Japonica Varieties Research Articles

Genome-wide association study reveals novel QTLs and candidate genes for panicle number in rice

IntroductionPanicle number (PN) is one of the three key yield components in rice, maintaining stable tiller and PN is a crucial characteristic of an ideal plant architecture. Understanding the molecular mechanisms underlying PN is essential for breeders aiming to improve rice yield.MethodsTo dissect the genetic architecture of panicle number, a genome-wide association study (GWAS) was conducted in 411 japonica rice varieties. GWAS analysis was carried out with the mixed linear model using 743,678 high-quality SNPs.ResultsOver two experimental years, we detected a total of seven quantitative trait loci (QTLs), located on chromosomes 1, 4, 6, 8, 11, and 12; notably, qPN1.1 and qPN8 were detected consistently in both years. By combining haplotype and expression analyses, OsCKX11 was identified as the candidate gene for qPN8, while LOC_Os01g07870 and LOC_Os01g07950 were identified as candidate genes for qPN1.1. Significant differences were observed among the haplotypes of these candidate genes. Additionally, qRT-PCR results showed that LOC_Os01g07870 expression levels were significantly lower in accessions with high panicle numbers compared to those with low panicle numbers.DiscussionTo understand the natural biological function of these candidate genes, further research involving overexpression or silencing in rice is needed. Despite these challenges, our results will lay the foundation for further study of panicle development and provide valuable genetic resources for developing high-panicle-number rice cultivars using genetic engineering and molecular breeding.

Revealing Physiological Basis for Floret Opening Difference Between Indica and Japonica Rice: Based on Floral Structure, Transcriptome, and Endogenous Floret Opening Regulator

Background: The differing floret opening times between subsp. indica and subsp. japonica in rice limit the potential for increased hybrid seed production. Objectives: To elucidate the physiological basis underlying the differences in floret opening time between indica and japonica rice. Materials: A comparative analysis involved nine indica and ten japonica rice varieties. Methods: Using paraffin sectioning, transcriptome sequencing, RT-PCR, and endogenous substance quantification, we investigated the structural variations in floral organs, the differences in the initiation timing of floret opening regulatory pathways, and endogenous regulators. Results: The results indicated insignificant differences in lemma thickness, lodicule thickness, lodicule area, and the coupling-lodicule length between indica and japonica rice. However, japonica rice exhibited larger lodicule-lemma gaps and more vascular bundles compared to indica rice. Within the 9:00 a.m. to 10:00 a.m. interval, the expression of OsAOS1 in α-linolenic acid metabolism and OsISA3 in starch and sucrose metabolism notably increased in indica rice, with no significant change in japonica rice. Additionally, the endogenous JA and α-amylase surged more significantly in indica rice than in japonica rice. The increase in soluble carbohydrate in indica rice is greater than in japonica rice, but the difference is not significant. Conclusions: These findings suggest that in the process of the floret opening, the α-linolenic acid metabolism and starch and sucrose metabolism are initiated earlier in indica rice, accompanied by a more pronounced elevation in endogenous JA and α-amylase. Furthermore, the smaller lodicule-lemma gap in indica rice contributes to earlier floret opening compared to japonica rice.

Identification of Genetic Loci for Grain Traits and Disease Resistance Reveals a Potential Trade-Off in Rice

Understanding how plants utilize limited resources for reproductivity and disease resistance can improve the efficiency of plant breeding. In the present study, we mapped genes for grain traits, including grain length and width and thousand grain weight (TGW). A previously constructed linkage map of a recombinant inbred line population (MHM) was used, which was derived from a cross between an indica restorer rice variety (Minghui 63) and a temperate japonica rice variety (M-202). The MHM population was grown in replicated field plots, and grain trait data were collected. Upon a 3-year field evaluation, a total of 16 loci were mapped on 9 of 12 chromosomes, including 7 for grain length, 4 for grain weight, and 5 for TGW. A TGW locus ( qTGW2) and a grain width locus ( qWIG2.2) were mapped at the known blast resistance locus qBLAST2 on chromosome 2 that harbors a major blast resistance allele Pi-b. Another TGW locus ( qTGW3.3) and a grain length locus ( qLNG3.3) were mapped at qBLAST3 on chromosome 3. These results reveal potential trade-offs between disease resistance and productivity, which are important for breeders to develop high-yielding and disease-resistant rice varieties. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2024.

