Rice Heading Research Articles

Research Progress on Photoperiod Gene Regulation of Heading Date in Rice.

Heading date is a critical physiological process in rice that is influenced by both genetic and environmental factors. The photoperiodic pathway is a primary regulatory mechanism for rice heading, with key florigen genes Hd3a (Heading date 3a) and RFT1 (RICE FLOWERING LOCUS T1) playing central roles. Upstream regulatory pathways, including Hd1 and Ehd1, also significantly impact this process. This review aims to provide a comprehensive examination of the localization, cloning, and functional roles of photoperiodic pathway-related genes in rice, and to explore the interactions among these genes as well as their pleiotropic effects on heading date. We systematically review recent advancements in the identification and functional analysis of genes involved in the photoperiodic pathway. We also discuss the molecular mechanisms underlying rice heading date variation and highlight the intricate interactions between key regulatory genes. Significant progress has been made in understanding the molecular mechanisms of heading date regulation through the cloning and functional analysis of photoperiod-regulating genes. However, the regulation of heading date remains complex, and many underlying mechanisms are not yet fully elucidated. This review consolidates current knowledge on the photoperiodic regulation of heading date in rice, emphasizing novel findings and gaps in the research. It highlights the need for further exploration of the interactions among flowering-related genes and their response to environmental signals. Despite advances, the full regulatory network of heading date remains unclear. Further research is needed to elucidate the intricate gene interactions, transcriptional and post-transcriptional regulatory mechanisms, and the role of epigenetic factors such as histone methylation in flowering time regulation. This review provides a detailed overview of the current understanding of photoperiodic pathway genes in rice, setting the stage for future research to address existing gaps and improve our knowledge of rice flowering regulation.

Rice response to fluridone following topsoil removal on a precision‐leveled field

AbstractFurrow‐irrigated rice (Oryza sativa L.) production requires additional management options without the cultural strategy of a flood. In 2023, fluridone (Brake) was registered for use in rice production. Precision‐leveling land is an important aspect of maintaining an effective irrigation flow path; however, the removal of topsoil can severely impact crop response from residual herbicides. The objective of this study was to evaluate the impact of fluridone on rice response when applied to a precision‐leveled field following topsoil removal. An on‐farm field study was conducted in 2023 near Osceola, AR, with a Sharkey‐Steele clay complex soil texture. The study consisted of six herbicide treatments applied at the rice three‐leaf stage. These treatments included clomazone, quinclorac, and fluridone at three rates (0.5×, 1×, and 2× of a label rate) and a nontreated control. Across evaluation times, maximum visual rice injury was greater than 25% and 65% for the fluridone 1× and 2× treatments, respectively. Rice canopy coverage was reduced in the fluridone 1× and 2× treatments compared to all other treatments from 6 to 10 weeks after application (WAA). Rice heading in the fluridone 2x treatment was delayed by more than 60 and 30 percentage points at 11 and 12 WAA, respectively, compared to all other treatments. Rough rice yield in the fluridone 2× treatment was reduced by 21% compared to all other treatments. Overall, fluridone 1× and 2× rates caused substantial rice injury and would not be recommended on a precision‐leveled field.

Comparative transcriptome analysis reveals major genes, transcription factors and biosynthetic pathways associated with leaf senescence in rice under different nitrogen application

