Research Article

Enhanced sustainable green revolution yield via nitrogen-responsive chromatin modulation in rice

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Science  07 Feb 2020:
Vol. 367, Issue 6478, eaaz2046
DOI: 10.1126/science.aaz2046

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Decoupling tillering and fertilization

For rice as an agricultural crop, more tillers, or branches that carry grains, are desired, as is less demand for nitrogen fertilization. Unfortunately, for many rice varieties, the number of tillers depends on the amount of nitrogen fertilization. Wu et al. now show that nitrogen status affects chromatin function through modification of histones, a process in which the transcription factor NGR5 recruits polycomb repressive complex 2 to target genes. Some of these genes regulate tillering, such that with more nitrogen, the plants develop more tillers. NGR5 is regulated by proteasomal destruction and mediates hormone signaling. An increase in NGR5 levels can drive increases in rice tillering and yield without requiring increases in nitrogen-rich fertilizer.

Science, this issue p. eaaz2046

Structured Abstract

INTRODUCTION

The green revolution of the 1960s boosted cereal crop yields in part through widespread adoption of semi-dwarf plant varieties. The beneficial semi-dwarfism is respectively conferred in wheat and rice green revolution varieties by mutant Reduced height-1 (Rht-1) and semi-dwarf1 (sd1) alleles. These alleles cause accumulation of growth-repressing DELLA proteins, the normal forms of which are characterized by the presence of an Asp-Glu-Leu-Leu-Ala amino acid motif. Resultant semi-dwarf plants resisted lodging but required high nitrogen fertilizer inputs to maximize yield. Normally, gibberellin promotes growth by stimulating DELLA degradation as regulated by the gibberellin receptor GID1 (GIBBERELLIN INSENSITIVE DWARF1), the F-box protein GID2 (GIBBERELLIN INSENSITIVE DWARF2), and the SCF (Skp, Cullin, F-box–containing) ubiquitin ligase complex. Nitrogen fertilization–induced increase in grain yield is determined by the integration of three components (tiller number, grain number, and grain weight), but exogenous application of gibberellin reduces tiller number in rice. Here, we asked how nitrogen fertilization affects the gibberellin signaling that regulates rice tillering. Nitrogen fertilization promotes crop yield, but overuse in agriculture degrades the environment. A future of sustainable agriculture demands improved nitrogen use efficiency.

RATIONALE

Increased tillering, nitrogen fertilization, and high-density planting all contribute to the high yield typical of green revolution rice varieties. Increases in tiller number despite reduced nitrogen fertilization could help to sustain yield while reducing the environmental impact of agriculture. To investigate the effect of gibberellin on nitrogen-promoted rice tillering, we used genetic screening to identify a mutation in the ngr5 (nitrogen-mediated tiller growth response 5) gene. Plants carrying the ngr5 mutant displayed fewer tillers; tiller number was insensitive to nitrogen supply. Further genetic and biochemical studies defined the mechanisms underlying the interaction between nitrogen- and gibberellin-mediated effects on tiller number.

RESULTS

We found that increased nitrogen supply enhanced transcription and abundance of the rice APETALA2-domain transcription factor encoded by an NGR5 (NITROGEN-MEDIATED TILLER GROWTH RESPONSE 5) allele. NGR5 interacts with a component of the polycomb repressive complex 2 (PRC2) and alters the genome-wide histone H3 lysine 27 trimethylation (H3K27me3) pattern response to changes in nitrogen availability. The extent of this alteration was reduced in ngr5 plants or by gibberellin treatment. RNA sequencing and chromatin immunoprecipitation (ChIP)–polymerase chain reaction analysis showed that an increase in nitrogen supply reduced the abundance of mRNAs specified by strigolactone signaling and other branching-inhibitory genes [such as Dwarf14 (D14) and squamosa promoter binding protein-like–14 (OsSPL14)] in a dosage-dependent manner. Lack of D14 or OsSPL14 function was epistatic to ngr5 in regulating rice tillering. We next found that the DELLA-mediated enhancement of nitrogen-induced tiller number, typical of green revolution rice varieties, was abolished in plants with the ngr5 mutation.

These observations suggest that NGR5-driven recruitment of PRC2 promotes repressive H3K27me3 modification of target branching-inhibitory genes, thus causing an increase in tiller number. On the other hand, a nitrogen-induced NGR5-dependent increase in tiller number is enhanced in green revolution rice varieties, and this effect is inhibited by gibberellin treatment. Although NGR5 abundance is negatively associated with gibberellin amount, gibberellin-promoted destabilization of NGR5 is neither dependent on nor downstream of gibberellin-induced DELLA destruction. Moreover, NGR5 interacts with the gibberellin receptor GID1 and DELLA proteins; this suggests that gibberellin-promoted proteasomal destruction of NGR5 is not due to gibberellin-promoted destruction of DELLAs, but is due to a gibberellin-potentiated interaction of NGR5-GID1, leading to polyubiquitination of NGR5 and subsequent destruction in the proteasome. Accumulation of DELLA proteins competitively inhibited the GID1-NGR5 interaction, thus stabilizing NGR5 by reducing its gibberellin-GID1–mediated destruction.

CONCLUSION

We conclude that nitrogen fertilization alters genome-wide reprogramming of H3K27me3 methylation via NGR5-dependent recruitment of PRC2. In rice, methylation represses genes that inhibit tillering and consequently promotes an increase in tiller number. NGR5 is a target of gibberellin-GID1–promoted proteasomal destruction. Modulation of competitive interactions among NGR5, DELLA proteins, and GID1 enables enhanced grain yield in elite rice varieties despite reduced nitrogen fertilizer inputs. Such shifts in yield and input use could promote agricultural sustainability and food security.

Nitrogen-responsive chromatin modulation enhances rice tillering.

The rice transcription factor NGR5 facilitates nitrogen-dependent recruitment of PRC2 to repress expression of shoot branching-inhibitory genes, thus promoting tillering in response to increasing nitrogen supply. NGR5 interacts with the gibberellin receptor GID1 and with growth-repressing DELLA proteins. DELLA accumulation competitively inhibits the GID1-NGR5 interaction, thus stabilizing NGR5 by reducing gibberellin- and GID1-promoted proteasomal destruction.

Abstract

Because environmentally degrading inorganic fertilizer use underlies current worldwide cereal yields, future agricultural sustainability demands enhanced nitrogen use efficiency. We found that genome-wide promotion of histone H3 lysine 27 trimethylation (H3K27me3) enables nitrogen-induced stimulation of rice tillering: APETALA2-domain transcription factor NGR5 (NITROGEN-MEDIATED TILLER GROWTH RESPONSE 5) facilitates nitrogen-dependent recruitment of polycomb repressive complex 2 to repress branching-inhibitory genes via H3K27me3 modification. NGR5 is a target of gibberellin receptor GIBBERELLIN INSENSITIVE DWARF1 (GID1)–promoted proteasomal destruction. DELLA proteins (characterized by the presence of a conserved aspartate-glutamate-leucine-leucine-alanine motif) competitively inhibit the GID1-NGR5 interaction and explain increased tillering of green revolution varieties. Increased NGR5 activity consequently uncouples tillering from nitrogen regulation, boosting rice yield at low nitrogen fertilization levels. NGR5 thus enables enhanced nitrogen use efficiency for improved future agricultural sustainability and food security.

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