Genetic Loci Mining and Candidate Gene Analysis for Determining Fatty Acid Composition in Rice

Fatty acid composition and its proportions are critical to the nutritional value and storage quality of rice (Oryza sativa L.) as the third major nutrient component in this staple food. This study involved crossing an indica rice variety, Huazhan (HZ), as the male parent, with a japonica variety, Nekken2, as the female parent, to produce the F1 generation. Subsequently, a population of 120 recombinant inbred lines (RILs) was developed through multiple generations of self-breeding. By utilizing a high-density molecular genetic linkage map and phenotypic data of four fatty acid components, we identified a total of 14 quantitative trait loci (QTLs) related to fatty acid composition across chromosomes 1, 3, 4, 6, 8, and 9. These included two QTLs for C14 content, three for C16:0 content, six for C18:1 content, and three for C18:2 content. Notably, the QTL qCOPT4.2 exhibited a high LOD score of 5.22. Within QTL intervals, genes such as OsACX3 and SLG affecting grain length were identified. The expression of candidate genes within these intervals was assessed and further analyzed by using quantitative real-time PCR. Genes such as LOC_Os01g15000, LOC_Os04g47120, LOC_Os04g49194, LOC_Os06g22080, LOC_Os06g23870, LOC_Os06g24704, LOC_Os06g30780, LOC_Os08g44840, and LOC_Os09g36860 were found to regulate fatty acid synthesis or metabolic pathways, potentially enhancing fatty acid content in rice. These QTLs are indispensable for breeding rice varieties with improved fatty acid profiles, offering new genetic resources for enhancing the nutritional and storage qualities of rice.

Indole-3-Acetic Acid (IAA) and Sugar Mediate Endosperm Development in Rice (Oryza sativa L.)

The yield potential of large-panicle rice is often limited by grain-filling barriers caused by the development of inferior spikelets (IS). Photoassimilates, which are the main source of rice grain filling, mainly enter the caryopsis through the dorsal vascular bundle. The distribution of assimilates between superior spikelets (SS) and IS is influenced by auxin-mediated apical dominance; however, the mechanism involved is still unclear. In this study, the effect of auxin signaling on the grain filling of SS and IS was investigated in two large-panicle japonica rice varieties, W1844 and CJ03. Compared to SS, IS displayed delayed initiation of filling and a significantly lower grain weight. Furthermore, the endosperm development in IS remained stagnant at the coenocytic stage. The development of the dorsal vascular bundle in the IS was also slow, and poor sucrose-unloading was observed during the initial grain filling stage. However, the endosperm development in IS immediately started after the improvement of dorsal vascular bundle development. GUS activity staining further revealed that indole-3-acetic (IAA) was localized in the dorsal vascular bundle and surrounding areas, suggesting that the low IAA content observed in the IS during the initial grain filling stage may have delayed the development of the dorsal vascular bundle. Therefore, these results demonstrate that IAA may control sugar transport and unloading by regulating dorsal vascular bundle development, consequently affecting endosperm development in IS.

Contrasting Alleles of OsNRT1.1b Fostering Potential in Improving Nitrogen Use Efficiency in Rice.

