Japonica Varieties Research Articles

QTL Mapping of Tiller Number in Korean Japonica Rice Varieties.

Tiller number is an important trait associated with yield in rice. Tiller number in Korean japonica rice was analyzed under greenhouse conditions in 160 recombinant inbred lines (RILs) derived from a cross between the temperate japonica varieties Odae and Unbong40 to identify quantitative trait loci (QTLs). A genetic map comprising 239 kompetitive allele-specific PCR (KASP) and 57 cleaved amplified polymorphic sequence markers was constructed. qTN3, a major QTL for tiller number, was identified at 132.4 cm on chromosome 3. This QTL was also detected under field conditions in a backcross population; thus, qTN3 was stable across generations and environments. qTN3 co-located with QTLs associated with panicle number per plant and culm diameter, indicating it had pleiotropic effects. The qTN3 regions of Odae and Unbong40 differed in a known functional variant (4 bp TGTG insertion/deletion) in the 5' UTR of OsTB1, a gene underlying variation in tiller number and culm strength. Investigation of variation in genotype and tiller number revealed that varieties with the insertion genotype had lower tiller numbers than those with the reference genotype. A high-resolution melting marker was developed to enable efficient marker-assisted selection. The QTL qTN3 will therefore be useful in breeding programs developing japonica varieties with optimal tiller numbers for increased yield.

Genomic variations combined with epigenetic modifications rewire open chromatin in rice.

Cis-regulatory elements (CREs) fine-tune gene transcription in eukaryotes. CREs with sequence variations play vital roles in driving plant or crop domestication. However, how global sequence and structural variations are responsible for multi-level changes between indica and japonica rice (Oryza sativa) is still not fully elucidated. To address this, we conducted multi-omics studies using MH-seq (MNase hypersensitivity sequencing) in combination with RNA-seq, ChIP-seq and BS-seq between the japonica rice variety Nipponbare (NIP) and indica rice variety 93-11. We found that differential MHSs exhibited some distinct intrinsic genomic sequence features between NIP and 93-11. Notably, through MHS-GWAS integration, we found that key sequence variations may be associated with differences of agronomic traits between NIP and 93-11, which is partly achieved by MHSs harboring CREs. In addition, SV-derived differential MHSs caused by TE insertion, especially by non-common TEs among rice varieties, were associated with genes with distinct functions, indicating that TE driven gene neo- or subfunctionalization is mediated by changes of chromatin openness. This study thus provides insights into how sequence and genomic structural variations control agronomic traits of NIP and 93-11; it also provides genome editing targets for molecular breeding aiming at improving favorable agronomic properties.

A Frameshift Mutation in the Mg-Chelatase I Subunit Gene OsCHLI Is Associated with a Lethal Chlorophyll-Deficient, Yellow Seedling Phenotype in Rice.

Chlorophyll biosynthesis is a crucial biological process in plants, and chlorophyll content is one of the most important traits in rice breeding programs. In this study, we identified a lethal, chlorophyll-deficient, yellow seedling (YS) phenotype segregating in progeny of CR5055-21, an F2 plant derived from a backcross between Korean japonica variety 'Hwaseong' (Oryza sativa) and CR5029, which is mostly Hwaseong with a small amount of Oryza grandiglumis chromosome segments. The segregation of the mutant phenotype was consistent with a single gene recessive mutation. Light microscopy of YS leaf cross-sections revealed loosely arranged mesophyll cells and sparse parenchyma in contrast to wildtype. In addition, transmission electron microscopy showed that chloroplasts did not develop in the mesophyll cells of the YS mutant. Quantitative trait loci (QTL)-seq analysis did not detect any significant QTL, however, examination of the individual delta-SNP index identified a 2-bp deletion (AG) in the OsCHLI gene, a magnesium (Mg)-chelatase subunit. A dCAPs marker was designed and genotyping of a segregating population (n = 275) showed that the mutant phenotype co-segregated with the marker. The 2-bp deletion was predicted to result in a frameshift mutation generating a premature termination. The truncated protein likely affects formation and function of Mg-chelatase, which consists of three different subunits that together catalyze the first committed step of chlorophyll biosynthesis. Transcriptome analysis showed that photosynthesis and carbohydrate metabolism pathways were significantly altered although expression of OsCHLI was not. Chlorophyll- and carotenoid-related genes were also differentially expressed in the YS mutant. Our findings demonstrated that OsCHLI plays an important role in leaf pigment biosynthesis and leaf structure development in rice.

