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The indica rice variety XYXZ carries elite traits including appearance and eating quality. Here, we report the de novo assembly of XYXZ using Illumine paired-end whole-genome shotgun sequencing and Nanopore sequencing. We annotated 39,722 protein-coding genes in the 395.04 Mb assembly. In comparison to other cultivars, XYXZ showed a larger gene size including the transcripts and introns, and more exons per gene. And hundreds of ultra-long genes were also detected. A total of 4362 complete LTRs were annotated, and among them, many were located next to or in protein-coding genes including several genes related to rice quality. We observed the different distributions of LTRs in these genes among XYXZ, Nipponbare, and R498, implying these LTRs might potentially affect expressions of the proximal genes and rice quality. Overall, This chromosome-length genome assembly of XYXZ provides a valuable resource for gene discovery, genetic variation and evolution, and the breeding of high-quality rice., (© 2023. The Author(s).)

Key Message: RIP2 serves as a negative regulator of leaf inclination through the coordination of BR signaling in rice. Leaf angle is considered as an important morphological trait in rice. Appropriate leaf angle increases the efficiency of sunlight capture and maintains a high level of photosynthesis, ultimately improving crop yield. Our present study demonstrates that RIP2 encodes a RING finger E3 ligase protein that directly binds to ROLLED AND ERECT LEAF 1 (REL1), a key regulator of leaf morphogenesis. Further studies reveal that RIP2 is extensively involved in leaf inclination through the coordination of BR signaling. Repression of RIP2 led to altered phenotypes, including enlarged leaf inclination and fewer tillers. Conversely, rice overexpressing RIP2 exhibited erect leaves. The double mutant rel1 rip2 displayed phenotypes similar to those of rel1, characterized by rolled leaves. Transcriptome profiling of WT, rel1, rip2, and rel1 rip2 mutants revealed that BR and IAA signaling pathways were impaired in rip2. Moreover, rel1, rip2, and rel1 rip2 were insensitive to BR treatment. In summary, these findings demonstrate that RIP2 serves as a negative regulator of leaf inclination, and therefore, provides an approach for the optimization of an ideal plant type., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Background: Mitogen-activated protein kinase (MAPK) cascades are conserved signaling modules in eukaryotic organisms and play essential roles in immunity and stress responses. However, the role of MAPKs in chloroplast development remains to be evidently established., Results: In this study, a rice chlorosis seedling lethality 1 (csl1) mutant with a Zhonghua11 (ZH11, japonica) background was isolated. Seedlings of the mutant were characterized by chlorotic leaves and death after the trefoil stage, and chloroplasts were observed to contain accumulated starch granules. Molecular cloning revealed that OsCSL1 encoded a MAPK kinase kinase22 (MKKK22) targeted to the endoplasmic reticulum (ER), and functional complementation of OsCSL1 was found to restore the normal phenotype in csl1 plants. The CRISPR/Cas9 technology was used for targeted disruption of OsCSL1, and the OsCSL1-Cas9 lines obtained therein exhibited yellow seedlings which phenocopied the csl1 mutant. CSL1/MKKK22 was observed to establish direct interaction with MKK4, and altered expression of MKK1 and MKK4 was detected in the csl1 mutant. Additionally, disruption of OsCSL1 led to reduced expression of chloroplast-associated genes, including chlorophyll biosynthetic genes, plastid-encoded RNA polymerases, nuclear-encoded RNA polymerase, and nuclear-encoded chloroplast genes., Conclusions: The findings of this study revealed that OsCSL1 played roles in regulating the expression of multiple chloroplast synthesis-related genes, thereby affecting their functions, and leading to wide-ranging defects, including chlorotic seedlings and severely disrupted chloroplasts containing accumulated starch granules., (© 2022. The Author(s).)

Plant architecture is an important factor for crop production. Plant height, tiller pattern, and panicle morphology are decisive factors for high grain yield in rice. Here, we isolated and characterized a T-DNA insertion rice mutant Osdmt1 (Oryza sativa dwarf and multi-tillering1) that exhibited a severe dwarf phenotype and multi-tillering. Molecular cloning revealed that DMT1 encodes a plasma membrane protein that was identified as a putative Ca 2+ permeable mechanosensitive channel. The transcript expression level was significantly higher in the dmt1 mutant compared to wild type (WT). Additionally, the dmt1 homozygous mutant displayed a stronger phenotype than that of the WT and heterozygous seedlings after gibberellic acid (GA) treatment. RNA-seq and iTRAQ-based proteome analyses were performed between the dmt1 mutant and WT. The transcriptome profile revealed that several genes involved in GA and strigolactone (SL) biosyntheses were altered in the dmt1 mutant. Ca 2+ and other ion concentrations were significantly enhanced in the dmt1 mutant, suggesting that DMT1 contributes to the accumulation of several ions in rice. Moreover, several EF-hand Ca 2+ sensors, including CMLs (CaM-like proteins) and CDPKs (calcium-dependent protein kinases), displayed markedly altered transcript expression and protein levels in the dmt1 mutant. Overall, these findings aid in the elucidation of the multiply regulatory roles of OsDMT1/OsMCA1 in rice., Competing Interests: The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Key Message: Rice leucine-rich repeat extensin-like protein OsPEX1 mediates the intersection of lignin deposition and plant growth. Lignin, a major structural component of secondary cell wall, is essential for normal plant growth and development. However, the molecular and genetic regulation of lignin biosynthesis is not fully understood in rice. Here we report the identification and characterization of a rice semi-dominant dwarf mutant (pex1) with stiff culm. Molecular and genetic analyses revealed that the pex1 phenotype was caused by ectopic expression of a leucine-rich repeat extension-like gene, OsPEX1. Interestingly, the pex1 mutant showed significantly higher lignin content and increased expression levels of lignin-related genes compared with wild type plants. Conversely, OsPEX1-suppresssed transgenics displayed low lignin content and reduced transcriptional abundance of genes associated with lignin biosynthesis, indicating that the OsPEX1 mediates lignin biosynthesis and/or deposition in rice. When OsPEX1 was ectopically expressed in rice cultivars with tall stature that lacks the allele of semi-dwarf 1, well-known green revolution gene, the resulting transgenic plants displayed reduced height and enhanced lodging resistance. Our study uncovers a causative effect between the expression of OsPEX1 and lignin deposition. Lastly, we demonstrated that modulating OsPEX1 expression could provide a tool for improving rice lodging resistance.

Single segment substitution lines (SSSLs) have been confirmed to be powerful tools to perform quantitative trait locus (QTL) analysis. This study illuminated the process and methods of QTL analysis with SSSLs on heading date (HD) in rice. QTL identification under two cropping seasons revealed 98 of 202 SSSLs associated with HD. A total of 22 QTLs were positioned in relative narrow regions on chromosomes by mrMLM.GUI software. QTL qHd3-1 was precisely positioned at 4.4 cM on chromosome 3 by a secondary F2 population. Through SSSL pyramiding, double segment substitution lines were constructed and used to analyze epistatic interactions of digenic loci. Epistatic effects for three pairs of QTLs were estimated, indicating the interactions of QTL qHd3-1 with other QTLs detected and the role to enhance the expression of early ripening or restraining of late flowering QTLs. Additionally, analysis of QTL in different environments provided information about the stability of HD QTLs. This type of research points out the way to excavate favorable genes for design breeding.