Nitrogen use efficiency (NUE) is important for the growth and development of rice and is significant in reducing the costs of rice production. OsNRT1.1b is involved in nitrate assimilation, and the alleles at position 21,759,092 on chromosome 10 clearly separate indica (Pathum Thani 1 (PTT1) and Homcholasit (HCS)) and japonica (Azucena and Leum Pua (LP)) rice varieties. Rice morphological and physiological traits were collected at three nitrogen levels (N0 = 0 kg ha-1, N7 = 43.75 kg ha-1, and N14 = 87.5 kg ha-1). Leaf and tiller numbers in PTT1 and HCS at N7 and N14 were two to three times higher than those at N0. At harvest, the biomass yield in PTT1 was the highest, while the total grain number in HCS was the maximum. The leaf widths and total chlorophyll contents (SPAD units) of Azucena and LP increased with nitrogen application as well as photosynthetic pigment parameters; for example, plant senescence reflectance indices (PSRIs), structure-insensitive pigment indices (SIPIs), and modified chlorophyll absorption ratio indices (MCARIs) were highly related in the japonica varieties. PTT1 and HCS, both carrying the A allele at OsNRT1.1b, had better NUE than Azucena and LP with the G allele. HCS, overall, had better NUE than PTT1. The translation to grain yield of assimilates was remarkable in PTT1 and HCS compared with Azucena and LP. In addition, HCS converted biomass for a 75% higher yield than PTT1. The ability of HCS to produce high yields was achieved even at N7 nitrogen fertilization, manifesting efficient use of nitrogen.

Differences in the Appearance Quality of Soft Japonica Rice with Different Grain Shapes in the Yangtze River Delta and Their Relationship with Grain-Filling

This study investigated the differences in appearance quality among different soft japonica rice varieties based on grain shape, with a particular focus on the broad-ovate soft japonica rice varieties Nanjing 9108 and Nanjing 5718, as well as the slender soft japonica rice varieties Shangshida 19 and Jiahe 218, all sourced from the Yangtze River Delta. The results showed that the slender soft japonica rice varieties exhibited significantly superior appearance quality compared to the broad-ovate varieties. In the case of superior grains, the chalky grain rate of the broad-ovate soft japonica rice was 4307.79 percent higher than that of the slender varieties, and the degree of chalkiness was 8275.00 percent higher. For inferior grains, the chalky grain rate of the broad-ovate soft japonica rice was 238.34 percent higher than the slender varieties, and the degree of chalkiness was 339.96 percent higher. In contrast to the slender soft japonica rice, the broad-ovate varieties had a lower percentage of high-weight grains and a higher percentage of low-weight grains. Compared to the broad-ovate soft japonica rice, the slender varieties exhibited a faster grain-filling rate and shorter effective grain-filling days. Correlation analysis revealed that chalkiness had a significant negative correlation with grain length and aspect ratio. Simultaneously, chalkiness also showed a positive correlation with the number of effective grain-filling days while demonstrating a negative correlation with both the maximum and average grain-filling rates. The slender soft japonica rice exhibited a lower likelihood of developing chalkiness and higher grain-filling efficiency and developed a favorable grain weight distribution. These distinctive attributes significantly contribute to the superior appearance quality of the slender japonica soft rice.

Exogenous MgH2-derived hydrogen alleviates cadmium toxicity through m6A RNA methylation in rice

