A novel Effective Panicle Number per Plant 4 haplotype enhances grain yield by coordinating panicle number and grain number in rice

Increasing effective panicle number per plant(EPN)is one approach to increase yield potential in rice.However,molecular mechanisms underlying EPN remain unclear.In this study,we integrated mapbased cloning and genome-wide association analysis to identify the EPN4 gene,which is allelic to NARROW LEAF1(NAL1).Overexpression lines containing the Teqing allele(TQ)of EPN4 had significantly increased EPN.NIL-EPN4^(TQ) in japonica(geng)cultivar Lemont(LT)exhibited significantly improved EPN but decreased grain number and flag leaf size relative to LT.Haplotype analysis indicated that accessions with EPN4-1 had medium EPN,medium grain number,and medium grain weight,but had the highest grain yield among seven haplotypes,indicating that EPN4-1 is an elite haplotype of EPN4 for positive coordination of the three components of grain yield.Furthermore,accessions carrying the combination of EPN4-1 and haplotype GNP1-6 of GNP1 for grain number per panicle showed higher grain yield than those with other allele combinations.Therefore,pyramiding of EPN4-1 and GNP1-6 could be a preferred approach to obtain high yield potential in breeding.

A 48-bp deletion upstream of LIGULELESS 1 alters rice panicle architecture

Panicle architecture is an agronomic determinant of crop yield and a target for cereal crop improvement.To investigate its molecular mechanisms in rice,we performed map-based cloning and characterization of OPEN PANICLE 1(OP1),a gain-of-function allele of LIGULELESS 1(LG1),controlling the spread-panicle phenotype.This allele results from a 48-bp deletion in the LG1 upstream region and promotes pulvinus development at the base of the primary branch.Increased OP1 expression and altered panicle phenotype in chimeric transgenic plants and upstream-region knockout mutants indicated that the deletion regulates spread-panicle architecture in the mutant spread panicle 1(sp1).Knocking out BRASSINOSTEROID UPREGULATED1(BU1)gene in the background of OP1 complementary plants resulted in compact panicles,suggesting OP1 may regulate inflorescence architecture via the brassinosteroid signaling pathway.We regard that manipulating the upstream regulatory region of OP1 or genes involved in BR signal pathway could be an efficient way to improve rice inflorescence architecture.

Border Sensitive Knowledge Distillation for Rice Panicle Detection in UAV Images

Research on panicle detection is one of the most important aspects of paddy phenotypic analysis.A phenotyping method that uses unmanned aerial vehicles can be an excellent alternative to field-based methods.Nevertheless,it entails many other challenges,including different illuminations,panicle sizes,shape distortions,partial occlusions,and complex backgrounds.Object detection algorithms are directly affected by these factors.This work proposes a model for detecting panicles called Border Sensitive Knowledge Distillation(BSKD).It is designed to prioritize the preservation of knowledge in border areas through the use of feature distillation.Our feature-based knowledge distillation method allows us to compress the model without sacrificing its effectiveness.An imitation mask is used to distinguish panicle-related foreground features from irrelevant background features.A significant improvement in Unmanned Aerial Vehicle(UAV)images is achieved when students imitate the teacher’s features.On the UAV rice imagery dataset,the proposed BSKD model shows superior performance with 76.3%mAP,88.3%precision,90.1%recall and 92.6%F1 score.

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.

QTL Analysis of Rice Peduncle Vascular Bundle System and Panicle Traits

A double haploid (DH) population of rice (Oryza sativa L.) derived from anther culture of ZYQ8/JX17, a typical indica and japonica hybrid, was used for genetic analysis of rice peduncle vascular system and panicle traits. The number of large vascular bundles (LVB), the number of small vascular bundles (SVB) in the peduncle, and the panicle traits including the number of primary rachis branches (PRB), the number of spikelets per panicle (SNP), peduncle top diameter (PTD), and panicle length (PL) were investigated in the parents and DH lines. The quantitative trait loci (QTLs) for each trait were analyzed based on the constructed molecular linkage map of this population. Three QTLs for LVB (qLVB_1, qLVB_6 and qLVB_7) were detected on chromosomes 1, 6, and 7, respectively. Two putative QTLs for SVB (qSVB_4 and qSVB_6) were mapped on chromosomes 4 and 6 respectively. Four QTLs (qPRB_4a, qPRB_4b, qPRB_6 and qPRB_7) on chromosomes 4, 6, and 7, respectively, were detected for PRB. Three QTLs (qSPN_4a, qSPN_4b and qSPN_6) were identified on chromosomes 4 and 6, respectively, which could significantly affect SPN. Five QTLs for PTD (qPTD_2, qPTD_5, qPTD_6, qPTD_8 and qPTD_12) were identified on chromosomes 2, 5, 6, 8, and 12, respectively. Three QTLs for PL (qPL_4, qPL_6 and qPL_8) were detected on chromosomes 4, 6, and 8, respectively. Clustering of QTLs, such as qLVB_6, qSVB_6, qSNP_6, qPTD_6, and qPL_6 detected in the interval G122_G1314b on chromosome 6, was found. These results suggest that some QTLs for peduncle vascular bundle system are possibly responsible for the panicle traits.

