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Strigolactones （SLs）, a group of carotenoid derived terpenoid lactones, are root-to-shoot phytohormones sup- pressing shoot branching by inhibiting the outgrowth of axillary buds. DWARF 53 （D53）, the key repressor of the SL signaling pathway, is speculated to regulate the downstream transcriptional network of the SL response. However, no downstream transcription factor targeted by D53 has yet been reported. Here we report that Ideal Plant Architecture 1 （IPA1）, a key regulator of the plant architecture in rice, functions as a direct downstream component of D53 in reg- ulating tiller number and SL-induced gene expression. We showed that D53 interacts with IPA1 in vivo and in vitro and suppresses the transcriptional activation activity of IPA1. We further showed that IPA1 could directly bind to the D53 promoter and plays a critical role in the feedback regulation of SL-induced D53 expression. These findings re- veal that IPA1 is likely one of the long-speculated transcription factors that act with D53 to mediate the SL-regulated tiller development in rice.

Plant architecture, a collection of genetically controlled agronomic traits, is one of the decisive factors that determine grain production. IDEAL PLANT ARCHITECTURE1 (IPA1) encodes a key transcription factor with pleiotropic effects on regulating plant architecture in rice (Oryza sativa), and IPA1 expression is controlled at the posttranscriptional level by microRNA156 and microRNA529. Here, we report the identification and characterization of IPA1 INTERACTING PROTEIN1 (IPI1), a RING-finger E3 ligase that can interact with IPA1 in the nucleus. IPI1 promotes the degradation of IPA1 in panicles, while it stabilizes IPA1 in shoot apexes. Consistent with these findings, the ipi1 loss-of-function mutants showed markedly altered plant architecture, including more tillers, enlarged panicles, and increased yield per plant. Moreover, IPI1 could ubiquitinate the IPA1-mediated complex with different polyubiquitin chains, adding K48-linked polyubiquitin chains in panicles and K63-linked polyubiquitin chains in the shoot apex. These results demonstrate that IPI1 affects plant architecture through precisely tuning IPA1 protein levels in different tissues in rice and provide new insight into the tissue-specific regulation of plant architecture and important genetic resources for molecular breeding.

Tiller angle in cereals is a key shoot architecture trait that strongly influences grain yield. Studies in rice (Oryza sativa) have implicated shoot gravitropism in the regulation of tiller angle. However, the functional link between shoot gravitropism and tiller angle is unknown. Here, we conducted a large-scale transcriptome analysis of rice shoots in response to gravistimulation and identified two new nodes of a shoot gravitropism regulatory gene network that also controls rice tiller angle. We demonstrate that HEAT STRESS TRANSCRIPTION FACTOR 2D (HSFA2D) is an upstream positive regulator of the LAZY1-mediated asymmetric auxin distribution pathway. We also show that two functionally redundant transcription factor genes, WUSCHEL RELATED HOMEOBOX6 (WOX6) and WOX11, are expressed asymmetrically in response to auxin to connect gravitropism responses with the control of rice tiller angle. These findings define upstream and downstream genetic components that link shoot gravitropism, asymmetric auxin distribution, and rice tiller angle. The results highlight the power of the high-temporal-resolution RNA-seq data set and its use to explore further genetic components controlling tiller angle. Collectively, these approaches will identify genes to improve grain yields by facilitating the optimization of plant architecture.

Jiayang Li, Xudong Zhu, Qian Qian and colleagues report cloning of the Grain Length on Chromosome 7 ( GL7 ) locus in rice and identify a copy number variant that increases grain length and improves grain quality. They demonstrate how interactions with other grain length–related genes may be used to improve breeding. Copy number variants (CNVs) are associated with changes in gene expression levels and contribute to various adaptive traits 1 , 2 . Here we show that a CNV at the Grain Length on Chromosome 7 ( GL7 ) locus contributes to grain size diversity in rice ( Oryza sativa L.). GL7 encodes a protein homologous to Arabidopsis thaliana LONGIFOLIA proteins, which regulate longitudinal cell elongation. Tandem duplication of a 17.1-kb segment at the GL7 locus leads to upregulation of GL7 and downregulation of its nearby negative regulator, resulting in an increase in grain length and improvement of grain appearance quality. Sequence analysis indicates that allelic variants of GL7 and its negative regulator are associated with grain size diversity and that the CNV at the GL7 locus was selected for and used in breeding. Our work suggests that pyramiding beneficial alleles of GL7 and other yield- and quality-related genes may improve the breeding of elite rice varieties.