Transcriptomic Analysis and Salt-Tolerance Gene Mining during Rice Germination.

Salt stress is an important environmental factor affecting crop growth and development. One of the important ways to improve the salt tolerance of rice is to identify new salt-tolerance genes, reveal possible mechanisms, and apply them to the creation of new germplasm and the breeding of new varieties. In this study, the salt-sensitive japonica variety Tong 35 (T35) and salt-tolerant japonica variety Ji Nongda 709 (JND709) were used. Salt stress treatment with a 150 mmol/L NaCl solution (the control group was tested without salt stress treatment simultaneously) was continued until the test material was collected after the rice germination period. Twelve cDNA libraries were constructed, and 5 comparator groups were established for transcriptome sequencing. On average, 9.57G of raw sequencing data were generated per sample, with alignment to the reference genome above 96.88% and alignment to guanine-cytosine (GC) content above 53.86%. A total of 16,829 differentially expressed genes were present in the five comparison groups, of which 2390 genes were specifically expressed in T35 (category 1), 3306 genes were specifically expressed in JND709 (category 2), and 1708 genes were differentially expressed in both breeds (category 3). Differentially expressed genes were subjected to gene ontology (GO), functional enrichment analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, which revealed that these genes belonged to three main classes: molecular function, cellular components, and biological processes. KEGG pathway analysis showed that the significantly enriched pathways for these differentially expressed genes included phenylpropane biosynthesis, phytohormone signaling, and the interaction of plants with pathogens. In this study, we provided a reference for studying the molecular mechanism underlying salt tolerance during germination.

Optimizing Nitrogen Regime Improves Dry Matter and Nitrogen Accumulation during Grain Filling to Increase Rice Yield

Nitrogen (N) fertilizer is a critical element that affects rice yield. However, its effects on dry matter accumulation (DMA), N accumulation, and their physiological mechanisms with grain yield and N utilization efficiency still lack in-depth study. Three large-scale japonica rice varieties—Jinxiangyu 1, Nanjing 46, and Huaidao 5—were used in two field experiments with varying N fertilizer application rates to examine grain yield and N utilization efficiency. The results showed that: (1) In the range of 0~360 kg ha−1 total N application rate (TNAR), the rice yields of the three cultivars were maximum under the TNAR at 270 kg ha−1. The optimal TNAR for the highest yield of Jinxiangyu 1, Nanjing 46, and Huaidao 5 were calculated based on quadratic regressions with values of 305.5 kg ha−1, 307.6 kg ha−1, and 298.0 kg ha−1, and the corresponding yields were 10.3 t ha−1, 10.6 t ha−1 and 10.2 t ha−1, respectively. The N utilization efficiency decreased gradually with the increase in TNAR, and the recovery efficiency decreased from 35.7~38.19% to 29.61~31.59%. (2) The yield was significantly positively correlated with DMA and N accumulation from the heading stage (HD) to the maturity stage (MA). The DMA and N accumulation of HD-MA were significantly positively correlated with leaf photosynthetic rate, non-structural carbohydrate (NSC) accumulation in stems, root oxidation activity, zeatin (Z) + zeatin riboside (ZR) contents in roots, and nitrate reductase (NR) and glutamate synthase (GOGAT) activity in HD. (3) In the range of 0~216 kg ha−1 panicle N application rate (PNAR), the rice yield was maximum under the PNAR at 108 kg ha−1. The optimal PNAR for the highest yield of Jinxiangyu 1 was calculated based on the quadratic regression with values of 139.5 kg ha−1, and the highest yield was 9.72 t ha−1. The leaf photosynthetic rate, NSC accumulation in stems, root oxidation activity, Z + ZR contents in roots, and NR activity in leaves in rice were higher under 108 kg ha−1 PNAR. Excessive application of panicle fertilizer reduced the above physiological indicators and rice yield. The above results showed that optimizing N fertilizer could increase the leaf photosynthetic rate, NSC accumulation in stems, root oxidation activity, Z + ZR contents in roots, and NR activity from HD to MA, which was beneficial to improving DMA and N uptake during HD-MA, thus improving grain yield and N utilization efficiency in rice.

