Regulates Rice Grain Research Articles

Transcription factor OsNF-YC1 regulates grain size by coordinating the transcriptional activation of OsMADS1 in Oryza sativa L.

Grain weight, grain number per panicle, and the number of panicles are the three factors that determine rice (Oryza sativa L.) yield. Of these, grain weight, which not only directly determines rice yield but also influences appearance and quality, is often considered the most important for rice production. Here, we describe OsNF-YC1, a member of the NF-Y transcription factor family that regulates rice grain size. OsNF-YC1 knockout plants (osnf-yc1), obtained using CRISPR-Cas9 technology, showed reduced grain weight due to reduced width and thickness, with no change in grain length, leading to a slenderer grain shape. Downregulation of OsNF-YC1 using RNA interference resulted in similar grain phenotypes as osnf-yc1. OsNF-YC1 affects grain formation by regulating both cell proliferation and cell expansion. OsNF-YC1 localizes in both the nucleus and cytoplasm, has transcriptional activation activity at both the N-terminus and C-terminus, and is highly expressed in young panicles. OsNF-YC1 interacts with OsMADS1 both in vivo and in vitro. Further analysis showed that the histone-like structural CBFD-NFYB-HMF domain of OsNF-YC1 conserved in the OsNF-YC transcription factor family can directly interact with the MADS-box domain of OsMADS1 to enhance its transcriptional activation activity. This interaction positively regulates the expression of OsMADS55, the direct downstream target of OsMADS1. Therefore, this paper reveals a potential grain size regulation pathway controlled by an OsNF-YC1-OsMADS1-OsMADS55 module in rice.

OsEXPA7 Encoding an Expansin Affects Grain Size and Quality Traits in Rice (Oryza sativa L.)

BackgroundYield 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.ResultsWe 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.ConclusionsThese 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.

DGS1 improves rice disease resistance by elevating pathogen-associated molecular pattern-triggered immunity.

The online version contains supplementary material available at 10.1007/s42994-024-00137-9.

DGW1, encoding an hnRNP-like RNA binding protein, positively regulates grain size and weight by interacting with GW6mRNA.

Grain size and weight determine rice yield. Although numerous genes and pathways involved in regulating grain size have been identified, our knowledge of post-transcriptional control of grain size remains elusive. In this study, we characterize a rice mutant, decreased grain width and weight 1 (dgw1), which produces small grains. We show that DGW1 encodes a member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family protein and preferentially expresses in developing panicles, positively regulating grain size by promoting cell expansion in spikelet hulls. Overexpression of DGW1 increases grain weight and grain numbers, leading to a significant rise in rice grain yield. We further demonstrate that DGW1 functions in grain size regulation by directly binding to the mRNA of Grain Width 6 (GW6), a critical grain size regulator in rice. Overexpression of GW6 restored the grain size phenotype of DGW1-knockout plants. DGW1 interacts with two oligouridylate binding proteins (OsUBP1a and OsUBP1b), which also bind the GW6 mRNA. In addition, the second RRM domain of DGW1 is indispensable for its mediated protein-RNA and protein-protein interactions. In summary, our findings identify a new regulatory module of DGW1-GW6 that regulates rice grain size and weight, providing important insights into the function of hnRNP-like proteins in the regulation of grain size.

Identification and characterization of BES1 genes involved in grain size development of Oryza sativa L.

BES1 (BRI1-EMS-SUPPRESSOR1) defines a unique class of plant-specific transcription factors that plays an essential role in response to Brassinosteroids (BRs) signal induction pathways. In our study, we conducted genome-wide scanning and comprehensive characterization of the BES1 gene family in rice and other eukaryotes, leading to valuable findings. Molecular docking experiments showed that all OsBES1 genes in rice could directly bind to BR small molecules. Among the identified genes, OsBES1–4 exhibited a remarkable response as it consistently showed induction upon exposure to various phytohormones after treatment. Further functional verification of OsBES1–4 revealed its impact on grain size. Overexpression of OsBES1–4 resulted in increased grain size, as confirmed by cytological observations showing an increase in cell length and cell number. Moreover, we identified that OsBES1–4 plays a role in rice grain size development by binding to the BR response element in the promoter region of the OsBZR1 gene. Evolutionary analysis indicated differentiation of OsBES1–4 between indica and japonica rice varieties, suggesting natural selection during the domestication process of cultivated rice. Therefore, we conclude that OsBES1–4 plays a crucial role in regulating rice grain size and has the potential to be an important target in rice breeding programs, and haplotype analysis found that all OsBES1 genes were associated with grain size development, either thousand-grain weight, grain length, or grain width. Overall, these findings suggest that the BES1 genes are involved in the regulation of grain size development in rice, and the utilization of SNPs in the OsBES1–4 gene promoter could be a favorable option for distinguishing indica and japonica.