BackgroundRice (Oryza sativa L.) is one of the most important food crops in the world and the application of nitrogen fertilizer is an effective means of ensuring stable and high rice yields. However, excessive application of nitrogen fertilizer not only causes a decline in the quality of rice, but also leads to a series of environmental costs. Nitrogen reutilization is closely related to leaf senescence, and nitrogen deficiency will lead to early functional leaf senescence, whereas moderate nitrogen application will help to delay leaf senescence and promote the production of photosynthetic assimilation products in leaves to achieve yield increase. Therefore, it is important to explore the mechanism by which nitrogen affects rice senescence, to search for genes that are tolerant to low nitrogen, and to delay the premature senescence of rice functional leaves.ResultsThe present study was investigated the transcriptional changes in flag leaves between full heading and mature grain stages of rice (O. sativa) sp. japonica ‘NanGeng 5718’ under varying nitrogen (N) application: 0 kg/ha (no nitrogen; 0N), 240 kg/ha (moderate nitrogen; MN), and 300 kg/ha (high nitrogen; HN). Compared to MN condition, a total of 10427 and 8177 differentially expressed genes (DEGs) were detected in 0N and HN, respectively. We selected DEGs with opposite expression trends under 0N and HN conditions for GO and KEGG analyses to reveal the molecular mechanisms of nitrogen response involving DEGs. We confirmed that different N applications caused reprogramming of plant hormone signal transduction, glycolysis/gluconeogenesis, ascorbate and aldarate metabolism and photosynthesis pathways in regulating leaf senescence. Most DEGs of the jasmonic acid, ethylene, abscisic acid and salicylic acid metabolic pathways were up-regulated under 0N condition, whereas DEGs related to cytokinin and ascorbate metabolic pathways were induced in HN. Major transcription factors include ERF, WRKY, NAC and bZIP TF families have similar expression patterns which were induced under N starvation condition.ConclusionOur results revealed that different nitrogen levels regulate rice leaf senescence mainly by affecting hormone levels and ascorbic acid biosynthesis. Jasmonic acid, ethylene, abscisic acid and salicylic acid promote early leaf senescence under low nitrogen condition, ethylene and ascorbate delay senescence under high nitrogen condition. In addition, ERF, WRKY, NAC and bZIP TF families promote early leaf senescence. The relevant genes can be used as candidate genes for the regulation of senescence. The results will provide gene reference for further genomic studies and new insights into the gene functions, pathways and transcription factors of N level regulates leaf senescence in rice, thereby improving NUE and reducing the adverse effects of over-application of N.

Effects of Pesticides Use on Pesticides Residues and Its Environmental Risk Assessment in Xingkai Lake（China）

Xingkai Lake, located in Heilongjiang Province, is an important fishery and agricultural base and is seriously polluted by agricultural non-point sources. To clarify the residual status of many pesticides in the surface water of Xingkai Lake, 27 types of pesticides, herbicides, and their degradation products were analyzed in rice paddy, drainage, and surface water around Xingkai Lake (China) during the rice heading and maturity periods. The results showed that all 27 types of pesticides, herbicides, and their degradation products were detected during the rice heading period, and the total concentration ranged from 247.97 to 6 094.49 ng·L-1. Additionally, 25 species were detected during the rice maturity period, and the total concentration ranged from 485.36 to 796.23 ng·L-1. In comparison, more pesticides, herbicides, and derived degradation products were detected during the heading period, and their total concentration was higher as well. During the rice heading period, atrazine, simetryn, and paclobutrazol were the main detected pesticides, atrazine and isoprothiolane were the main pesticides detected during the maturity period. The distribution characteristics of pesticides and herbicides in the surface water around Xingkai Lake (China) was similar to that in drainage, so they were probably imported from the drainage and rice paddy. The average risk quotient (RQ) values of atrazine, simetryn, prometryn, butachlor, isoprothiolane, and oxadiazon were higher than 0.1 in drainage and Xingkai Lake (China), which showed a potential risk to aquatic organisms.

Estimation of the rice aboveground biomass based on the first derivative spectrum and Boruta algorithm.