Optimum Basic Seedling Density and Yield and Quality Characteristics of Unmanned Aerial Seeding Rice

Unmanned aerial seeding (UAS) is an efficient unmanned rice planting method with broad application prospects. But its optimum basic seedling number and yield and quality characteristics remain unclear. Field experiments were conducted to compare UAS, unmanned dry direct seeding (UDDS), and unmanned carpet transplanting (UCT) methods using inbred japonica rice variety Nanjing 5718. The UAS method was subdivided into four planting density treatments (UAS105, UAS150, UAS195, and UAS240 = 105, 150, 195, and 240 seedlings/m2, respectively). The results showed that increasing the basic seedling density first increased the yield but then it decreased, and UAS195 produced a significantly higher yield. On the other hand, the grain processing, appearance, and taste quality deteriorated with improved nutritional quality. Among the three planting methods, UAS (UAS195) yielded less than UCT due to there being fewer spikelets per panicle, a lower grain-filling rate, and less photosynthetic activity after heading. However, UAS (UAS195) produced more yields than UDDS by having more panicles, more spikelets per panicle, and more biomass accumulation. Both UAS195 and UDDS had poorer grain processing, appearance, and nutritional quality than UCT, but increased amylose content and taste values. Therefore, UAS195 could be an alternative planting method for inbred japonica rice with coordinated yield, quality, and production efficiency.

Camellia japonica Flowers as a Source of Nutritional and Bioactive Compounds.

In recent decades, plants have strengthened their relevance as sources of molecules potentially beneficial for health. This underpinning effect also arises from the extensive research that has been conducted on plants that are typically undervalued, besides being scarcely used. This is the case with Camellia japonica in Galicia (NW Spain), where, despite its abundance, it is exclusively used for ornamental purposes and has been studied only for its proximate composition. Thus, the present study was conducted on several additional parameters in the flowers of eight C. japonica varieties. Our results show that camellia has a high nutritional value, with carbohydrates as the most abundant macronutrients followed by a moderate protein content (4.4-6.3 g/100 g dry weight) and high levels of polyunsaturated fatty acids (especially ω-3 fatty acids, which represent 12.9-22.7% of the total fatty acids), raising its potential for use for nutritional purposes. According to the thermochemical characterization and elemental composition of camellia, the raw material has poor mineralization and low nitrogen content, but high percentages of volatile matter and high carbon-fixation rates, making it a promising alternative for biofuel production. Furthermore, preliminary analysis reveals a high concentration of different bioactive compounds. As a result of these findings, camellias can be used as food or functional ingredients to improve the nutritional quality of food formulations.

Natural variation in OsSEC13 HOMOLOG 1 modulates redox homeostasis to confer cold tolerance in rice.

Rice (Oryza sativa L.) is a cold-sensitive species that often faces cold stress, which adversely affects yield productivity and quality. However, the genetic basis for low-temperature adaptation in rice remains unclear. Here, we demonstrate that two functional polymorphisms in Oryza sativa SEC13 Homolog 1 (OsSEH1), encoding a WD40-repeat nucleoporin, between the two subspecies Oryza sativa japonica and Oryza sativa indica rice may have facilitated cold adaptation in japonica rice. We show that OsSEH1 of the japonica variety expressed in OsSEH1MSD plants (transgenic line overexpressing the OsSEH1 allele from Mangshuidao [MSD], cold-tolerant landrace) has a higher affinity for metallothionein 2b (OsMT2b) than that of OsSEH1 of indica. This high affinity of OsSEH1MSD for OsMT2b results in inhibition of OsMT2b degradation, with decreased accumulation of reactive oxygen species and increased cold tolerance. Transcriptome analysis indicates that OsSEH1 positively regulates the expression of the genes encoding dehydration-responsive element-binding transcription factors, i.e., OsDREB1 genes, and induces the expression of multiple cold-regulated genes to enhance cold tolerance. Our findings highlight a breeding resource for improving cold tolerance in rice.