OsMADS1 Regulates Grain Quality, Gene Expressions, and Regulatory Networks of Starch and Storage Protein Metabolisms in Rice.

OsMADS1 plays a vital role in regulating floret development and grain shape, but whether it regulates rice grain quality still remains largely unknown. Therefore, we used comprehensive molecular genetics, plant biotechnology, and functional omics approaches, including phenotyping, mapping-by-sequencing, target gene seed-specific RNAi, transgenic experiments, and transcriptomic profiling to answer this biological and molecular question. Here, we report the characterization of the 'Oat-like rice' mutant, with poor grain quality, including chalky endosperms, abnormal morphology and loose arrangement of starch granules, and lower starch content but higher protein content in grains. The poor grain quality of Oat-like rice was found to be caused by the mutated OsMADS1Olr allele through mapping-by-sequencing analysis and transgenic experiments. OsMADS1 protein is highly expressed in florets and developing seeds. Both OsMADS1-eGFP and OsMADS1Olr-eGFP fusion proteins are localized in the nucleus. Moreover, seed-specific RNAi of OsMADS1 also caused decreased grain quality in transgenic lines, such as the Oat-like rice. Further transcriptomic profiling between Oat-like rice and Nipponbare grains revealed that OsMADS1 regulates gene expressions and regulatory networks of starch and storage protein metabolisms in rice grains, hereafter regulating rice quality. In conclusion, our results not only reveal the crucial role and preliminary mechanism of OsMADS1 in regulating rice grain quality but also highlight the application potentials of OsMADS1 and the target gene seed-specific RNAi system in improving rice grain quality by molecular breeding.

The kinase OsSK41/OsGSK5 negatively regulates amylose content in rice endosperm by affecting the interaction between OsEBP89 and OsBP5.

Amylose content (AC) is the main factor determining the palatability, viscosity, transparency, and digestibility of rice (Oryza sativa) grains. AC in rice grains is mainly controlled by different alleles of the Waxy (Wx) gene. The AP2/EREBP transcription factor OsEBP89 interacts with the MYC-like protein OsBP5 to synergistically regulate the expression of Wx. Here, we determined that the GLYCOGEN SYNTHASE KINASE 5 (OsGSK5, also named SHAGGY-like kinase 41 [OsSK41]) inhibits the transcriptional activation activity of OsEBP89 in rice grains during amylose biosynthesis. The loss of OsSK41 function enhanced Wx expression and increased AC in rice grains. By contrast, the loss of function of OsEBP89 reduced Wx expression and decreased AC in rice grains. OsSK41 interacts with OsEBP89 and phosphorylates four of its sites (Thr-28, Thr-30, Ser-238, and Thr-257), which makes OsEBP89 unstable and attenuates its interaction with OsBP5. Wx promoter activity was relatively weak when regulated by the phosphomimic variant OsEBP89E -OsBP5 but relatively strong when regulated by the nonphosphorylatable variant OsEBP89A -OsBP5. Therefore, OsSK41-mediated phosphorylation of OsEBP89 represents an additional layer of complexity in the regulation of amylose biosynthesis during rice grain development. In addition, our findings provide four possible sites for regulating rice grain AC via precise gene editing.

The miR167-OsARF12 module regulates rice grain filling and grain size downstream of miR159

Grain weight and quality are always determined by grain filling. Plant microRNAs have drawn attention as key targets for regulation of grain size and yield. However, the mechanisms that underlie grain size regulation remain largely unclear because of the complex networks that control this trait. Our earlier studies demonstrated that suppressed expression of miR167 (STTM/MIM167) substantially increased grain weight. In a field test, the yield increased up to 12.90%–21.94% because of a significantly enhanced grain filling rate. Here, biochemical and genetic analyses revealed the regulatory effects of miR159 on miR167 expression. Further analysis indicated that OsARF12 is the major mediator by which miR167 regulates rice grain filling. Overexpression of OsARF12 produced grain weight and grain filling phenotypes resembling those of STTM/MIM167 plants. Upon in-depth analysis, we found that OsARF12 activates OsCDKF;2 expression by directly binding to the TGTCGG motif in its promoter region. Flow cytometry analysis of young panicles from OsARF12-overexpressing plants and examination of cell number in cdkf;2 mutants verified that OsARF12 positively regulates grain filling and grain size by targeting OsCDKF;2. Moreover, RNA sequencing results suggested that the miR167-OsARF12 module is involved in the cell development process and hormone pathways. OsARF12-overexpressing plants and cdkf;2 mutants exhibited enhanced and reduced sensitivity to exogenous auxin and brassinosteroid (BR) treatment, confirming that targeting of OsCDKF;2 by OsARF12 mediates auxin and BR signaling. Our results reveal that the miR167-OsARF12 module works downstream of miR159 to regulate rice grain filling and grain size via OsCDKF;2 by controlling cell division and mediating auxin and BR signals.