Cadmium (Cd) contamination poses a substantial threat to crop yields and human health. While magnesium hydride (MgH2) has been reported as a hydrogen (H2) donor that promotes plant growth under heavy metal contamination, its role in rice remains elusive. Herein, seedlings of Oryza sativa L. Japonica variety Zhonghua 11 (ZH11) were selected and exposed to 20 µL of 1-mol/L cadmium chloride (CdCl2) solution via hydroponics to simulate Cd stress. Meanwhile, 0.1 mg of MgH2 was used to slow-release H2 to the experimental group to explore its potential effects on rice over a 2-week period. The results indicated that Cd exposure severely inhibited the growth and development of ZH11 rice seedlings. However, the exogenous slow-release of H2 from MgH2 effectively mitigated this inhibitory effect by restoring the balance of reactive oxygen species (ROS), maintaining endogenous H2 homeostasis, and supporting the photosynthetic system. High-performance liquid chromatography analysis revealed that exogenous H2 reduces m6A RNA methylation levels in mRNA under Cd stress. Consequently, MeRIP-seq was conducted to investigate the effect of Cd exposure in rice in the presence and absence of H2. The m6A modifications were enriched at the start codon, stop codon, and 3′ UTR. By integrating RNA-seq data, 118 transcripts were identified as differentially methylated and expressed genes under Cd stress. These gene annotations were associated with ROS, biological stress, and hormonal responses. Notably, 297 differentially methylated and expressed genes were identified under Cd stress in the presence of H2, linked to heavy metals, protein kinases, and calcium signaling regulation. Cd strongly activates the MAPK pathway in response to stress. Exogenous H2 reduces Cd accumulation as well as enhances plant tolerance and homeostasis by lowering m6A levels, thereby decreasing the mRNA stability of these genes. Our findings indicate that MgH2, by supplying H2, regulates gene expression through m6A RNA methylation and confers Cd tolerance in rice. This study provides potential candidate genes for studying the remediation of heavy metal pollution in plants.

Genetic Diversity and Divergence between Southern Japonica and Northern Japonica Rice Varieties in China.

Given the notable ecological and breeding disparities between southern and northern rice regions, delving into the genetic diversity and divergence between southern and northern japonica rice contributes to enhancing the genetic pool for japonica rice breeding. In this study, we analyzed 90 southern and 51 northern japonica rice varieties, focusing on nucleotide diversity (Pi), agronomic trait variations, population structure, genetic divergence, and a neutral test. For genetic diversity, the results demonstrated higher Pi in northern japonica rice varieties (NJRVs) on Chr2, Chr5, Chr6, Chr8, and Chr10, whereas in southern japonica rice varieties (SJRVs) on Chr7 and Chr9. In addition, SJRVs exhibited higher grain width and thickness, whereas NJRVs featured a higher grain aspect ratio, filled grain number, and grain number per panicle. Regarding genetic divergence, geographic differentiation existed between NJRVs and SJRVs, with Chr5 exhibiting numerous higher genetic differentiation windows, including cloned grain shape-controlling genes RGA1 and SFD5, stemming from intensified selection pressure on SJRVs. In summary, SJRVs and NJRVs exhibited diversity differences and genetic differentiation. Hence, it was suggested to conduct genetic introgression between NJRVs and SJRVs to broaden the genetic basis of the local japonica rice germplasm. By exploiting their heterotic advantage, new japonica rice cultivars with superior comprehensive traits could be developed.

Molecular Evolution of Rice Blast Resistance Gene bsr-d1

Rice blast, caused by the fungus Magnaporthe oryzae, reduces rice yields by 10% to 35%. Incorporating plant blast resistance genes into breeding programs is an effective strategy to combat this disease. Understanding the genetic variants that confer resistance is crucial to this strategy. The gene Bsr-d1 encodes a C2H2-like transcription factor, and its recessive allele confers broad-spectrum resistance against infections by various strains of M. oryzae. In this study, we investigated the molecular evolution of the rice blast resistance gene bsr-d1 in a representative population consisting of 827 cultivated and wild rice varieties. Our results revealed that wild rice exhibited significantly higher nucleotide diversity, with polymorphic regions primarily concentrated in the promoter region, in contrast to indica and japonica rice varieties. The Bsr-d1 gene displayed significant differentiation between indica and japonica, with the bsr-d1 resistance allele being unique to indica. Haplotype network and phylogenetic analyses suggested that the bsr-d1 resistance allele most likely originated from Oryza nivara in the region adjacent to the Indian Peninsula and the Indochina Peninsula. Moreover, we explored the utilization of bsr-d1 resistance alleles in China and designed a pair of DNA primers based on the polymorphic sites for the detection of the bsr-d1 resistance gene. In summary, our study uncovering the origin and evolution of bsr-d1 will enhance our comprehension of resistance gene variation and expedite the resistance breeding process.