Exogenous Application of Methyl Jasmonate Promotes Yield and Grain Quality of Rice under Terminal Drought Stress

Exogenous application of methyl jasmonate (MeJA) improves rice drought tolerance, but its effects on rice yield and quality under drought stress during the reproductive phase remain unclear. A pot experiment was conducted to measure rice yield, grain quality, and starch physicochemical properties under three treatments: continuous flooding irrigation throughout the whole growth season (CF), ten days of −40 kPa drought stress at the heading stage (DS), and foliar spraying 100 μmol L−1 MeJA on the first three days of the ten-day −40 kPa heading stage drought stress (DM). An inbred japonica rice variety, Huaidao 5, was the experimental material, and each treatment had 11 replicates for sampling. The results indicated that DS significantly reduced rice yield and quality compared to CF. With increases in superoxide dismutase (+22.2%), peroxidase activities (+10.5%), catalase (+5.0%), and proline content (+5.7%), DM significantly increased 1000-grain weight (+8.6%), filled grain percentage (+3.6%), and yield (+11.1%) compared with DS. Regarding grain quality, DM significantly decreased the chalkiness degree (−12.3%) and protein content (−3.9%) but increased the amylose content (+17.2%) and taste value (+7.3%) relative to DS. In addition, DM improved breakdown viscosity (+17.8%), gelatinization enthalpy (+17.2%), retrogradation enthalpy (+28.0%), 1045/1022 cm−1 ratio (+3.0%), and starch granule morphology compared to DS. In conclusion, exogenous application of 100 μmol L−1 MeJA enhanced the antioxidant capacity of rice leaves, and thus improved starch physicochemical properties to increase grain yield and quality under terminal drought stress.

Fine Mapping and Candidate Gene Analysis of Rice Grain Length QTL qGL9.1.

Grain length (GL) is one of the crucial determinants of rice yield and quality. However, there is still a shortage of knowledge on the major genes controlling the inheritance of GL in japonica rice, which severely limits the improvement of japonica rice yields. Here, we systemically measured the GL of 667 F2 and 1570 BC3F3 individuals derived from two cultivated rice cultivars, Pin20 and Songjing15, in order to identify the major genomic regions associated with GL. A novel major QTL, qGL9.1, was mapped on chromosome 9, which is associated with the GL, using whole-genome re-sequencing with bulked segregant analysis. Local QTL linkage analysis with F2 and fine mapping with the recombinant plant revealed a 93-kb core region on qGL9.1 encoding 15 protein-coding genes. Only the expression level of LOC_Os09g26970 was significantly different between the two parents at different stages of grain development. Moreover, haplotype analysis revealed that the alleles of Pin20 contribute to the optimal GL (9.36 mm) and GL/W (3.31), suggesting that Pin20 is a cultivated species carrying the optimal GL variation of LOC_Os09g26970. Furthermore, a functional-type mutation (16398989-bp, G>A) located on an exon of LOC_Os09g26970 could be used as a molecular marker to distinguish between long and short grains. Our experiments identified LOC_Os09g26970 as a novel gene associated with GL in japonica rice. This result is expected to further the exploration of the genetic mechanism of rice GL and improve GL in rice japonica varieties by marker-assisted selection.

Reduced Nitrogen Input Combined with Nitrogen-Saving japonica Rice Varieties Balances Yield and Nitrogen Use Efficiency in The Lower Reaches of the Yangtze River in China