Heat Stress Decreases Rice Grain Weight: Evidence and Physiological Mechanisms of Heat Effects Prior to Flowering.

Heat stress during the preflowering panicle initiation stage seriously decreases rice grain weight in an invisible way and has not been given enough attention. The current review aims to (i) specify the heat effects on rice grain weight during the panicle initiation stage compared with the most important grain-filling stage; and (ii) discuss the physiological mechanisms of the decreased rice grain weight induced by heat during panicle initiation in terms of assimilate supply and phytohormone regulation, which are key physiological processes directly regulating rice grain weight. We emphasize that the effect of heat during the panicle initiation stage on rice grain weight is more serious than that during the grain-filling stage. Heat stress during the panicle initiation stage induces alterations in endogenous phytohormones, leading to the inhibition of the photosynthesis of functional leaves (source) and the formation of vascular bundles (flow), thus reducing the accumulation and transport of nonstructural carbohydrates and the growth of lemmata and paleae. The disruptions in the “flow” and restrictions in the preanthesis “source” tissue reduce grain size directly and decrease grain plumpness indirectly, resulting in a reduction in the final grain weight, which could be the direct physiological causes of the lower rice grain weight induced by heat during the panicle initiation stage. We highlight the seriousness of preflowering heat stress on rice grain weight, which can be regarded as an invisible disaster. The physiological mechanisms underlying the lower grain weight induced by heat during panicle initiation show a certain novelty because they distinguish this stage from the grain-filling stage. Additionally, a number of genes that control grain size through phytohormones have been summarized, but their functions have not yet been fully tested under heat conditions, except for the Grain Size and Abiotic stress tolerance 1 (GSA1) and BRASSINOSTEROID INSENSITIVE1 (OsBRI1) genes, which are reported to respond rapidly to heat stress. The mechanisms of reduced rice grain weight induced by heat during the panicle initiation stage should be studied in more depth in terms of molecular pathways.

Combined Effect of Nitrogen Fertilizer Application and High Temperature on Grain Quality Properties of Cooked Rice.

Ambient temperature and nitrogen (N) fertilizer are two of the most important factors that affect rice grain quality. However, less information has been available on the interactive effect of N fertilizer and ambient temperature on grain quality under stressful high temperature (HT). In this article, the effects of panicle N fertilizer, ambient temperature, and their interaction on starch composition, particle size distribution of starch granules, starch physicochemical properties, and storage protein accumulation in milled grains were investigated to clarify the potential role of panicle N fertilizer topdressing in regulating rice grain quality under stressful HT by using a two-factor experiment of three N levels in combination with two temperature regimes. Results showed that appropriate application of panicle N fertilizer could attenuate the adverse effect of HT during grain filling on milling quality and chalky occurrence to some extent, particularly for the effective alleviation of HT-induced decrease in milling quality. However, the topdressing of panicle N fertilizer tended to enhance starch gelatinization enthalpy (ΔH) and its setback viscosity in HT-ripening grains, with the simultaneous decrements in the number and surface area proportions of smaller starch granules under the higher N fertilizer in combination with HT exposure. The effects of higher nitrogen fertilizer and HT exposure on total protein content and gluten composition of grains were additively increased. Hence, the topdressing of panicle N fertilizer exacerbated HT-induced deterioration in cooking and eating quality, rather than alleviating the negative impact of HT exposure on the palatability of cooked rice.