Research on Rice Panicle L-system Model Based on Substructure Algorithm

In order to decrease model complexity of rice panicle for its complicated morphological structure,an interactive L-system based on substructure algorithm was proposed to model rice panicle in this study.Through the analysis of panicle morphology,the geometrical structure models of panicle spikelet,axis and branch were constructed firstly.Based on that,an interactive panicle L-system model was developed by using substructure algorithm to optimize panicle geometrical models with the similar structure.Simulation results showed that the interactive L-system panicle model based on substructure algorithm could fast construct panicle morphological structure in reality.In addition,this method had the well reference value for other plants model research.

Mapping QTLs for Panicle Traits Based on Rice RIL Population Derived from TD70 and Kasalath

Two hundred and forty recombinant inbred lines （RIL） derived from a cross TD70/Kasalath and its linkage map including 141 SSR markers were used to map QTLs controlling panicle length （PL）, total seeds per panicle （TSP） and grain density （GD） in 2010 and 2011. The results showed that a total of 23 QTLs controlling three panicle traits were detected on chromosomes 2, 3, 4, 6, 7, 8 and 10, respec- tively, including 5 QTLs controlling PL, 8 QTLs controlling TSP, 10 QTLs controlling GD, with the LOD value ranging between 2.5-9.3, and the QTLs explained the ob- served phenotypic by 4.0%-20.8%. The marker interval RM5699-RM424 on chro- mosome 2, RM489-RM1278 on chromosome 3, RM3367-RM1018 on chromosome 4, RM3343-RM412 on chromosome 6 were common marker intervals for TSP and GD; six QTLs （qPL3, qTSP4, qTSP6-2, qTSP7, qGD3-2 and qGDT） were detected in two years. Among these QTLs, the qPL3, qTSP6-2, qGD3-2 and qGD7 were major QTLs. All QTLs for PL mapped in the present study had been mapped QTLs previously by other research groups, 16 QTLs controlling TSP and GD were new ones which contributed the observed phenotypic variance range by 4%-9.5%. These results laid a founda^ion for further fine positioning or cloning these QTLs.

Grain-filling Characteristics of Two Differentpanicle Type Rice Cultivars in Heilongjiang Province

The grain-filling processes at different grain positions of curved-panicle type Longjing 29 and semi-erect-panicle type Longjing 31, two major rice （Oryza sativa L.） cultivars in Heilongjiang Province, were simulated by Richards growth eq-uation, so as to determine the reason of great differences in head rice rate of different rice cul- tivar among different years and to improve the processing quality of different rice cul- tivar through cultivation regulation measures. The results showed that the yield of Longjing 29 was slightly higher than that of Longjing 31, but the head rice rate of Longjing 29 was significantly lower than that of Longjing 31. More grains on sec- ondary rachis branch resulted in lower plumpness, lower seed-setting rate and lower milled rice rate of Longjing 29. The grain-filling rates at the six grain positions of Longjing 31 reached the peaks simultaneously, so the synchronous grain filling char- acteristic of Longjing 31 was more obvious. The grain-filling rate on the primary rachis branch of Longjing 31 was higher, and it reached the peak in the middle peri- od. Although the grain-filling rate on the secondary rachis branch of Longjing 31 was lower, it early reached the peak. In addition, the middle and late filling period of Longjing 31 was longer, resulting in plump and compact grains on the secondary rachis branch of Longjing 31. After the grain-filling rate on the primary rachis branch was decreased, the grain-filling rate on the secondary rachis branch of Longjing 29 started to be increased greatly, characterized by asynchronous grain filling. In the early grain filling stage, the grains on the upper, middle and basal secondary rachis branch were all significantly suppressed by those on the primary rachis branch of Longjing 29. The initial growth potential and maximum filling rate of grains on the secondary rachis branch of Longjing 29 were all lower. The grain-filling rate on the secondary rachis branch of Longjing 29 late reached the peak. Even worse, the mid- dle and late filling period of Longjing 29 was shorter. Therefore, the grains of Longjing 29 had poor plumpness. Synchronous grain filling led to small difference in grain quality within the same panicle, and this was also the reason for stable head rice rate of Longjing 31 among different years. In contrast, asynchronous grain filling led to great difference in grain quality within the same panicle of Longjing 29. In addi- tion, low temperature often occurred during the fast filling of grains on the secondary rachis branch of Longjing 29. Thus, the head rice rate of Longjing 29 was decreased.