Comprehensive phenotyping of SKUAST-K released rice varieties reveals significant role of root traits in drought resilience

The North Western Himalayan region, particularly the Kashmir valley, harbors a rich diversity of rice landraces, yet systematic studies on climate resilience are lacking. The present study was aimed at investigating the root traits and their interplay with shoot morphological and physiological traits under drought stress using seven indica and three japonica rice varieties released by SKUAST-Kashmir and their possible role in adaptive capacity to different environments. Significant variability was observed in root and shoot traits across the varieties. Root traits exhibited a wide phenotypic range, including rooting depth, fresh and dry weight, diameter, length, volume, surface area, and length density. Associations between root and shoot traits were identified, with notable correlations such as shoot weight with root shoot ratio, shoot length with root dry weight, diameter, and surface area, and tiller number with various root traits. Additionally, physiological traits like canopy temperature depression showed significant correlations with root depth and surface area. Principal component analysis (PCA) analysis grouped japonica type varieties together with a notable outlier, Chenab, due to its superior root traits among indica varieties. These findings emphasize the substantial contribution of root traits to productivity and advocate for their integration into varietal development processes. In view of the increasing evidences in crop plants about their role of root traits in defining plant productivity and reproductive fitness, study of root traits could provide valuable insights into the patterns of crop adaptation to diverse areas and growing environments.

Multi-omics reveals the metabolic changes and genetic basis of post-flowering rice caryopsis under blue light

BackgroundThe effects of blue light on photosynthetic organs have been studied. However, its effects on non-photosynthetic organs, in particular, on the early stages of rice caryopsis development, are unclear. Thus, we aimed to determine the metabolic characteristics of caryopsis development under blue light to improve the metabolic quality of crop kernels.ResultsWe conducted a multi-omics analysis of each of the three periods from the beginning of cellular differentiation to the end of morphogenesis in post-pollination seeds of a japonica rice variety to explore the effect of blue light on metabolic levels during these metabolic changes and its genetic basis. It was found that blue light caused a gradual decrease in auxin content, a significant increase in the accumulation of JA and flavonoids, and a downregulation of the expression of many starch-related genes and proteins, leads to reduced starch synthesis and smaller starch granules. In addition, the gene co-expression network identified three transcription factors that may regulate starch and two that may regulate flavonoids.ConclusionsIt was found through multi-omics testing that hormones such as jasmonic acid and auxins, and metabolites including alkaloids, flavonoids, lipids, organic acids, phenolic acids, and terpenoids altered significantly. Transcriptome and proteome analyses showed that blue light affected the seed nutrient repository activity. Specifically, starch- and gluten-related genes and proteins were significantly downregulated. Co- and WGCNA analyses identified several transcription factors that were regulated under blue light and identified key regulators of starch. Our study provides an understanding of the effects of blue light on post-flowering development in Gramineae and provides a framework for blue light-induced synthesis of secondary metabolites.Graphical

Developing a new active canopy sensor- and machine learning-based in-season rice nitrogen status diagnosis and recommendation strategy

