Comparative proteomics analysis of superior and inferior spikelets in hybrid rice during grain filling and response of inferior spikelets to drought stress using isobaric tags for relative and absolute quantification

Abstract The biological functions of the differentially abundant proteins between superior and inferior spikelet grains were investigated based on the isobaric tags for relative and absolute quantification to further clarify the mechanism of rice grain filling at the proteomic level, as well as the response of inferior spikelets to drought dress (− 20 kPa or − 40 kPa). Compared with superior spikelets, inferior ones had lower sink strength due to the lower sink activities (lower abundances of ADP-glucose pyrophosphorylase, granule-bound starch synthase, starch branching enzyme and pullulanase) and smaller sink sizes (lower abundances of structural proteins). The slower and later grain filling resulted from the weaker decomposition and conversion of photoassimilate and the slower cell division. Moderate drought stress (− 20 kPa) promoted the grain filling of inferior spikelets through regulating the proteins associated with photoassimilate supply and conversion. These proteins may be important targets for rice breeding programs that raise the rice yield under drought condition. The findings offer new insights into rice grain-filling and provide theoretical evidences for better quality control and scientific improvement of super rice in practice. Biological significance Rice cultivars with large panicles do not always guarantee high yield and grain quality probably due to the slow grain filling and many unfilled grains of inferior spikelets. In general, earlier-flowering superior spikelets, which are usually located on apical primary branches, fill faster and produce larger and heavier grains. In contrast, later-flowering inferior spikelets located on proximal secondary branches are either sterile or fill slowly and poorly, and the differences are more significant in large panicle rice or super rice. The increase of rice yield has been limited by the unsatisfactory grain filling of inferior spikelets, and the inferior spikelets are more prone to environmental factors during grain filling. Thus, we herein investigated the biological functions of differently abundant proteins between superior and inferior spikelet grains by using iTRAQ to unravel the mechanism of rice grain filling and the response of inferior spikelets to drought stress at proteomic level. This study offers new insights into rice grain-filling and provides valuable evidences for better quality control and scientific improvement of super rice in practice.