Aboveground biomass (AGB) is regarded as a critical variable in monitoring crop growth and yield. The use of hyperspectral remote sensing has emerged as a viable method for the rapid and precise monitoring of AGB. Due to the extensive dimensionality and volume of hyperspectral data, it is crucial to effectively reduce data dimensionality and select sensitive spectral features to enhance the accuracy of rice AGB estimation models. At present, derivative transform and feature selection algorithms have become important means to solve this problem. However, few studies have systematically evaluated the impact of derivative spectrum combined with feature selection algorithm on rice AGB estimation. To this end, at the Xiaogang Village (Chuzhou City, China) Experimental Base in 2020, this study used an ASD FieldSpec handheld 2 ground spectrometer (Analytical Spectroscopy Devices, Boulder, Colorado, USA) to obtain canopy spectral data at the critical growth stage (tillering, jointing, booting, heading, and maturity stages) of rice, and evaluated the performance of the recursive feature elimination (RFE) and Boruta feature selection algorithm through partial least squares regression (PLSR), principal component regression (PCR), support vector machine (SVM) and ridge regression (RR). Moreover, we analyzed the importance of the optimal derivative spectrum. The findings indicate that (1) as the growth stage progresses, the correlation between rice canopy spectrum and AGB shows a trend from high to low, among which the first derivative spectrum (FD) has the strongest correlation with AGB. (2) The number of feature bands selected by the Boruta algorithm is 19~35, which has a good dimensionality reduction effect. (3) The combination of FD-Boruta-PCR (FB-PCR) demonstrated the best performance in estimating rice AGB, with an increase in R² of approximately 10% ~ 20% and a decrease in RMSE of approximately 0.08% ~ 14%. (4) The best estimation stage is the booting stage, with R2 values between 0.60 and 0.74 and RMSE values between 1288.23 and 1554.82 kg/hm2. This study confirms the accuracy of hyperspectral remote sensing in estimating vegetation biomass and further explores the theoretical foundation and future direction for monitoring rice growth dynamics.

Impact of Duckweed (Lemna minor L.) Growing in Paddy Fields on Rice Yield and Its Underlying Causes

Duckweed growing in paddy fields (DGP) has substantially increased because of the effects of climate warming and/or eutrophication in irrigated water. Previous studies have primarily focused on investigating the effects of DGP as a nonchemical agent for enhancing rice productivity on nitrogen utilization in rice paddy fields. However, how DGP impacts rice yield remains poorly understood. Therefore, a field experiment with three representative rice cultivars was conducted to determine the effects of DGP on rice yield, considering ecological factors, photosynthetic capacity, spectral changes, and plant growth. The results showed that DGP significantly reduced the pH value by 0.6 and the daily water temperature by 0.6 °C, accelerated rice heading by 1.6 days and increased the soil and plant analyzer development (SPAD) and photosynthetic rate of leaves by 10.8% and 14.4% on average, respectively. DGP also markedly enhanced the values of various vegetation indices such as RARSc, MTCI, GCI, NDVI705, CI, CIrededge, mND705, SR705, and GM, and the first derivative curve of the rice canopy reflectance spectrum exhibited a ‘red shift’ phenomenon upon DGP treatment. Changes in the aforementioned factors may lead to average increases of 4.7% in plant height, 15.0% in dry matter weight, 10.6% in panicles m−2, 2.3% in 1000-grain weight, and ultimately a 10.2% increase in grain yield. The correlation observed suggested that the DGP-induced enhancement in grain yield can be achieved by reducing the pH and temperature of the paddy water, thus enhancing the SPAD value and photosynthesis of leaves and stimulating rice plant growth. These results could offer valuable theoretical support for the future sustainable development of agriculture and the environment through the biological synergy between rice and duckweed.

Can ethylenediurea (EDU) alter the effects of ozone on the source-sink regulation of nitrogen uptake and remobilization during grain filling period in rice?