Determination of rice panicle numbers during heading by multi-angle imaging

Plant phenomics has the potential to accelerate progress in understanding gene functions and environmental responses. Progress has been made in automating high-throughput plant phenotyping. However, few studies have investigated automated rice panicle counting. This paper describes a novel method for automatically and nonintrusively determining rice panicle numbers during the full heading stage by analyzing color images of rice plants taken from multiple angles. Pot-grown rice plants were transferred via an industrial conveyer to an imaging chamber. Color images from different angles were automatically acquired as a turntable rotated the plant. The images were then analyzed and the panicle number of each plant was determined. The image analysis pipeline consisted of extracting the i2 plane from the original color image, segmenting the image, discriminating the panicles from the rest of the plant using an artificial neural network, and calculating the panicle number in the current image. The panicle number of the plant was taken as the maximum of the panicle numbers extracted from all 12 multi-angle images. A total of 105 rice plants during the full heading stage were examined to test the performance of the method. The mean absolute error of the manual and automatic count was 0.5, with 95.3% of the plants yielding absolute errors within ± 1. The method will be useful for evaluating rice panicles and will serve as an important supplementary method for high-throughput rice phenotyping.

Rice DENSE AND ERECT PANICLE 2 is essential for determining panicle outgrowth and elongation

The architecture of the panicle, including grain size and panicle morphology, directly determines grain yield. Panicle erectness, which is selected for achieving ideal plant arehitecture in the northern part of China, has drawn increasing attention of rice breeders. Here, dense and erect panicle 2 （dep2） mutant, which shows a dense and erect panicle phenotype, was identified. DEP2 encodes a plant-specific protein without any known functional domain. Expression profiling of DEP2 revealed that it is highly expressed in young tissues, with most abundance in young panicles. Morphological and expression analysis indicated that mutation in DEP2 mainly affects the rapid elongation of rachis and primary and secondary branches, but does not impair the initiation or formation of panicle primordia. Further analysis suggests that decrease of panicle length in dep2 is caused by a defect in cell proliferation during the exponential elongation of panicle. Despite a more compact plant type in the dep2 mutant, no significant alteration in grain production was found between wild type and dep2 mutant. Therefore, the study of DEP2 not only strengthens our understanding of the molecular genetic basis of panicle architecture but also has important implications for rice breeding.

Decrement of Sugar Consumption in Rice Young Panicle Under High Temperature Aggravates Spikelet Number Reduction

Two rice genotypes Huanghuazhan(HHZ, heat-resistant) and IR36(heat-susceptible) were subjected to high-temperature(HT, 40℃) and normal-temperature(NT, 32℃) treatments at the spikelet differentiation stage. HT treatment inhibited spikelet differentiation, aggravated spikelet degeneration, reduced spikelet size, and disordered carbohydrate allocation. Meanwhile, HT treatment increased nonstructural carbohydrate content in leaves, but decreased that in stems and young panicles, and the same tendencies of sucrose and starch contents were observed in leaves and stem. However, HT treatment significantly increased the sucrose content and sharply decreased the glucose and fructose contents in young panicles. Lower activity levels of soluble acid invertase(EC3.2.1.26) and sucrose synthase(EC2.4.1.13) were observed under HT treatment. Moreover, HT treatment reduced the activities of key enzymes associated with glycolysis and the tricarboxylic acid cycle, which indicated sucrose consumption was inhibited in young panicles under HT treatment. Exogenous glucose and fructose applied under HT treatment increased the spikelet number more than exogenous sucrose. In conclusion, the results demonstrated that the reduction of spikelet number under high temperature was more affected by the decrease in sugar consumption than the blocking of sucrose transport. The impairment of sucrose hydrolysis was the main reason for the inhibition of sugar utilization.