The genetic editing of GS3 via CRISPR/Cas9 accelerates the breeding of three-line hybrid rice with superior yield and grain quality

Grain size is one of the major traits that determine rice grain yield and quality. The GS3 gene is the first major quantitative trait locus (QTL) that was identified in regulating rice grain length and weight. It was reported that the gs3 allele with a mutation in the organ size regulation (OSR) domain of the GS3 protein produced longer grains. In this study, we used the CRISPR/Cas9 gene editing technology to introduce an edited gs3 allele into our indica maintainer line, Mei1B, to enhance its grain yield and quality. Through molecular analysis and sequencing, a homologous edited-gs3 mutant line without any transgene was obtained in the T1 generation and was named Mei2B. A superior male sterile line Mei2A was generated by backcrossing the cytoplasmic male sterile (CMS) line Mei1A with Mei2B. Mei2B had a higher grain quality and yield compared to its wild-type Mei1B. Its grain length increased by 7.9%, its length/width ratio increased from 3.89 to 4.19, TGW increased by 6.7%, and grain yield per plant increased by 14.9%. In addition, genetic improvement of other quality traits including brown rice length (6.83 mm), brown rice grain length/width ratio (3.61), matched the appearance standards set for traditional Simiao (silk seedling) type cultivars. Two restorer lines were outcrossed to both Mei1A and Mei2A to produce hybrid rice. Compared to two hybrids of Mei1A, the hybrids of Mei2A had longer grains, higher length/width ratio, TGW, and yield per plant. In addition, the hybrids of Mei2A showed a better grain appearance including better translucency, a lower chalky rice rate, and degree of chalkiness than the hybrids of Mei1A. These results demonstrated that the introduction of an elite gs3 allele into Mei1A via CRISPR/Cas9 gene editing technology led to significant genetic improvement of the rice grain. The resultant CMS line Mei2A(gs3) displayed much higher grain quality and yield than the original Mei1A. Therefore, our study demonstrated that the targeted genetic improvement via gene editing technology can enhance rice breeding, especially the breeding of three-line hybrid rice.

KNOX II transcription factor HOS59 functions in regulating rice grain size.

Plant Knotted1-like homeobox (KNOX) genes encode homeodomain-containing transcription factors. In rice (Oryza sativa L.), little is known about the downstream target genes of KNOX Class II subfamily proteins. Here we generated chromatin immunoprecipitation (ChIP)-sequencing datasets for HOS59, a member of the rice KNOX Class II subfamily, and characterized the genome-wide binding sites of HOS59. We conducted trait ontology (TO) analysis of 9705 identified downstream target genes, and found that multiple TO terms are related to plant structure morphology and stress traits. ChIP-quantitative PCR (qPCR) was conducted to validate some key target genes. Meanwhile, our IP-MS datasets showed that HOS59 was closely associated with BELL family proteins, some grain size regulators (OsSPL13, OsSPL16, OsSPL18, SLG, etc.), and some epigenetic modification factors such as OsAGO4α and OsAGO4β, proteins involved in small interfering RNA-mediated gene silencing. Furthermore, we employed CRISPR/Cas9 editing and transgenic approaches to generate hos59 mutants and overexpression lines, respectively. Compared with wild-type plants, the hos59 mutants have longer grains and increased glume cell length, a loose plant architecture, and drooping leaves, while the overexpression lines showed smaller grain size, erect leaves, and lower plant height. The qRT-PCR results showed that mutation of the HOS59 gene led to upregulation of some grain size-related genes such as OsSPL13, OsSPL18, and PGL2. In summary, our results indicate that HOS59 may be a repressor of the downstream target genes, negatively regulating glume cell length, rice grain size, plant architecture, etc. The identified downstream target genes and possible interaction proteins of HOS59 improve our understanding of the KNOX regulatory networks.

OsCOMT, encoding a caffeic acid O-methyltransferase in melatonin biosynthesis, increases rice grain yield through dual regulation of leaf senescence and vascular development.

SummaryMelatonin, a natural phytohormone in plants, plays multiple critical roles in plant growth and stress responses. Although melatonin biosynthesis‐related genes have been suggested to possess diverse biological functions, their roles and functional mechanisms in regulating rice grain yield remain largely unexplored. Here, we uncovered the roles of a caffeic acid O‐methyltransferase (OsCOMT) gene in mediating rice grain yield through dual regulation of leaf senescence and vascular development. In vitro and in vivo evidence revealed that OsCOMT is involved in melatonin biosynthesis. Transgenic assays suggested that OsCOMT significantly delays leaf senescence at the grain filling stage by inhibiting degradation of chlorophyll and chloroplast, which, in turn, improves photosynthesis efficiency. In addition, the number and size of vascular bundles in the culms and leaves were significantly increased in the OsCOMT‐overexpressing plants, while decreased in the knockout plants, suggesting that OsCOMT plays a positive role in vascular development of rice. Further evidence indicated that OsCOMT‐mediated vascular development might owe to the crosstalk between melatonin and cytokinin. More importantly, we found that OsCOMT is a positive regulator of grain yield, and overexpression of OsCOMT increase grain yield per plant even in a high‐yield variety background, suggesting that OsCOMT can be used as an important target for enhancing rice yield. Our findings shed novel insights into melatonin‐mediated leaf senescence and vascular development and provide a possible strategy for genetic improvement of rice grain yield.

