Suppressing a phosphohydrolase of cytokinin nucleotide enhances grain yield in rice.

One-step and two-step pathways are proposed to synthesize cytokinin in plants. The one-step pathway is mediated by LONELY GUY (LOG) proteins. However, the enzyme for the two-step pathway remains to be identified. Here, we show that quantitative trait locus GY3 may boost grain yield by more than 20% through manipulating a two-step pathway. Locus GY3 encodes a LOG protein that acts as a 5'-ribonucleotide phosphohydrolase by excessively 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 to produce iPR. 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, which demonstrates the great value of GY302428 in indica rice production.

Fixation of hybrid sterility genes and favorable alleles of key yield-related genes with dominance contribute to the high yield of the Yongyou series of intersubspecific hybrid rice.

In rice, the Yongyou series of Xian-Geng intersubspecific hybrids have excellent production performance, as shown by their extremely high yield. However, the mechanisms underlying the success of these rice hybrids are unclear. In this study, three F2 populations are generated from three Yongyou hybrids to determine the genetic basis of the extremely high yield of intersubspecific hybrids. Genome constitution analysis reveals that the female and male parental lines belong to the Geng and Xian subspecies, respectively, although introgression of 20% of the Xian ancestry and 14% of the Geng ancestry are observed. Twenty-five percent of the hybrid genomes carries homozygous Xian or Geng fragments, which harbors hybrid sterility genes such as Sd, Sc, f5, and qS12 and favorable alleles of key yield-related genes, including NAL1, Ghd7, and Ghd8. None of the parents carries the S5+ killer of the S5 killer-protector system. Compatible allele combinations of hybrid sterility genes ensure the fertility of these intersubspecific hybrids and overcome the bottleneck in applying intersubspecific hybrids. Additive effects of favorable alleles of yield-related genes fixed in both parents enhances midparent values. Many QTLs for yield and its key component spikelets per panicle shows dominance and the net positive dominant effects lead to heterosis. These factors result in an extremely high yield of the hybrids. These findings will aid in the development of new intersubspecific rice hybrids with diverse genetic backgrounds.