, which is a homolog of OsINV3 and generated double knockout (KO) mutants of OsINV2 and OsINV3 using CRISPR/Cas9. Genetic data showed that OsINV2, that has no effect on grain size by itself, reduces grain length and width in the absence of OsINV3. Altered sugar content with increased sucrose and decreased hexose levels, as well as changes vacuolar invertase activities and starch constitution in INV3^KO, INV2^KO, INV3^KOINV2^KO mutants indicate that OsINV2 and OsINV3 affect sucrose metabolism in sink organs. In summary, we identified OsINV3 as a positive regulator of grain size in rice, and while OsINV2 has no function on grain size by itself. In the absence of OsINV3, it is possible to detect a role of OsINV2 in the regulation of grain size. Both OsINV3 and OsINV2 are involved in sucrose metabolism, and thus regulate grain size. Our findings increase our understanding of the role of OsINV3 and its homolog, OsINV2, in grain size development and also suggest a potential strategy to improve grain yield in rice.

The role of rice genomics in breeding progress is becoming increasingly important. Deeper research into the rice genome will contribute to the identification and utilization of outstanding functional genes, enriching the diversity and genetic basis of breeding materials and meeting the diverse demands for various improvements. Here, we review the significant contributions of rice genomics research to breeding progress over the last 25 years, discussing the profound impact of genomics on rice genome sequencing, functional gene exploration, and novel breeding methods, and we provide valuable insights for future research and breeding practices.

Background: Male sterility is a critical trait for large-scale hybrid rice seed production, yet the genetic and molecular regulatory networks governing tapetal degradation during anther development remain incompletely understood. This study aimed to clone the causal gene underlying a novel rice non-pollen male sterility mutant and elucidate its role in tapetal development and microsporogenesis. Methods: The nms1 (non-pollen male sterility 1) sterile mutant was screened from the ethyl methanesulfonate (EMS)-mutagenized progeny of the elite indica restorer line Shuhui 498 (R498). Map-based cloning and whole-genome resequencing-assisted bulked segregant analysis were used to identify the causal variant. Gene function was verified via cytological observation, genetic complementation testing, RNA sequencing, and quantitative real-time PCR (qRT-PCR) to profile sterility-associated transcriptional changes. Results: Gene mapping identified a T635A single-nucleotide substitution within OsR498G0305626400.01 on chromosome 3, which encodes a strictosidine synthase-like protein. This nucleotide alteration causes a Val212Glu amino acid change and is associated with delayed tapetal degradation and pollen abortion. Transgenic complementation experiments verified that functional NMS1 restores fertility in nms1 mutant plants. Spatiotemporal expression analysis showed predominant NMS1 expression in late-developing spikelets. Furthermore, combined RNA sequencing and qRT-PCR analyses demonstrated that loss of NMS1 function leads to significant transcriptional dysregulation of key regulators of programmed cell death (PCD) in the tapetum (PTC2, TIP2) and pollen wall biosynthesis genes (TIP3, OsMS2). Conclusions: This study demonstrates that NMS1 plays a crucial role in coordinating tapetal degradation and microspore development in rice. The discovered functional SNP of NMS1 provides a novel theoretical foundation and a valuable sterile genetic resource for hybrid rice breeding.