Mapping the Expression Profiles of Grain Yield QTL Associated miRNAs in Rice Varieties with Different Grain Size

microRNAs (miRNAs) are key regulatory molecules that fine tune gene expression at the transcriptional and post-transcriptional levels through the RNA silencing pathways. They play an important role in regulating plant growth, development and response to a/biotic stress conditions. Grain yield is a complex trait that is governed by the coordinated action of several genetic and environmental factors. A number of genes and miRNAs have been identified to affect the grain productivity and yield. In this study, we identified the miRNAs that map to grain yield QTLs in rice. The expression variations of these miRNAs and their target transcript were studied across different tissues of three indica rice varieties with different grain morphology. The varieties used include the extra-long and slender grained Pusa Basmati 1 (PB1), medium grain sized IR64 and the short grained Pokkali (PK). The windows for miRNA target correlation were captured and their putative role in regulating rice grain yield is discussed.

Moonlighting PPKL1 reveals a role of cytokinin in regulating rice grain size

Rice is the staple food of more than half of the world’s population, and major efforts are being made to improve rice yield. Rice yield is mainly determined by three components: number of panicles per plant, number of grains per panicle, and grain weight, which is positively associated with grain size. Therefore, grain size is an important agricultural trait for yield improvement in rice, and it is controlled by multiple genetic factors and environmental cues (Li et al., 2018). The final size of rice grains is largely determined by cell proliferation and cell expansion in the spikelet hull (husk), which sets the storage capacity of the grain and limits grain filling (Li et al., 2018).

A rice QTL GS3.1 regulates grain size through metabolic-flux distribution between flavonoid and lignin metabolons without affecting stress tolerance

Grain size is a key component trait of grain weight and yield. Numbers of quantitative trait loci (QTLs) have been identified in various bioprocesses, but there is still little known about how metabolism-related QTLs influence grain size and yield. The current study report GS3.1, a QTL that regulates rice grain size via metabolic flux allocation between two branches of phenylpropanoid metabolism. GS3.1 encodes a MATE (multidrug and toxic compounds extrusion) transporter that regulates grain size by directing the transport of p-coumaric acid from the p-coumaric acid biosynthetic metabolon to the flavonoid biosynthetic metabolon. A natural allele of GS3.1 was identified from an African rice with enlarged grains, reduced flavonoid content and increased lignin content in the panicles. Notably, the natural allele of GS3.1 caused no alterations in other tissues and did not affect stress tolerance, revealing an ideal candidate for breeding efforts. This study uncovers insights into the regulation of grain size though metabolic-flux distribution. In this way, it supports a strategy of enhancing crop yield without introducing deleterious side effects on stress tolerance mechanisms.

Exogenous melatonin confers enhanced salinity tolerance in rice by blocking the ROS burst and improving Na+/K+ homeostasis

Melatonin (MT; N-acetyl-5-methoxytryptamine) has been reported to enhance the salt tolerance of rice seedlings and other crop species, yet its role in regulating rice grain yield formation and the underlying mechanism have received little attention. In this study, exogenous MT markedly mitigated the adverse effect of salinity on final rice grain yield, which was increased by 4.0 %–13.0 % compared with that under the same salt concentration in the absence of MT. Under the MT treatment, the number of rice green leaves was significantly (P < 0.05) increased, accompanied by increased leaf photosynthesis and enhanced photosynthetic pigment contents. MT protected leaf cell membranes by scavenging H2O2 and O2·− that accumulated (whose contents decreased by 6.5 %–28.9 % and 1.1 %–5.1 %, respectively, at heading stage) and enhanced the activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) (whose average activity increased by 5.0 %–12.8 %, 14.9 %–27.0 % and 3.4 %–12.2 %, respectively). The leaf K+ content and expression of OsHAK genes didn’t show significant changes under low salt concentration (0.1 % NaCl) but both parameters were greatly increased under relatively high salt concentrations, especially after MT application. Thus, we concluded that the mechanism through which MT provided enhanced rice salinity tolerance was different under various salt concentrations. MT prioritized activation of the ROS scavenging system to improve salinity tolerance in rice under relatively low salt concentration but alleviated damage from salinity both by blocking the reactive oxygen species (ROS) burst and by increasing K+ retention in leaf mesophyll cells via regulation of OsHAK expression (especially that of OsHAK5) under relatively high salt concentrations.