The phytohormone auxin regulates nearly all aspects of plant growth and development. Tremendous achievements have been made in elucidating the tryptophan (Trp)-dependent auxin biosynthetic pathway; however, the genetic evidence, key components, and functions of the Trp-independent pathway remain elusive. Here we report that the Arabidopsis indole synthase mutant is defective in the long-anticipated Trp-independent auxin biosynthetic pathway and that auxin synthesized through this spatially and temporally regulated pathway contributes significantly to the establishment of the apical–basal axis, which profoundly affects the early embryogenesis in Arabidopsis . These discoveries pave an avenue for elucidating the Trp-independent auxin biosynthetic pathway and its functions in regulating plant growth and development. Significance The phytohormone indole-3-acetic acid (IAA) plays a vital role in plant growth and development. IAA can be synthesized through the precursor tryptophan (Trp), known as the Trp-dependent IAA biosynthetic pathway. However, IAA may also be synthesized through a proposed Trp-independent IAA biosynthetic pathway. Although the Trp-independent IAA biosynthesis was hypothesized 20 years ago, it remains a mystery. In this paper, we provide compelling evidence that the cytosol-localized indole synthase (INS) initiates the Trp-independent IAA biosynthetic pathway and that the spatial and temporal expression of INS plays an important role in the establishment of the apical–basal pattern during early embryogenesis, demonstrating that the Trp-dependent and -independent IAA biosynthetic pathways coordinately regulate embryogenesis of higher plants.

Pan-genomes from large natural populations can capture genetic diversity and reveal genomic complexity. Using de novo long-read assembly, we generated a graph-based super pan-genome of rice consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice. Our pan-genome reveals extensive structural variations (SVs) and gene presence/absence variations. Additionally, our pan-genome enables the accurate identification of nucleotide-binding leucine-rich repeat genes and characterization of their inter- and intraspecific diversity. Moreover, we uncovered grain weight-associated SVs which specify traits by affecting the expression of their nearby genes. We characterized genetic variants associated with submergence tolerance, seed shattering and plant architecture and found independent selection for a common set of genes that drove adaptation and domestication in Asian and African rice. This super pan-genome facilitates pinpointing of lineage-specific haplotypes for trait-associated genes and provides insights into the evolutionary events that have shaped the genomic architecture of various rice species.

IDEAL PLANT ARCHITECTURE1 (IPA1) is critical in regulating rice (Oryza sativa) plant architecture and substantially enhances grain yield. To elucidate its molecular basis, we first confirmed IPA1 as a functional transcription activator and then identified 1067 and 2185 genes associated with IPA1 binding sites in shoot apices and young panicles, respectively, through chromatin immunoprecipitation sequencing assays. The SQUAMOSA PROMOTER BINDING PROTEIN-box direct binding core motif GTAC was highly enriched in IPA1 binding peaks; interestingly, a previously uncharacterized indirect binding motif TGGGCC/T was found to be significantly enriched through the interaction of IPA1 with proliferating cell nuclear antigen PROMOTER BINDING FACTOR1 or PROMOTER BINDING FACTOR2. Genome-wide expression profiling by RNA sequencing revealed IPA1 roles in diverse pathways. Moreover, our results demonstrated that IPA1 could directly bind to the promoter of rice TEOSINTE BRANCHED1, a negative regulator of tiller bud outgrowth, to suppress rice tillering, and directly and positively regulate DENSE AND ERECT PANICLE1, an important gene regulating panicle architecture, to influence plant height and panicle length. The elucidation of target genes of IPA1 genome-wide will contribute to understanding the molecular mechanisms underlying plant architecture and to facilitating the breeding of elite varieties with ideal plant architecture.

Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching. SL signalling requires the hormone-dependent interaction of DWARF 14 (D14), a probable candidate SL receptor, with DWARF 3 (D3), an F-box component of the Skp–Cullin–F-box (SCF) E3 ubiquitin ligase complex. Here we report the characterization of a dominant SL-insensitive rice ( Oryza sativa ) mutant dwarf 53 ( d53 ) and the cloning of D53 , which encodes a substrate of the SCF D3 ubiquitination complex and functions as a repressor of SL signalling. Treatments with GR24, a synthetic SL analogue, cause D53 degradation via the proteasome in a manner that requires D14 and the SCF D3 ubiquitin ligase, whereas the dominant form of D53 is resistant to SL-mediated degradation. Moreover, D53 can interact with transcriptional co-repressors known as TOPLESS-RELATED PROTEINS. Our results suggest a model of SL signalling that involves SL-dependent degradation of the D53 repressor mediated by the D14–D3 complex. Strigolactones (SLs), key regulators of plant growth, are believed to mediate their responses through a proposed receptor (D14) that interacts with an F-box protein (D3) to form a D14–SCF D3 protein complex; here the perception of SLs by the D14–SCF D3 complex and the control of gene expression are linked by the finding that DWARF 53, a repressor protein of SL signalling, interacts with the D14–SCF D3 complex and is ubiquitinated and degraded in a SL-dependent manner. Strigolactone receptor identified The strigolactones are key regulators of plant growth, controlling the formation of secondary shoots and regulating root branching. Strigolactone responses are mediated through a proposed receptor (D14) that interacts with an F-box protein (D3). Now, in two related publications, Liang Jiang et al . and Feng Zhou et al . demonstrate a functional link between the perception of strigolactones by D14/D3 and the control of gene expression in rice. They show that the protein DWARF53 (D53), of previously unknown function, acts as a repressor of strigolactone signalling and that strigolactones induce its degradation. D53 interacts with the D14–D3 complex and is ubiquitinated and degraded by the proteasome in a strigolactone-dependent manner.

Programmed cell death （PCD） is of fundamental importance to development and defense in animals and plants. In plants, a well-recognized form of PCD is hypersensitive response （HR） triggered by pathogens, which involves the generation of reactive oxygen species （ROS） and other signaling molecules. While the mitochondrion is a master reg- ulator of PCD in animals, the chloroplast is known to regulate PCD in plants. Arabidopsis Mosaic Death 1 （MOD1）, an enoyl-acyl carrier protein （ACP） reductase essential for fatty acid biosynthesis in chloroplasts, negatively regulates PCD in Arabidopsis. Here we report that PCD in modl results from accumulated ROS and can be suppressed by mu- tations in mitochondrial complex I components, and that the suppression is confirmed by pharmaceutical inhibition of the complex 1-generated ROS. We further show that intact mitochondria are required for full HR and optimum disease resistance to the Pseudomonas syringae bacteria. These findings strongly indicate that the ROS generated in the electron transport chain in mitochondria plays a key role in triggering plant PCD and highlight an important role of the communication between chloroplast and mitochondrion in the control of PCD in plants.

Phytohormones performed critical roles in regulating plant architecture and thus determine grain yield in rice. However, the roles of brassinosteroids (BRs) compared to other phytohormones in shaping rice architecture are less studied. In this study, we report that BR hypersensitive1 (BHS1) plays a negative role in BR signaling and regulate rice architecture. BHS1 encodes the kinesin-13a protein and regulates grain length. We found that bhs1 was hypersensitive to BR, while BHS1-overexpression was less sensitive to BR compare to WT. BHS1 was down-regulated at RNA and protein level upon exogenous BR treatment, and proteasome inhibitor MG132 delayed the BHS1 degradation, indicating that both the transcriptional and posttranscriptional regulation machineries are involved in BHS1-mediated regulation of plant growth and development. Furthermore, we found that the BR-induced degradation of BHS1 was attenuated in Osbri1 and Osbak1 mutants, but not in Osbzr1 and Oslic mutants. Together, these results suggest that BHS1 is a novel component which is involved in negative regulation of the BR signaling downstream player of BRI1.