ContextTraditional critical nitrogen (N) dilution curve (CNDC) construction for N nutrition index (NNI) determination has limitations for in-season crop N diagnosis and recommendation under diverse on-farm conditions. ObjectivesThis study was conducted to (i) develop a new rice (Oryza sativa L.) critical N concentration (Nc) determination approach using vegetation index-based CNDCs; and (ii) develop an N recommendation strategy with this new Nc determination approach and evaluate its reliability and practicality. MethodsFive years of plot and on-farm experiments involving three japonica rice varieties were conducted at fourteen sites in Qixing Farm, Northeast China. Two machine learning (ML) methods, random forest (RF) and extended gradient boosting (XGBoost) regression, were used to fuse multi-source data including genotype, environment, management, growth stage, normalized difference vegetation index (NDVI) and normalized difference red edge (NDRE) from portable active canopy sensor RapidSCAN. The CNDC was established using NDVI and NDRE instead of aboveground biomass (AGB) measured by destructive sampling. A new in-season N diagnosis and recommendation strategy was further developed using direct and indirect NNI prediction using multi-source data fusion and ML models. ResultsThe new CNDC based on NDVI or NDRE explained 94−96 % of Nc variability in the evaluation dataset when it was coupled with environmental and agronomic factors using ML models. The ML-based PNC and NNI prediction models explained 85 % and 21–36 % more variability over simple regression models using NDVI or NDRE in the evaluation dataset, respectively. The new in-season N diagnosis strategy using the NDVI and NDRE-based CNDCs and plant N concentration (PNC) predicted with RF model and multi-source data fusion performed slightly better than direct NNI prediction, explaining 7 % more of NNI variability and achieving 89 % of the areal agreement for N diagnosis across all evaluation experiments. Integrating this new N management strategy into the precision rice management system (as ML_PRM) increased yield, N use efficiency (NUE) and economic benefits over farmer’s practice (FP) by 7–15 %, 11–71 % and 4–16 % (161–596 $ ha−1), respectively, and increased NUE by 11–26 % and economic benefits by 8–97 $ ha−1 than regional optimum rice management (RORM) under rice N surplus status under on-farm conditions. ConclusionsIn-season rice N status diagnosis can be improved using NDVI- and NDRE-based CNDC and PNC predicted by ML modeling with multi-source data fusion. ImplicationsThe active canopy sensor- and ML-based in-season N diagnosis and management strategy is more practical for applications under diverse on-farm conditions and has the potential to improve rice yield and ecological and economic benefits.

Paclobutrazol Enhanced Stem Lodging Resistance of Direct-Seeded Rice by Affecting Basal Internode Development.

The objectives of this study were to explore the mechanism of stem mechanical strength in direct-seeded rice (DSR) as affected by paclobutrazol, especially its related endogenous hormone and cell wall component changes in culm tissue and response to the application of paclobutrazol. Field experiments were conducted in Changchun County, Jilin Province, China, by using two japonica rice varieties, Jiyujing and Jijing305, with soaking seeds in paclobutrazol at concentrations of (0 mg L-1, S0; 50 mg L-1; S1; 100 mg L-1; S2; 150 mg L-1, S3; 200 mg L-1, S4) in 2021 and 2022. The results suggest that the application of paclobutrazol increased the grain yield and reduced the lodging rate of DSR. Compared with the S0 treatments, soaking the seeds in paclobutrazol treatments rapidly shortened the length of the basal internode by decreasing the endogenous indole acetic acid (IAA) and gibberellin A3 (GA3) contents in culm tissue. The larger breaking strength (M) was attributed to a higher section modulus (SM) and bending stress (BS). The higher mechanical tissue thickness in culm tissue under paclobutrazol treatments, which was raised by higher endogenous zeatin and zeatin riboside (Z+ZR) content in culm tissue, increased the culm diameter, culm wall thickness, and section modulus (SM) of the internode. Compared with the S0 treatments, soaking the seeds in paclobutrazol treatments increased the cellulose content, lignin content, activities of lignin-related enzymes, and expression of key genes in lignin biosynthesis, as well as resulted in a higher bending stress (BS) to enhance the culm breaking strength (M).

Knocking out isopropylmalate synthase simultaneously improves grain appearance and nutritional quality in rice.