Pleiotropic Effect of GNP1 Underlying Grain Number per Panicle on Sink, Source and Flow in Rice.

Rice yield potential is largely determined by the balance among source capacity, sink strength, and flow fluency. Our previous study indicated that the gene GNP1 encoding gibberellin biosynthesis gene GA20ox1 affects grain number per panicle (GNP) in rice, thus resulting in increase of grain yield. To clarify GNP1 effect on sink, source and flow in regulating rice grain yield, we compared Lemont, a japonica (geng) cultivar, with its near-isogenic line (NIL-GNP1TQ) in Lemont background with introgression of the allele at GNP1 from Teqing, a high-yielding indica (xian) cultivar. NIL-GNP1TQ exhibited averagely 32.8% more GNP than Lemont with the compensation by reduced seed setting rate, panicle number and single-grain weight. However, NIL-GNP1TQ still produced averagely 7.2% higher grain yield than Lemont in two years, mainly attributed to significantly more filled grain number per panicle, and greater vascular system contributing to photoassimilates transport to spikelets. The significantly decreased grain weight of superior spikelets (SS) in NIL-GNP1TQ was ascribed to a significant decrease of grain size while the significantly decreased grain weight of inferior spikelets (IS) ascribed to both grain size and poor grain-filling as compared with Lemont. The low activities of key enzymes of carbon metabolism might account for the poor grain-filling in IS, which resulted in more unfilled grains or small grain bulk density in NIL-GNP1TQ. In addition, low seed setting rate and grain weight of IS in NIL-GNP1TQ might be partially resulted from significantly lower carbohydrate accumulation in culms and leaf sheath before heading compared with Lemont. Our results indicated that significantly increased GNP from introgression of GNP1TQ into Lemont did not highly significantly improve grain yield of NIL-GNP1TQ as expected, due primarily to significant low sink activities in IS and possible insufficient source supply which didn’t fully meet the increased sink capacity. The results provided useful information for improving rice yield potential through reasonably introgressing or pyramiding the favorable alleles underlying source-related or panicle number traits by marker-assisted selection.

The PLATZ Transcription Factor GL6 Affects Grain Length and Number in Rice.

Grain size is one of the key determinants of grain yield. Although a number of genes that control grain size in rice (Oryza sativa) have been identified, the overall regulatory networks behind this process remain poorly understood. Here, we report the map-based cloning and functional characterization of the quantitative trait locus GL6, which encodes a plant-specific plant AT-rich sequence- and zinc-binding transcription factor that regulates rice grain length and spikelet number. GL6 positively controls grain length by promoting cell proliferation in young panicles and grains. The null gl6 mutant possesses short grains, whereas overexpression of GL6 results in large grains and decreased grain number per panicle. We demonstrate that GL6 participates in RNA polymerase III transcription machinery by interacting with RNA polymerase III subunit C53 and transcription factor class C1 to regulate the expression of genes involved in rice grain development. Our findings reveal a further player involved in the regulation of rice grain size that may be exploited in future rice breeding.

Overexpressing lncRNA LAIR increases grain yield and regulates neighbouring gene cluster expression in rice

Long noncoding RNAs (lncRNAs) are essential regulators of gene expression in eukaryotes. Despite increasing knowledge on the function of lncRNAs, little is known about their effects on crop yield. Here, we identify a lncRNA transcribed from the antisense strand of neighbouring gene LRK (leucine-rich repeat receptor kinase) cluster named LAIR (LRK Antisense Intergenic RNA). LAIR overexpression increases rice grain yield and upregulates the expression of several LRK genes. Additionally, chromatin immunoprecipitation assay results indicate H3K4me3 and H4K16ac are significantly enriched at the activated LRK1 genomic region. LAIR binds histone modification proteins OsMOF and OsWDR5 in rice cells, which are enriched in LRK1 gene region. Moreover, LAIR is demonstrated to bind 5′ and 3′ untranslated regions of LRK1 gene. Overall, this study reveals the role of lncRNA LAIR in regulating rice grain yield and lncRNAs may be useful targets for crop breeding.