Transcriptomic analysis offers deep insights into the Increased Grain Length 1 (IGL1) regulation of grain length

Although great progress has been made in recent years in identifying novel genes or natural alleles for rice yield improvement, the molecular mechanisms of how these genes/natural alleles regulate yield-associated traits, such as grain length and 1000-grain weight, remain largely unclear. An in-depth understanding of the roles of these genes/natural alleles in controlling yield traits become a necessity to ultimately increase rice yield via novel molecular techniques, such as gene editing.

In this study, the roles of IGL1, which was previously identified through a map-based cloning approach, in the regulation of grain length were investigated by overexpressing and knocking out it in the Nipponbare genetic background. Overexpression and knockout of IGL1 (the resulting transgenic lines were hereafter designated IGL1-OE and IGL1-CR lines, respectively) led to elongation and shortening of grains, respectively. To further elucidate the molecular mechanisms behind the IGL1 action, young panicles from IGL1-OE and IGL1-CR lines were subjected to mRNA sequencing. The results showed that both overexpression and knockout of IGL1 all resulted in a large number of upregulated and downregulated differentially expression genes (DEGs) relative to wild-type NPB control lines. A total of 984 DEGs overlapped between upregulated DEGs from IGL1-OE and downregulated DEGs from IGL1-CR; 1146 DEGs were common to downregulated DEGs from IGL1-OE and upregulated DEGs from IGL1-CR. GO term and KEGG pathway analysis revealed that IGL1-upregulated DEGs were associated with extracellular region, protein ubiquitination, cell-wall modification, BR signaling, cell cycle, etc.; by comparison, the IGL1-downregulated DEGs were connected with extracellular region, response to wounding, flavonoid biosynthesis, jasmonic-acid signaling, glucose/sucrose metabolism, etc. Some phytohormone-associated genes (like OsYUCCA4, OsPIN10b, OsBAK1, and OsDLT), TF genes (like OsMADS1 and OsGASR9), grain length-regulating genes (like An-1, GS9, OsIQD14, and TGW2) showed significant upregulation or downregulation in IGL1-OE or IGL1-CR.

Our result clearly demonstrated that IGL1 is an important regulator of grain length, and has profound impacts on genome-wide gene expression, suggesting that it may work together with certain TFs. Overexpression or knockout of IGL1 appears to cause complex expression changes of genes associated with phytohormones, TFs, grain length-regulating factors, which ultimately brings about the grain elongation.