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Background Caryopsis development consists of several processes in the production of grain yield in field crops. This study evaluated the effect of silicon (Si) on spikelet formation, spikelet fertility, and grain filling and its impact on grain yield in rice. Results Applying Si increased grain yield by 44% in Chainat 1( CNT1) and by 23% in Pathumthani 1 (PTT1). With no Si application, CNT1 had fewer total spikelets, and the fertilized and filled spikelets responded more strongly to Si than PTT1 did. Grain yield in both genotypes increased with increasing number of spikelets and filled fertilized grains. There were close relationships between Si concentration in the shoots, flag leaf, and the husk, which were positively correlated with grain yield, the number of spikelets, and fertilized and filled grains. Applying Si fertilizer also increased the expression level of Lsi6 in both CNT1 and PTT1 by 202% and 144% respectively compared with the expression of plants with no Si supplied. Conclusion This study has shown how rice grain yield can be limited by Si deficiency through the spikelet formation, fertilization, and grain filling processes. Applying Si fertilizer could improve rice grain yield through increasing spikelet formation, fertilization, and grain filling, which is in parallel with Lsi6 gene expression. This information can be used for improving rice productivity by Si fertilization management. © 2020 Society of Chemical Industry.