Maintaining rice yield and reducing nitrogen (N) input are two important targets in sustainable agriculture practices. The adoption of a nitrogen-saving variety (NSV) provides a unique opportunity to achieve this. However, limited options in NSV japonica rice and a lack of information on their responses to N reduction make management decisions difficult. This study aims to explore the responses of yield and nitrogen use efficiency (NUE) in NSV to N reduction. Two newly released NSVs and two popular general varieties (GVs) of japonica rice were field tested in Yangzhou, located at the lower reaches of Yangtze River of China, in two consecutive years. The results showed that for NSVs, with a 40–60% reduction in common practice N rate (300 Kg ha−1), the rice yield could maintain a record average level (p < 0.05), whereas the yield for the GV would drop 20–30% (p < 0.05). This indicates that combining the practices of adoption of NSV and N reduction to 120–180 Kg N ha−1 could balance the yield and N consumption. Moderate N reduction promotes the N accumulation and NUE, and it increases the number of tillers, the productive tiller percentage and the total amount of spikelets in the population, and increases the carbon and N metabolism of the population in the NSV. Compared with GV, NSV showed higher NUE and non-structural carbohydrate re-mobilization in the reduced N rate. The results showed that the practice of N reduction has to adopt NSV at the same time in order to maintain the grain yield level in rice.

Storage performance of non-waxy Japonica rice varieties preferred by Japanese consumers: Evaluation of physicochemical properties and in vitro starch digestibility

This study aimed to evaluate the changes during storage in the composition, texture, and starch digestibility of non-waxy Japonica rice varieties (cv. Yudai 21, Koshihikari, and Milky Queen) preferred by Japanese consumers. Stored grains were prepared by storing fresh grains at 30 °C for 6 months. Changes in pH of the rinse water and the color reaction of catalase activity showed a decrease in freshness and significant differences between varieties, between storage periods and by interaction. The total and resistant starch content decreased during storage and had significant correlations with pH and color reaction. Yudai 21 had higher surface adhesiveness, surface adhesion, and overall adhesiveness than Koshihikari with a similar apparent amylose (AA) content and Milky Queen with a lower AA content, regardless of storage. The equilibrium concentration of starch hydrolysis ranged from 84.1% to 94.9% with no significant difference and showed a significant correlation with pH (r = 0.78). The estimated glycemic index (eGI) was significantly affected by variety, with Koshihikari having the highest eGI and Yudai 21 having the lowest eGI, but was not affected by storage. Among the varieties, Yudai 21 was a suitable variety not only for fresh grains but also for stored grains, with high eating quality and low starch digestibility.

First Report of Aphelenchoides besseyi Causing White Tip Disease of Rice in Heilongjiang Province of China.