Increased surface ozone (O3) pollution seriously threatens crop production, and ethylenediurea (EDU) can alleviate crop yield reduction caused by O3. However, the reason for the decrease in grain nitrogen (N) accumulation caused by O3 and whether EDU serves as N fertilizer remain unclear. An experiment was conducted to investigate the impacts of factorial combinations of O3 enrichment (ambient air plus 60 ppb) and EDU (foliage spray with 450 ppm solutions) on N concentration, accumulation and remobilization in hybrid rice seedlings. Compared to ambient condition, elevated O3 significantly inhibited the N accumulation in vegetative organs during anthesis and grain N accumulation during the maturity stage. Elevated O3 significantly decreased the total N accumulation during anthesis and maturity stages, with a greater impact at the latter stage. The decrease in grain N accumulation caused by O3 was attributed to a decrease in N remobilization of vegetative organs during the grain filling period as well as to a decrease in post-anthesis N uptake. However, there was no significant change in the proportion of N remobilization and N uptake in grain N accumulation. The inhibitory effect of O3 on N remobilization in the upper canopy leaves was greater than that in the lower canopy leaves. In addition, elevated O3 increased the N accumulation of panicles at the anthesis stage, mainly by resulting in earlier heading of rice. EDU only increased N accumulation at the maturity stage, which was mainly attributed to an increase in rice biomass by EDU. EDU had no significant effect on N concentration, N remobilization process, and N harvest index. The findings are helpful to better understand the utilization of N fertilizer by rice under O3 pollution, and can also provide a theoretical basis for sustainable nutrient management to alleviate the negative impact of O3 on crop yield and quality.

QTL-seq analysis identified the genomic regions of plant height and days to heading in high-latitude rice.

Introduction: Rice (Oryza sativa L.) is one of the most extensive crops in the world. China's Heilongjiang Province is the northernmost rice-growing region in the world. However, rice cultivars suitable for growth in low-latitude regions may not mature normally due to their distinct climate and short frost-free period. It is necessary to precisely determine the frost-free period for each region to make the best use of the rice growth stage so as to ensure the maturity and yield of different rice cultivars in Heilongjiang Province. The time span of the heading stage is a key parameter for evaluating the adaptability of a rice cultivar to a specific rice-growing region. Given the above facts, it is of high importance to study the associated genes and sites controlling days to heading (DH) and plant height (PH) of rice in Heilongjiang Province. Bulked segregant analysis (BSA) combined with high-throughput sequencing can effectively exclude interferences from background genomic differences, making it suitable for analyzing the associated sites of complex agronomic traits in early generations. Methods: In this study, an F3 segregating population was obtained by crossing two main cultivars that are grown under different temperatures and day-light conditions in Heilongjiang. Two pools of extreme phenotypes were built for the DH and PH of the population. For SNP and InDel variants obtained from whole-genome resequencing in the pools, an association analysis was performed using the Euclidean distance (ED) algorithm and the SNP/InDel index algorithm. Results: The intersection of SNP and InDel regions associated with the phenotypes was considered to obtain the final associated sites. After excluding interferences from the cloned genes on chromosomes 2 and 7, a total length of 6.34Mb on chromosomes 1, 3, and 10 and 3.16Mb on chromosomes 1 and 10 were left associated with PH and DH, respectively. Then, we performed a gene annotation analysis for candidate genes in the remaining regions using multiple genome annotation databases. Our research provides basic data for subsequent gene mapping and cloning. Discussion: By mining more genetic loci associated with the days to heading and plant height of rice, we may provide abundant genetic resources for refined molecular breeding in Heilongjiang Province.

Phosphatidyl Ethanolamine Binding Protein FLOWERING LOCUS T-like 12 (OsFTL12) Regulates the Rice Heading Date under Different Day-Length Conditions.

Plant FLOWERING LOCUS T-Like (FTL) genes often redundantly duplicate on chromosomes and functionally diverge to modulate reproductive traits. Rice harbors thirteen FTL genes, the functions of which are still not clear, except for the Hd3a and RFT genes. Here, we identified the molecular detail of OsFTL12 in rice reproductive stage. OsFTL12 encoding protein contained PEBP domain and localized into the nucleus, which transcripts specifically expressed in the shoot and leaf blade with high abundance. Further GUS-staining results show the OsFTL12 promoter activity highly expressed in the leaf and stem. OsFTL12 knock-out concurrently exhibited early flowering phenotype under the short- and long-day conditions as compared with wild-type and over-expression plants, which independently regulates flowering without an involved Hd1/Hd3a and Ehd1/RFT pathway. Further, an AT-hook protein OsATH1 was identified to act as upstream regulator of OsFTL12, as the knock-out OsATH1 elevated the OsFTL12 expression by modifying Histone H3 acetylation abundance. According to the dissection of OsFTL12 molecular functions, our study expanded the roles intellectual function of OsFTL12 in the mediating of a rice heading date.