Grain appearance and nutritional quality are critical traits for rice marketing. However, how to simultaneously improve grain appearance (slender grain and low chalkiness) and nutritional quality (improved protein and amino acid contents) in rice remains a major challenge. Here, we show that knocking out rice isopropylmalate synthase genes OsIPMS1 and OsIPMS2 can improve both grain appearance and nutritional quality. We find that OsIPMS1 directly interacts with OsIPMS2 to form heterodimers. Meanwhile, we observe that OsIPMS1 and OsIPMS2 influence the expression of genes previously reported to be involved in the determination of grain size and nutritional quality in the developing panicles and grains. Furthermore, we show that Osipms1/2 double mutants exhibit significantly improved grain appearance and nutritional quality in polished rice in both the japonica (Wuyungeng 23) and indica (Huanghuazhan) varieties. Our findings indicate that OsIPMS is a useful target gene for breeding of rice varieties appealing for marketing and with health-benefiting properties.

Improvement of Flowering Stage in Japonica Rice Variety Jiahe212 by Using CRISPR/Cas9 System.

The flowering period of rice significantly impacts variety adaptability and yield formation. Properly shortening the reproductive period of rice varieties can expand their ecological range without significant yield reduction. Targeted genome editing, like CRISPR/Cas9, is an ideal tool to fine-tune rice growth stages and boost yield synergistically. In this study, we developed a CRISPR/Cas9-mediated multiplex genome-editing vector containing five genes related to three traits, Hd2, Ghd7, and DTH8 (flowering-stage genes), along with the recessive rice blast resistance gene Pi21 and the aromatic gene BADH2. This vector was introduced into the high-quality japonica rice variety in Zhejiang province, Jiahe212 (JH212), resulting in 34 T0 plants with various effective mutations. Among the 17 mutant T1 lines, several displayed diverse flowering dates, but most exhibited undesirable agronomic traits. Notably, three homozygous mutant lines (JH-C15, JH-C18, and JH-C31) showed slightly earlier flowering dates without significant differences in yield-related traits compared to JH212. Through special Hyg and Cas marker selection of T2 plants, we identified seven, six, and two fragrant glutinous plants devoid of transgenic components. These single plants will serve as sib lines of JH212 and potential resources for breeding applications, including maintenance lines for indica-japonica interspecific three-line hybrid rice. In summary, our research lays the foundation for the creation of short-growth-period CMS (cytoplasmic male sterility, CMS) lines, and also provides materials and a theoretical basis for indica-japonica interspecific hybrid rice breeding with wider adaptability.

A QTL GN1.1, encoding FT-L1, regulates grain number and yield by modulating polar auxin transport in rice.

Rice grain number is a crucial agronomic trait impacting yield. In this study, we characterized a quantitative trait locus (QTL), GRAIN NUMBER 1.1 (GN1.1), which encodes a Flowering Locus T-like1 (FT-L1) protein and acts as a negative regulator of grain number in rice. The elite allele GN1.1B, derived from the Oryza indica variety, BF3-104, exhibits a 14.6% increase in grain yield compared with the O. japonica variety, Nipponbare, based on plot yield tests. We demonstrated that GN1.1 interacted with and enhanced the stability of ADP-ribosylation factor (Arf)-GTPase-activating protein (Gap), OsZAC. Loss of function of OsZAC results in increased grain number. Based on our data, we propose that GN1.1B facilitates the elevation of auxin content in young rice panicles by affecting polar auxin transport (PAT) through interaction with OsZAC. Our study unveils the pivotal role of the GN1.1 locus in rice panicle development and presents a novel, promising allele for enhancing rice grain yield through genetic improvement.

Genetic Dissection of Major Rice QTLs for Strong Culms and Fine Mapping of qWS5 for Breeding Application in Transplanted System