Aphelenchoides besseyi is considered one of the most damaging plant parasitic nematodes to rice and can cause white tip disease. It was first discovered in Kyushu, Japan in 1915 and introduced into China from Japan in the 1940s. The disease is mainly found in rice-planting areas in South China (Zhu et al. 2016; Wang et al. 2017; Xu et al. 2019), causing yield losses of 30%-50% in irrigated rice (Wang et al. 2014). In summer 2021, rice plants displaying distortion and discoloration on new leaves, white tips on flag leaves, erect and shorter panicles, and fewer or less filled spikelets were observed in the rice field in Acheng district, Harbin city, Heilongjiang Province, China (13°32'33″S, 58°48'51″W). Plant samples with the typical symptoms of 'white tip' in the flag leaves were collected and transported to the laboratory for further pathogen identification. Nematodes were extracted from the leaves and panicles of diseased plants using Baermann funnel method, and the population density of nematode was an average of 57 individuals per sample (total 28 diseased samples). The main morphological characteristics of females (n = 20) and males (n = 15) were individually determined using a microscope (LEICA, DM2500). Female body was slender, and straight to ventrally curved when heat-relaxed, with a rounded cephalic region, the lateral field with four incisures, the excretory pore close to the anterior edge of the nerve ring, a narrow post-vulval sac and less than 1/3 the distance from the vulva to the anus, and a conoid tail with star-shaped mucro. Female measurements: body length = 724.6 (593.3 to 867.5) μm, stylet = 11.7 (10.9 to 12.5) μm, tail length = 39.4 (35.8 to 44.4) μm, a = 45.2 (38.6 to 51.0), b = 10.1 (9.4 to 10.7), c = 18.47 (14.7 to 21.4), and V = 71.1 (65.0 to 79.6). The body of male usually showed in a 'J' shape when relaxed, spicule length between 17.1 and 19.4 μm, and a conoid tail, with terminal mucro bearing two to four pointed processes. Male measurements: body length = 546.3 (521.7 to 587.6) μm, stylet = 11.9 (10.7 to 12.6) μm, tail length = 32.54 (29.53 to 34.35) μm, a = 37.7 (35.7 to 40.4), b = 8.7 (8.5 to 9.1), c = 17.8 (15.8 to19.4). The key morphological characteristics were coincident with the description of A. besseyi by Christie (1942), Ou et al. (2014) and Chen et al. (2020). DNA was extracted from six fresh nematodes, and the partial 18S-rRNA was amplified with a pair of primers 1813F/2646R (5'-CTGCGTGAGAGGTGAAAT-3'; 5'-GCTACCTTGTTACGACTTTT-3') (Holterman et al. 2006). PCR products of expected size were purified and sequenced. The newly obtained sequence (accession no. ON629604) was submitted to GenBank and displayed more than 99.5% identity with that of A. besseyi isolates (KT943536, KT454963, JQ957877). Additionally, the isolated nematodes were further confirmed using the species-specific primers Abess_11F/Abess_11R (5'-GTATTCAATCCCGCGACACT-3'; 5'-CATCCTGTTCGGGCATAGTT-3'), and the PCR amplification generated a 570 bp fragment which was specific to the 28S rDNA region of A. besseyi reported previously (Noronha et al. 2020). The pathogenicity test was confirmed in a pot assay. Approximately 2000 mixed-stage A. besseyi (juveniles, males and females) were obtained from the field-diseased rice plants, and ten-day-old rice seedlings (Japonica rice variety, Keyou 1) (n = 5) were inoculated with 400 nematodes per seedling and maintained in a greenhouse. During early growth stages (fifty days after inoculation), some young leaves of infected plants showed the chlorotic tips. Ninety days after inoculation, similar field symptoms (white tip on leaves) were observed on the aerial tissues of the inoculated plants, and an average of 237 A. besseyi were re-isolated from each plant. To the best of our knowledge, this is the first report of A. besseyi on rice plant in Heilongjiang Province of Northeast China. This finding indicates that A. besseyi could become a severe threat to rice production in Heilongjiang Province and contributes to the further inspection and prevention of white tip disease in rice-growing areas of Heilongjiang Province.

Bioinformatics approach for developing a minimum set of SNP markers for identification of temperate japonica rice varieties cultivated in Spain.

The use of molecular markers for plant variety identification and protection is increasing. For this purpose, SNP markers have provided a reliable and stable tool for plant genotyping. The availability of small and low-cost SNP panels to accelerate the identification of the cultivated rice varieties should be beneficial for breeders, seed certification entities and rice industry. With the intention of providing of such a facility, we first developed a simple and easy-handle bioinformatics tool based on the widely used and freely available software R to generate small sets of SNPs that can discriminate varieties, by selecting markers from a larger genotyping dataset. By applying this algorithm to data from a previously genotyped collection of temperate japonica varieties from different countries, we identified a minimal set of 31 SNPs markers to distinguish 210 varieties. In addition, we used this algorithm to discriminate the 43 most cultivated in Spain rice varieties with minimal sets of 8 SNPs. We then developed and tested 22 Kompetitive Allele-Specific PCR (KASP) assays for the markers included in these panels, and obtained reliable genotype patterns for rice varieties identification. The complete 22 markers panel and the rice genotypes data could offer a useful and low-cost tool for rice breeders and industry to identify varieties and therefore to guarantee the quality of rice. The provided R-based algorithm can be applied to other genomic resources to develop core sets of discriminating markers.

Adaptation to high latitudes through a novel allele of Hd3a strongly promoting heading date in rice.

