Suppressing a phosphohydrolase of cytokinin nucleotide enhances grain yield in rice

One-step and two-step pathways are proposed to synthesize cytokinin. One-step pathway is mediated by LONELY GUY (LOG) proteins. However, the enzyme for two-step pathway has not been identified yet. Here, we show that a QTL GY3 boosts grain yield by more than 20% via manipulating two-step pathway. GY3 encodes a LOG protein that acts as a 5’-ribonucleotide phosphohydrolase by excessive consuming the cytokinin precursors, which contrasts with the activity of canonical LOG members as phosphoribohydrolases in a one-step pathway. The residue S41 of GY3 is crucial for the dephosphorylation of iPRMP. A solo-LTR insertion within the promoter of GY3 suppressed its expression and resulted in a higher content of active cytokinins in young panicles. Introgression of GY302428 increased grain yield per plot by 7.4% to 16.3% in all investigated indica backgrounds both under long-day and short-day conditions, which demonstrates the great value of GY302428 in indica rice production. eChip-seq of panicle with two replicates