Xiaojin Luo

Summary: Improving plant architecture and increasing yields are the main goals of rice breeders. However, yield is a complex trait influenced by many yield‐related traits. Identifying and characterizing important genes in the coordinated network regulating complex rice traits and their interactions is conducive to cultivating high‐yielding rice varieties. In this study, we determined that the interaction between mitogen‐activated protein kinase kinase kinase5 (OsMAPKKK5) and brassinosteroid‐signalling kinase1–1 (OsBSK1–1) regulates yield‐related traits in rice. Specifically, OsMAPKKK5 phosphorylates OsBSK1–1, which enhances the interaction between these two proteins, but adversely affects the OsBSK1–1–OsBRI1 (BR insensitive1) and OsBSK1–1–OsPPKL1 (protein phosphatase with two Kelch‐like domains) interactions. Additionally, OsMAPKKK5 disrupts brassinosteroid signal transduction, which prevents OsBZR1 (brassinazole‐resistant1) from efficiently entering the nucleus, thereby negatively modulating its function as a transcription factor regulating downstream effector genes, ultimately adversely affecting plant architecture and yield. This study revealed the relationship between the MAPK cascade and the regulatory effects of brassinosteroid on the rice grain yield involves OsMAPKKK5 and OsBSK1–1. The study data may be important for future investigations on the rice yield‐regulating molecular network.

Background: Yield and quality are the two most important traits in crop breeding. Exploring the regulatory mechanisms that affect both yield and quality traits is of great significance for understanding the molecular genetic networks controlling these key crop attributes. Expansins are cell wall loosening proteins that play important roles in regulating rice grain size. Results: We investigated the effect of OsEXPA7, encoding an expansin, on rice grain size and quality. OsEXPA7 overexpression resulted in increased plant height, panicle length, grain length, and thousand-grain weight in rice. OsEXPA7 overexpression also affected gel consistency and amylose content in rice grains, thus affecting rice quality. Subcellular localization and tissue expression analyses showed that OsEXPA7 is localized on the cell wall and is highly expressed in the panicle. Hormone treatment experiments revealed that OsEXPA7 expression mainly responds to methyl jasmonate, brassinolide, and gibberellin. Transcriptome analysis and RT-qPCR experiments showed that overexpression of OsEXPA7 affects the expression of OsJAZs in the jasmonic acid pathway and BZR1 and GE in the brassinosteroid pathway. In addition, OsEXPA7 regulates the expression of key quantitative trait loci related to yield traits, as well as regulates the expression levels of BIP1 and bZIP50 involved in the seed storage protein biosynthesis pathway. Conclusions: These results reveal that OsEXPA7 positively regulates rice yield traits and negatively regulates grain quality traits by involving plant hormone pathways and other trait-related pathway genes. These findings increase our understanding of the potential mechanism of expansins in regulating rice yield and quality traits and will be useful for breeding high-yielding and high-quality rice cultivars.

RNA‐binding proteins (RBPs) are components of the post‐transcriptional regulatory system, but their regulatory effects on complex traits remain unknown. Using an integrated strategy involving map‐based cloning, functional characterizations, and transcriptomic and population genomic analyses, we revealed that RBP‐K (LOC_Os08g23120), RBP‐A (LOC_Os11g41890), and RBP‐J (LOC_Os10g33230) encode proteins that form an RBP‐A‐J‐K complex that negatively regulates rice yield‐related traits. Examinations of the RBP‐A‐J‐K complex indicated RBP‐K functions as a relatively non‐specific RBP chaperone that enables RBP‐A and RBP‐J to function normally. Additionally, RBP‐J most likely affects GA pathways, resulting in considerable increases in grain and panicle lengths, but decreases in grain width and thickness. In contrast, RBP‐A negatively regulates the expression of genes most likely involved in auxin‐regulated pathways controlling cell wall elongation and carbohydrate transport, with substantial effects on the rice grain filling process as well as grain length and weight. Evolutionarily, RBP‐K is relatively ancient and highly conserved, whereas RBP‐J and RBP‐A are more diverse. Thus, the RBP‐A‐J‐K complex may represent a typical functional model for many RBPs and protein complexes that function at transcriptional and post‐transcriptional levels in plants and animals for increased functional consistency, efficiency, and versatility, as well as increased evolutionary potential. Our results clearly demonstrate the importance of RBP‐mediated post‐transcriptional regulation for the diversity of complex traits. Furthermore, rice grain yield and quality may be enhanced by introducing various complete or partial loss‐of‐function mutations to specific RBP genes using clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR‐associated protein 9 technology and by exploiting desirable natural tri‐genic allelic combinations at the loci encoding the components of the RBP‐A‐J‐K complex through marker‐assisted selection.