A novel Hd3a allele strongly promoting rice heading date was identified, and it functions through florigen activation complex (FAC) and was selected during the spread of rice cultivation to high-latitude areas. Heading date is a critical agronomic trait for rice that determines the utilization of light and temperature conditions and thereby affects grain yield. Rice is a short day (SD) plant, and its photoperiodic information is processed by complex pathways and integrated by florigens to control flowering. In this study, we identified a novel allele for the florigen gene Heading date 3a (Hd3a), characterized by a C435G substitution in its coding region, by a genome-wide association study (GWAS) approach in a panel of 199 high-latitude japonica rice varieties. The C435G substitution induces plants to flower 10days earlier in high-latitude area (long day condition). Then, we mutated C435 to G in Hd3a by prime editing and found the point mutation plants flowered 12days earlier. Further molecular experiments showed the novel Hd3a protein can interact with GF14b protein and increase the expression of OsMADS14, the output gene of florigen activation complex (FAC). Molecular signatures of selection indicated that the novel Hd3a allele was selected during the process of rice cultivation expansion into high-latitude areas. Collectively, these results provide new insights into heading date regulation in high-latitude areas and advance improvements to rice adaptability to enhance crop yield.

A hybrid CNN-LSTM model for diagnosing rice nutrient levels at the rice panicle initiation stage

Nitrogen (N) and potassium (K) are two key mineral nutrient elements involved in rice growth. Accurate diagnosis of N and K status is very important for the rational application of fertilizers at a specific rice growth stage. Therefore, we propose a hybrid model for diagnosing rice nutrient levels at the early panicle initiation stage (EPIS), which combines a convolutional neural network (CNN) with an attention mechanism and a long short-term memory network (LSTM). The model was validated on a large set of sequential images collected by an unmanned aerial vehicle (UAV) from rice canopies at different growth stages during a two-year experiment. Compared with VGG16, AlexNet, GoogleNet, DenseNet, and inceptionV3, ResNet101 combined with LSTM obtained the highest average accuracy of 83.81% on the dataset of Huanghuazhan (HHZ, an indica cultivar). When tested on the datasets of HHZ and Xiushui 134 (XS134, a japonica rice variety) in 2021, the ResNet101-LSTM model enhanced with the squeeze-and-excitation (SE) block achieved the highest accuracies of 85.38 and 88.38%, respectively. Through the cross-dataset method, the average accuracies on the HHZ and XS134 datasets tested in 2022 were 81.25 and 82.50%, respectively, showing a good generalization. Our proposed model works with the dynamic information of different rice growth stages and can efficiently diagnose different rice nutrient status levels at EPIS, which are helpful for making practical decisions regarding rational fertilization treatments at the panicle initiation stage.

Relationship between characteristics of basal internodes and lodging and its physiological mechanism in direct‐seeded rice

AbstractLodging is an important factor that limits rice yield and the large‐scale promotion of direct‐seeded rice (DSR). The objective of this study was to clarify the relationship between the characteristics of basal internodes and lodging and the physiological mechanism underlying this process in DSR. A field study was conducted in Changchun, Jilin Province, China, using a japonica rice variety Jiyujing with two direct seeding cultivation methods, including dry DSR (DDSR), wet DSR (WDSR) and conventional‐transplanted rice (CTSR) as a control in 2019 and 2020. Lodging‐related physical parameters, morphological characteristics and carbohydrate components of basal internodes were investigated at heading stage (HS) and 30 days after heading stage (HS30). The results showed that WDSR increased lodging index (LI) and lodging rate compared with CTSR and DDSR. LI increased rapidly from HS to HS30, primarily because of the significant reduction in the breaking strength (M). Correlation analysis revealed that the M of N4 internode was significantly positively correlated with culm plumpness and structural carbohydrate proportions at HS30. Culm plumpness decreased significantly, due to a decrease in nonstructural carbohydrate (NSC) content then primarily the decrease in starch proportions and content. Compared with CTSR and DDSR, WDSR decreased culm wall thickness, dry weight per centimetre of the culm and leaf sheaths, and the proportions and contents of cellulose, lignin and starch of internode, resulting in the decrease in internode breaking strength. Thus, it was concluded that the DSR reduced internode strength by reducing internode plumpness and carbohydrate content, thus decreasing lodging resistance.

Effects of Source Strength and Sink Size on Starch Metabolism, Starch Properties and Grain Quality of Rice (Oryza sativa L.)

