Transcriptomic analyses of IGL1 effects on grain elongation

In this study, the roles of IGL1, which is previously identified through the map-based cloning, in the regulation of grain length are investigated by overexpressing and knocking out it in the Nipponbare genetic background. Overexpression and knockout of IGL1 (the resulting transgenic lines are hereafter designated IGL1-OE and IGL1-CR lines, respectively) lead to elongation and shortening of grain, respectively. To further elucidate the molecular mechanism behind IGL1 action, the young panicles from IGL1-OE and IGL1-CR lines are subjected to RNA sequencing. The results show that both overexpression and knockout of IGL1 all result in a large number of upregulated and downregulated differentially expression genes (DEGs). A total of 984 DEGs overlapping between upregulated DEGs from IGL1-OE and downregulated DEGs from IGL1-CR; 1146 DEGs are common to downregulated DEGs from IGL1-OE and upregulated DEGs from IGL1-CR. GO term and KEGG pathway analysis reveal that IGL1-upregulated DEGs are associated with extracellular region, protein ubiquitination, cell-wall modification, BR singaling, cell cycle, etc.; by comparison, the IGL1-downregulated DEGs are connected with extracellular region, response to wounding, flavonoid biosynthesis, jasmonic-acid signaling, glucose/sucrose metabolism, etc. Some phytohormone-associated genes (like OsYUCCA4, OsPIN10b, OsBAK1, OsDLT), transcription factor genes (like OsMADS1, OsGASR9), grain length-regulating genes (like An-1, GS9, OsIQD14, TGW2) show significant upregulation or downregulation in IGL1-OE or IGL1-CR line relative to wild-type NPB line. Our result clearly demonstrate that IGL1 is an important regulator of grain length, and has profound impact on genome-wide gene expression.