Mechanical Analysis of Rice Canopy Using Explicit Dynamics and Practical Applications of Canopy Opener

Open-canopy pesticide application technology is not affected by the canopy structure and can substantially increase droplet penetration and deposition in the middle and lower rice canopy. However, the optimal working position of the canopy opener is difficult to determine. The purpose of this study was to examine the characteristics of rice canopy disturbances under the action of a canopy opener, verify simulation results using high-speed photography tests, and identify the spraying effect of the optimal operating parameters of a canopy opener through spray tests. The mechanical characteristic parameters of the rice heading stage were determined through experiments, and the canopy-opening process was simulated based on the finite element method of explicit dynamics. The simulation results show that when the speed of the canopy opener is 1.2 m s−1 and the height is 0.6 m, the rice canopy is the most disturbed. The spray experiment results show that under this condition, the overall coverage rate of the rice canopy is relatively high, and the coverage rates of the upper, middle, and lower layers of rice are 92.18%, 66.43%, and 52.84%, respectively.

Improving rice eating and cooking quality by enhancing endogenous expression of a nitrogen-dependent floral regulator.

Improving rice eating and cooking quality (ECQ) is one of the primary tasks in rice production to meet the rising demands of consumers. However, improving grain ECQ without compromising yield faces a great challenge under varied nitrogen (N) supplies. Here, we report the approach to upgrade rice ECQ by native promoter-controlled high expression of a key N-dependent floral and circadian clock regulator Nhd1. The amplification of endogenous Nhd1 abundance alters rice heading date but does not affect the entire length of growth duration, N use efficiency and grain yield under both low and sufficient N conditions. Enhanced expression of Nhd1 reduces amylose content, pasting temperature and protein content while increasing gel consistence in grains. Metabolome and transcriptome analyses revealed that increased expression of Nhd1 mainly regulates the metabolism of carbohydrates and amino acids in the grain filling stage. Moreover, expression level of Nhd1 shows a positive relationship with grain ECQ in some local main cultivars. Thus, intensifying endogenous abundance of Nhd1 is a promising strategy to upgrade grain ECQ in rice production.

UAV time-series imagery with novel machine learning to estimate heading dates of rice accessions for breeding

Timely monitoring of rice heading dates is essential for estimating growth status and grain yield in rice breeding. This study aims to develop a machine learning method to classify growth stages and estimate the days from sowing to initial heading (IHD) and days from sowing to full heading (FHD) of rice accessions from unmanned aerial vehicle (UAV)-based imagery. A two-year field experiment was conducted on different rice accessions, including doubled-haploid (DH) lines, early maturing F1 hybrids, and cultivars at two different locations (i.e., EXP 1 and EXP 2). A neural network, namely Res2Net50, was first used to classify the rice growth stages based on UAV RGB images. The partial least squares regression (PLSR) model was then developed to predict IHD and FHD by using canopy reflectance extracted from multispectral images. The results showed that the Res2Net50 model successfully identified five growth stages with overall accuracies of 86% and 83% in EXP 1 and EXP 2, respectively. PLSR models developed with image data after the Res2Net50 classification achieved good performances on predicting IHD and FHD with the coefficient of determination (R2) of 0.60–0.78, root mean square error (RMSE) ranging from 3.9 days to 5.1 days, and relative root mean square error (rRMSE) varied between 4% to 6%. Model validation with ten cultivars further demonstrated the capability of proposed method for IHD and FHD predictions and achieved the rRMSE of 3%-4%, which was comparable with that obtained by field inspection. Furthermore, the feasibility of the proposed method in monitoring of the rice heading dynamics was validated by EXP 2 using the model transfer. The proposed approach enables quantification of heading dates of diverse rice accessions in breeding and could be used as a high-throughput screening technique for accelerating rice breeding.