The source strength and sink demand as well as their interaction have been demonstrated to co-regulate the synthesis of starch and determine the grain quality, but the knowledge of the underlying physiological mechanisms is limiting. An indica variety, Yangdao 6, and a japonica variety, Jinxiangyu 1, were planted with three treatments, including normal growth plant (CK), leaf-cutting (LC) and spikelet-thinning (ST). The transcript levels of starch metabolic genes, physicochemical characteristics of starch and appearance, milling, cooking and tasting qualities of rice under different treatments were determined. The ST treatment increased the relative expression of genes related to the synthesis of short branch-chains of amylopectin (SSI, BEI, BEIIb) and amylose (GBSSI) and reduced the relative expression of medium-long to long branch-chains of amylopectin synthesis genes (SSIIa, SSIIIa, SSIIIb, ISA1). When comparing ST with the CK treatment, starch granules became smoother with higher contents of short branch-chains and lower ratios of medium-long and long branch-chains of amylopectin; the crystallinity and the value of 1045/1022 cm−1 was decreased; for pasting properties, the setback and pasting temperature were decreased; the peak viscosity, hot viscosity, breakdown and final viscosity were significantly increased. Meanwhile, the ST treatment improved the appearance, milling and cooking and tasting qualities. The opposite results were observed under the LC treatment. These results indicated that source strength and sink size would regulate expression levels of starch metabolic genes, which is pivotal for the contents of amylose and short/long branch chains ratio of amylopectin, thus changing the structure and physicochemical properties of starch and grain quality. Here, we speculated that the improved source strength in terms of higher leaf/canopy photosynthesis and small sink size, such as small panicle size, would be preferred traits in high grain quality rice breeding.

Double Mutation of Days to Heading 2 and CONSTANS 3 Improves Agronomic Performance of Japonica Rice under Short Daylight Conditions in Southern China.

Some progress has been made in understanding the pathways related to rice heading, but their applications to breeding japonica rice varieties adapted to grow in low-latitude areas ("indica to japonica") are limited. We edited eight adaptation-related genes via a lab-established CRISPR/Cas9 system in a japonica variety, Shennong265 (SN265). All T0 plants and their progeny bearing random mutation permutations were planted in southern China and screened for changes in heading date. We found that the double mutant of Days to heading 2 (DTH2) and CONSTANS 3 (OsCO3) (dth2-osco3), two CONSTANS-like (COL) genes, showed significantly delayed heading under both short-day (SD) and long-day (LD) conditions in Guangzhou and manifested great yield increase under SD conditions. We further demonstrated that the heading-related Hd3a-OsMADS14 pathway was down-regulated in the dth2-osco3 mutant lines. The editing of the COL genes DTH2 and OsCO3 greatly improves the agronomic performance of japonica rice in Southern China.

Ornithine δ-aminotransferase OsOAT is critical for male fertility and cold tolerance during rice plant development.

Cold stress is a major factor limiting the production and geographical distribution of rice (Oryza sativa) varieties. However, the molecular mechanisms underlying cold tolerance remain to be elucidated. Here, we report that ornithine δ-aminotransferase (OsOAT) contributes to cold tolerance during the vegetative and reproductive development of rice. osoat mutant was identified as a temperature-sensitive male sterile mutant with deformed floral organs and seedlings sensitive to cold stress. Comparative transcriptome analysis showed that OsOAT mutation and cold treatment of the wild-type plant led to similar changes in the global gene expression profiles in anthers. OsOAT genes in indica rice Huanghuazhan (HHZ) and japonica rice Wuyungeng (WYG) are different in gene structure and response to cold. OsOAT is cold-inducible in WYG but cold-irresponsive in HHZ. Further studies showed that indica varieties carry both WYG-type and HHZ-type OsOAT, whereas japonica varieties mostly carry WYG-type OsOAT. Cultivars carrying HHZ-type OsOAT are mainly distributed in low-latitude regions, whereas varieties carrying WYG-type OsOAT are distributed in both low- and high-latitude regions. Moreover, indica varieties carrying WYG-type OsOAT generally have higher seed-setting rates than those carrying HHZ-type OsOAT under cold stress at reproductive stage, highlighting the favorable selection for WYG-type OsOAT during domestication and breeding to cope with low temperatures.