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Background  Rice ( Oryza sativa  L.) Chalkiness, the opaque part in the kernel endosperm formed by loosely piled starch and protein bodies. Chalkiness is a complex quantitative trait regulated by multiple genes and various environmental factors. Phytohormones play important roles in the regulation of chalkiness formation but the underlying molecular mechanism is still unclear at present.    Results  In this research, Xiangzaoxian24 (X24, pure line of  indica  rice with high-chalkiness) and its origin parents Xiangzaoxian11 (X11, female parent, pure line of  indica  rice with high-chalkiness) and Xiangzaoxian7 (X7, male parent, pure line of  indica  rice with low-chalkiness) were used as materials. The phenotype, physiological and biochemical traits combined with transcriptome analysis were conducted to illustrate the dynamic process and transcriptional regulation of rice chalkiness formation. Impressively, phytohormonal contents and multiple phytohormonal signals were significantly different in chalky caryopsis, suggesting the involvement of phytohormones, particularly ABA and auxin, in the regulation of rice chalkiness formation, through the interaction of multiple transcription factors and their downstream regulators.    Conclusion  These results indicated that chalkiness formation is a dynamic process associated with multiple genes, forming a complex regulatory network in which phytohormones play important roles. These results provided informative clues for illustrating the regulatory mechanisms of chalkiness formation in rice.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-021-03109-z.

Dynamic formation and transcriptional regulation mediated by phytohormones during chalkiness formation in rice