The Significance of Florigen Activation Complex in Controlling Flowering in Rice

Yield potential, plant height and flowering time are three classes of traits that determine the productivity of rice. Rice heading greatly depends on the accurate measurement of environment changes, particularly in day length and temperature. We discuss all genes reported to be related to the heading time in this review. The accumulation of florigen, such as Hd3a or RFT1, is the key factor for rice heading. Florigen is found in the rice leaf and then transports into the shoot apical meristem (SAM), where floral initiation occurs. We discuss the formation of florigen activation complex (FAC) with 14-3-3 and FD1 proteins to induce the expression of flowering genes. In addition, two key pathways related to heading date, GI-Hd1-Hd3a and Ghd7-Ehd1-Hd3a/RFT1 are introduced in this review. We summarize proteins with histone modification functions, due to the modification of histone is also significant for heading date. The flowering time also extremely dependent on the environments, including nutrient availability, abiotic and biotic stresses, we argue the phenotypes of rice heading date under different extreme environments, as well. Lastly, we gather genes that are reported having a change in heading time, but their detail molecular regulation is still elusive. Thus, this review introduces heading time systematically, providing knowledge and ideas for researchers to study further the phenotype of heading time.

The amino acid residue E96 of Ghd8 is crucial for the formation of the flowering repression complex Ghd7-Ghd8-OsHAP5C in rice.

Ghd7 is an important gene involved in the photoperiod flowering pathway in rice. A Ghd7-involved transcriptional regulatory network has been established, but its translational regulatory pathway is poorly understood. The mutant suppressor of overexpression of Ghd7 (sog7) was identified from EMS-induced mutagenesis on the background of ZH11 overexpressing Ghd7. MutMap analysis revealed that SOG7 is allelic to Ghd8 and delayed flowering under long-day (LD) conditions. Biochemical assays showed that Ghd8 interacts with OsHAP5C and Ghd7 both in vivo and in vitro. Surprisingly, a point mutation E96K in the α2 helix of the Ghd8 histone fold domain (HFD) destroyed its ability to interact with Ghd7. The prediction of the structure shows that mutated amino acid is located in the interaction region of CCT/NF-YB/YC complexes, which alter the structure of α4 of Ghd8. This structural difference prevents the formation of complex NF-YB/YC. The triple complex of Ghd8-OsHAP5C-Ghd7 directly bound to the promotor of Hd3a and downregulated the expression of Ehd1, Hd3a and RFT1, and finally resulted in a delayed heading. These findings are helpful in deeply understanding the Ghd7-involved photoperiod flowering pathway and promote the elucidation of rice heading.

Genetic basis of the early heading of high-latitude weedy rice

Japonica rice (Oryza sativa L.) is an important staple food in high-latitude regions and is widely distributed in northern China, Japan, Korea, and Europe. However, the genetic diversity of japonica rice is relatively narrow and poorly adapted. Weedy rice (Oryza sativa f. spontanea) is a semi-domesticated rice. Its headings are earlier than the accompanied japonica rice, making it a potential new genetic resource, which can make up for the defects of wild rice that are difficult to be directly applied to japonica rice improvement caused by reproductive isolation. In this study, we applied a natural population consisting of weedy rice, japonica landrace, and japonica cultivar to conduct a genome-wide association study (GWAS) of the heading date and found four loci that could explain the natural variation of the heading date in this population. At the same time, we developed recombinant inbred lines (RILs) crossed by the early-heading weedy rice WR04-6 and its accompanied japonica cultivar ShenNong 265 (SN265) to carry out a QTL mapping analysis of the heading date and mapped four quantitative trait locus (QTLs) and three epistatic effect gene pairs. The major locus on chromosome 6 overlapped with the GWAS result. Further analysis found that two genes, Hd1 and OsCCT22, on chromosome 6 (Locus 2 and Locus 3) may be the key points of the early-heading character of weedy rice. As minor effect genes, Dth7 and Hd16 also have genetic contributions to the early heading of weedy rice. In the process of developing the RIL population, we introduced fragments of Locus 2 and Locus 3 from the weedy rice into super-high-yielding japonica rice, which successfully promoted its heading date by at least 10 days and expanded the rice suitable cultivation area northward by about 400km. This study successfully revealed the genetic basis of the early heading of weedy rice and provided a new idea for the genetic improvement of cultivated rice by weedy rice.