BackgroundRice is one of the major staples that feeds about one half of the global populations, and it is important to identify the genetic loci for the traits related to yield improvement. Lodging will cause severe yield loss when it happens, and stem diameter has been characterized as an important trait for lodging resistance. However, most QTLs for stem diameter have not been finely dissected due to their sensitivity to environmental fluctuation.ResultIn this study, we performed QTL analysis for stem diameter using populations derived from Nipponbare (NIP) and strong culm variety YYP1, and confirmed the single and combined effect of three major QTLs by recombinant inbred lines (RILs). Based on the QTL location, we found that qWS5 is a novel QTL not well characterized before. To finely dissect the novel locus, several recombinant heterogeneous inbred families (HIFs) were selected from the RILs for linkage analysis and their derived nearly isogenic lines (NILs) were subjected to detailed trait investigation throughout different years. The HIF-NILs strategy confined the QTL to about 380 kb region supported by repeated genotype and phenotype data, and it lays the foundation for QTL cloning in the future. In addition, introgression of the QTL to an elite japonica variety SD785 was performed by successive backcrossing, and it confirmed the value of qWS5 in increasing stem diameter and other agronomic traits during rice breeding.ConclusionsWe prove that qWS5 is a novel QTL with relatively stable effect for stem diameter and the QTL can be finely mapped to small region by the HIF-NILs strategy. The result will facilitate the improvement of rice lodging resistance by molecular marker assisted selection breeding.

Transcription factor OsbZIP10 modulates rice grain quality by regulating OsGIF1.

Understanding and optimizing the process of grain filling helps the quest to maximize rice (Oryza sativa L.) seed yield and quality, yet the intricate mechanisms at play remain fragmented. Transcription factors (TFs) are major players in the gene networks underlying the grain filling process. Here, we employed grain incomplete filling (OsGIF1)/cell wall invertase 2, a key gene involved in grain filling, to explore its upstream TFs and identified a bZIP family TF, OsbZIP10, to be a transcriptional activator of OsGIF1. Rice grains of the knockouts of OsbZIP10 showed increased white-core rates but lower amylose content (AC), leading to better eating and cooking qualities in all genetic backgrounds investigated, though the impact of mutations in OsbZIP10 on grain weight depended on genetic background. Multi-omics analyses suggested that, in addition to OsGIF1, multiple genes involved in different biological processes contributing to grain filling were targeted by OsbZIP10, including OsAGPS1, a gene encoding the ADP-Glc pyrophosphorylase (AGPase) small subunit, and genes contributing to homeostasis of reactive oxygen species. Distinct genetic make-up was observed in OsbZIP10 between japonica and indica rice varieties, with the majority varieties of each subspecies belonging to two different haplotypes that were closely associated with AC. Overexpressing the haplotype linked to high-AC in the low-AC genetic background increased AC. Overall, this study sheds crucial light on the significance of the OsbZIP10-OsGIF1 module in the determination of rice grain quality, offering a potential avenue for genetic engineering of rice to produce seeds with tailored attributes.

The OsMYC2-JA feedback loop regulates diurnal flower-opening time via cell wall loosening in rice.

Diurnal flower-opening time (DFOT), the time of spikelet opening during the day, is an important trait for hybrid rice (Oryza sativa L.) seed production. Hybrids between indica and japonica rice varieties have strong heterosis, but the parental lines usually have different, nonoverlapping DFOTs. This reduces the success of hybrid seed production in crosses between indica and japonica subspecies, thus hindering the utilization of indica and japonica inter-subspecies heterosis. However, little is known about the molecular mechanisms regulating DFOT in rice. Here, we obtained japonica rice lines with a DFOT 1.5 h earlier than the wild type by overexpressing OsMYC2, a gene encoding a key transcription factor in the jasmonate (JA) signaling pathway. OsMYC2 is activated by JA signaling and directly regulates the transcription of genes related to JA biosynthesis and cell wall metabolism. Overexpressing OsMYC2 led to significantly increased JA contents and decreased cellulose and hemicellulose contents in lodicule cells, as well as the softening of lodicule cell walls. This may facilitate the swelling of lodicules, resulting in early diurnal flower-opening. These results suggest that the OsMYC2-JA feedback loop regulates DFOT in rice via cell wall remodeling. These findings shed light on the understanding of regulatory mechanism of the DFOT of plants, which should promote the development of indica and japonica varieties suitable for hybrid rice breeding.