Editorial: Mining and utilization of favorable gene resources in rice

Spikelet number per panicle (SNP) is one of the most important yield components in rice. Rice ENHANCING BIOMASS AND SPIKELET NUMBER (OsEBS), a gene involved in improved SNP and yield, has been cloned from an accession of Dongxiang wild rice. However, the mechanism of OsEBS increasing rice SNP is poorly understood. In this study, the RNA-Seq technology was used to analyze the transcriptome of wildtype Guichao 2 and OsEBS over-expression line B102 at the heading stage, and analysis of the evolution of OsEBS was also conducted. A total of 5369 differentially expressed genes (DEGs) were identified between Guichao2 and B102, most of which were down-regulated in B102. Analysis of the expression of endogenous hormone-related genes revealed that 63 auxin-related genes were significantly down-regulated in B102. Gene Ontogeny (GO) enrichment analysis showed that the 63 DEGs were mainly enriched in eight GO terms, including auxin-activated signaling pathway, auxin polar transport, auxin transport, basipetal auxin transport, and amino acid transmembrane transport, most of which were directly or indirectly related to polar auxin transport. Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis further verified that the down-regulated genes related to polar auxin transport had important effects on increased SNP. Analysis of the evolution of OsEBS found that OsEBS was involved in the differentiation of indica and japonica, and the differentiation of OsEBS supported the multi-origin model of rice domestication. Indica (XI) subspecies harbored higher nucleotide diversity than japonica (GJ) subspecies in the OsEBS region, and XI experienced strong balancing selection during evolution, while selection in GJ was neutral. The degree of genetic differentiation between GJ and Bas subspecies was the smallest, while it was the highest between GJ and Aus. Phylogenetic analysis of the Hsp70 family in O. sativa, Brachypodium distachyon, and Arabidopsis thaliana indicated that changes in the sequences of OsEBS were accelerated during evolution. Accelerated evolution and domain loss in OsEBS resulted in neofunctionalization. The results obtained from this study provide an important theoretical basis for high-yield rice breeding.

Plant height and grain size are important agronomic traits affecting rice yield. Various plant hormones participate in the regulation of plant height and grain size in rice. However, how these hormones cooperate to regulate plant height and grain size is poorly understood. In this study, we identified a brassinosteroid-related gene, hfr131, from an introgression line constructed using Oryza longistaminata, that caused brassinosteroid insensitivity and reduced plant height and grain length in rice. Further study showed that hfr131 is a new allele of OsBRI1 with a single-nucleotide polymorphism (G to A) in the coding region, leading to a T988I conversion at a conserved site of the kinase domain. By combining yeast one-hybrid assays, chromatin immunoprecipitation-quantitative PCR and gene expression quantification, we demonstrated that OsARF17, an auxin response factor, could bind to the promoter region of HFR131 and positively regulated HFR131 expression, thereby regulating the plant height and grain length, and influencing brassinosteroid sensitivity. Haplotype analysis showed that the consociation of OsAFR17^Hap1/HFR131^Hap6 conferred an increase in grain length. Overall, this study identified hfr131 as a new allele of OsBRI1 that regulates plant height and grain length in rice, revealed that brassinosteroid and auxin might coordinate through OsARF17–HFR131 interaction, and provided a potential breeding target for improvement of rice yield.

Developing methods for increasing the biomass and improving the plant architecture is important for crop improvement. We herein describe a gene belonging to the RING_Ubox (RING (Really Interesting New Gene) finger domain and U-box domain) superfamily, PLANT ARCHITECTURE and GRAIN NUMBER 1 (PAGN1), which regulates the number of grains per panicle, the plant height, and the number of tillers. We used the CRISPR/Cas9 system to introduce loss-of-function mutations to OsPAGN1. Compared with the control plants, the resulting pagn1 mutant plants had a higher grain yield because of increases in the plant height and in the number of tillers and grains per panicle. Thus, OsPAGN1 may be useful for the genetic improvement of plant architecture and yield. An examination of evolutionary relationships revealed that OsPAGN1 is highly conserved in rice. We demonstrated that OsPAGN1 can interact directly with OsCNR10 (CELL NUMBER REGULATOR10), which negatively regulates the number of rice grains per panicle. A transcriptome analysis indicated that silencing OsPAGN1 affects the levels of active cytokinins in rice. Therefore, our findings have clarified the OsPAGN1 functions related to rice growth and grain development.

Significance: Rice breeding programs aim to develop cultivars with improved traits, including high grain yield and superior quality. In rice, OsPDCD5 encodes a programmed cell death 5 protein. Targeted mutagenesis of OsPDCD5 enhanced grain yield and plant architecture. Statistical analysis indicated that plot grain yield of OsPDCD5 knockout lines was enhanced by 6.25 to 20.13% in 11 popular or newly bred rice cultivars compared with the corresponding wild types. The OsPDCD5 knockout lines showed increases in milled rice percentage and gel consistency, and a decrease in amylose content. Our results provide insight into the molecular mechanism by which OsPDCD5 influences grain yield and plant architecture, and highlight a promising candidate gene for use in breeding programs designed to develop super rice cultivars.