Identification of QTLs for Heat Tolerance at the Flowering Stage Using Chromosome Segment Substitution Lines in Rice

High temperature is a major stress in rice production. Although considerable progress has been made in investigating heat tolerance (HT) in rice, the genetic basis of HT at the heading stage remains largely unknown. In this study, a novel set of chromosome segment substitution lines (CSSLs) consisting of 113 lines derived from a heat-resistant indica variety N22 and a heat-sensitive indica variety 9311 was developed and used for the analysis of the genetic basis of HT. The heat sensitivity index (HSI) calculated based on seed-setting rates under natural and high-temperature environments was used to evaluate the influence of HT at the rice heading stage. In total, five quantitative trait loci (QTLs) associated with HT were detected based on seed-setting rate (SSR) evaluation; these were named qSSR6-1, qSSR7-1, qSSR8-1, qSSR9-1 and qSSR11-1 located on chromosomes 6, 7, 8, 9 and 11, respectively. Heat-tolerant alleles of the QTLs were all derived from N22. Among them, qSSR9-1 overlapped with QTLs identified previously, while the remaining QTLs were found novel. In particular, qSSR7-1 explained a high phenotypic variation of 26.35% with a LOD score of 10.75, thus deserved to be further validated. These findings will increase our understanding of the genetic mechanism underlying HT and facilitate the breeding of heat-tolerant rice varieties.

Functional Conservation and Divergence of MOS1 That Controls Flowering Time and Seed Size in Rice and Arabidopsis.

The heading date and grain size are two essential traits affecting rice yield. Here, we found that OsMOS1 promotes rice heading and affects its grain size. Knocking out OsMOS1 delayed heading, while the overexpression of OsMOS1 promoted heading in rice under long-day conditions. The transcriptions of the heading activators Ehd1, Hd3a, and RFT1 were decreased and the heading repressor Hd1 was increased in the osmos1 mutant. Conversely, the overexpression of OsMOS1 promoted the expressions of Ehd1, Hd3a, and RFT1, but inhibited the expression of Hd1. This suggests that OsMOS1 may control heading in rice by modulating the transcriptions of Ehd1, Hd3a, RFT1, and Hd1. In addition, knocking out OsMOS1 led to larger grains with longer grain lengths and higher grain weights. The seed cell size measurement showed that the cell lengths and cell widths of the outer glume epidermal cells of the osmos1 mutant were greater than those of the wild type. Furthermore, we also found that the overexpression of OsMOS1 in the Arabidopsis mos1 mutant background could suppress its phenotypes of late flowering and increased seed size. Thus, our study shows a conserved function of MOS1 in rice and Arabidopsis, and these findings shed light on the heading and seed size regulation in rice and suggest that OsMOS1 is a promising target for rice yield improvement.

Temporal dynamics of total and active root-associated diazotrophic communities in field-grown rice

Plant-associated nitrogen-fixing microorganisms (diazotrophs) are essential to host nutrient acquisition, productivity and health, but how host growth affects the succession characteristics of crop diazotrophic communities is still poorly understood. Here, Illumina sequencing of DNA- and RNA-derived nifH genes was employed to investigate the dynamics of total and active diazotrophic communities across rhizosphere soil and rice roots under four fertilization regimes during three growth periods (tillering, heading and mature stages) of rice in 2015 and 2016. Our results indicated that 71.9–77.2% of the operational taxonomic units (OTUs) were both detected at the DNA and RNA levels. According to the nonmetric multidimensional scaling ordinations of Bray–Curtis distances, the variations in community composition of active rhizosphere diazotrophs were greater than those of total rhizosphere diazotrophs. The community composition (β-diversity) of total and active root-associated diazotrophs was shaped predominantly by microhabitat (niche; R2 ≥ 0.959, p < 0.001), followed by growth period (R2 ≥ 0.15, p < 0.001). The growth period had a stronger effect on endophytic diazotrophs than on rhizosphere diazotrophs. From the tillering stage to the heading stage, the α-diversity indices (Chao1, Shannon and phylogenetic diversity) and network topological parameters (edge numbers, average clustering coefficient and average degree values) of total endophytic diazotrophic communities increased. The proportions of OTUs shared by the total rhizosphere and endophytic diazotrophs in rhizosphere diazotrophs gradually increased during rice growth. Moreover, total diazotrophic α-diversity and network complexity decreased from rhizosphere soil to roots. Collectively, compared with total diazotrophic communities, active diazotrophic communities were better indicators of biological response to environmental changes. The host microhabitat profoundly drove the temporal dynamics of total and active root-associated diazotrophic communities, followed by the plant growth period.

QHD5 encodes an AP2 factor that suppresses rice heading by down-regulating Ehd2 expression

Heading date is crucial for rice reproduction and the geographical expansion of cultivation. We fine-mapped qHD5 and identified LOC_Os05g03040, a gene that encodes an AP2 transcription factor, as the candidate gene of qHD5 in our previous study. In this article, using two near-isogenic lines NIL(BG1) and NIL(XLJ), which were derived from the progeny of the cross between BigGrain1 (BG1) and Xiaolijing (XLJ), we verified that LOC_Os05g03040 represses heading date in rice through genetic complementation and CRISPR/Cas9 gene-editing experiments. Complementary results showed that qHD5 is a semi-dominant gene and that the qHD5XLJ and qHD5BG1 alleles are both functional. The homozygous mutant line generated from knocking out qHD5XLJ in NIL(XLJ) headed earlier than NIL(XLJ) under both short-day and long-day conditions. In addition, the homozygous mutant line of qHD5BG1 in NIL(BG1) also headed slightly earlier than NIL(BG1). All of these results show that qHD5 represses the heading date in rice. Transient expression showed that the qHD5 protein localizes to the nucleus. Transactivation activity assays showed that the C-terminus is the critical site that affects self-activation in qHD5XLJ. qRT-PCR analysis revealed that qHD5 represses flowering by down-regulating Ehd2. qHD5 may have been selected during indica rice domestication.

Remote Sensing-Based Evaluation of Heat Stress Damage on Paddy Rice Using NDVI and PRI Measured at Leaf and Canopy Scales

Extremely high air temperature at the heading stage of paddy rice causes a yield reduction due to the increasing spikelet sterility. Quantifying the damage to crops caused by high temperatures can lead to more accurate estimates of crop yields. The remote sensing technique evaluates crop conditions indirectly but provides information related to crop physiology, growth, and yield. In this study, we aim to assess the crop damage caused by heat stress in paddy rice examined under elevated air temperatures in a temperature gradient field chamber from 2016 to 2019, using remote-sensed vegetation indices. A leaf-spectrometer, field-spectrometers, and a multi-spectral camera were used to monitor the conditions of paddy rice. Although, in the leaf- and canopy-scales, the values of normalized difference vegetation index (NDVI) and photochemical reflectance index (PRI) decreased after the heading of rice under normal conditions, the decreasing sensitivity of NDVI and PRI was different depending on the degree of physiological heat stress by high temperature conditions. The NDVI after the heading under extremely high air temperature was not dropped and remained the value before heading. The PRI decreased at all air temperature conditions after the heading; the PRI of the plot exposed to the elevated air temperature was higher than that under ambient air temperature. Further, the relative change in NDVI and PRI after the heading exhibited a strong relationship with the ripening ratio of paddy rice, which is the variable related to crop yield. These remote-sensing results aid in evaluating the crop damage caused by heat stress using vegetation indices.