Genetical and Physiological Basis of Plant Type Model of Erect and Large Panicle Japonica Super Rice in Northern China

The historical changes in rice yields across China were explored. The physiological mechanisms and genetic basis of the erect and large panicle super-high-yield plant type model for breeding japonica super rice were analyzed mainly on the panicle type, number of large vascular bundles （LVB） in the panicle neck, and the panicle type index （PTI）. In the production point of view, we suggested that, for the breeding of super-high-yield japonica rice, the erect panicle types with more LVB numbers in the panicle neck and superior upper grains in the secondary branches would be the key factors. The information has potential significance in the rice breeding and productivity not only in China but also throughout the rice production areas of the world.

Description of Aphelenchoides besseyi from Abnormal Rice with ‘Small Grains and Erect Panicles’ Symptom in China

The abnormal rice with small grains and erect panicles were found on a large scale in China, which showed shortend rice panicle and decreased number of grains in comparison with normal rice, and the grain was small and black-brown, and some of them were distorted, while the flag leaf was normal. A kind of nematode of Aphelenchoides was isolated from the grains of rice variety Wuyujing 3 which performed ＇small grains and erect panicles＇ symptom. There were 2014 nematodes in one hundred grains infected, and up to 74 in single grain, 92 percent of the grains tested had nematodes in the infested panicles. The diagnosis characters of nematode include lateral fields about one-fourth as wide as body, with 4 incisures. The terminus bears a mucro of diverse shape with 3-4 pointed processes. The female post-vulval uterine sac extends less than 50% of distance from vulva to anus, no sperm in it. Oocytes usually arrange in 2-4 rows. The male spicules have a moderately developed rostrum. Morphological measurements showed it to be conspecific with Aphelenchoides besseyi Christie, 1942.

Effects of Panicle Nitrogen Fertilization on Non-Structural Carbohydrate and Grain Filling in Indica Rice

Grain filling, a crucial stage of grain yield formation in rice, is usually affected by the panicle nitrogen （N） fertilization. Field and pot culture experiments were conducted to explore the underlying mechanisms of N effect. Two rice cultivars with high lodging resistance were grown in the field and pot. Four panicle N fertilization treatments were conducted in 2006 and repeated in 2007. The result showed that medium level of panicle N fertilization treatment （NM） enhanced the accumulation and translocation of non-structural carbohydrate （NSC） in the stem and sheath. Compared with non-nitrogen treatment （NO）, NM promoted the translocation of labeled ^13C from stem and sheath to grain. But, low level of panicle N fertilization treatment （NL） and high level of panicle N fertilization treatment （NH） showed the negative effect. The endosperm cell, grain length, and grain width of NM increased more quickly than that of NO from 4 to 10 d after anthesis. During the early period of grain filling, sucrose-phosphate synthase （EC 2.4.1.14, SPS） activity were significantly higher for the NM treatment than those of the NL and NH treatments. Sucrose synthase （EC 2.4.1.13, SuSase） activity in the grains was substantially enhanced by NM, with the duration of higher activity being longer than those of the other treatments. At maturing stage, NM significantly increased the filled grain number, the seed-setting rate, and the grain weight compared with NL and NH. The results suggest that NM have a positive effect on the activities of enzymes of physiological importance, thereby increasing the grain size and promoting grain filling.

Erect panicle super rice varieties enhance yield by harvest index advantages in high nitrogen and density conditions

The erect panicle （Ep） type is an important characteristic for japonica super rice in Northeast China and plays a significant role in enhancing yield. The Ep type is considered to be a genetic ideotype resource to the japonica super rice group by virtue of its agronomic advantages such as grain number per panicle and biomass. This study addresses the effects of nitrogen and planting density conditions on yielding performance regarding panicle type （PT） using the recombinant inbred line （RIL） population derived from the cross between an Ep variety Liaogeng 5 and non-Ep variety Wanlun 422. The genetics underlying the Ep type proved to be robust not only for panicle-type optimization but also plant height, panicle length, flag leaf length and seed density. We also found that regardless of nitrogen and density, correlation between harvest index （HI） and plant height was not significant in Ep type whatever the nitrogen and density. The application of Ep type provides a potential strategy for yield improvement by increasing biomass through HI maintainable in rice.

Genetic control of panicle architecture in rice

Rice panicle architecture affects grain number per panicle and thereby grain yield.Many genes involved in control of panicle architecture have been identified in the past decades.According to their effect on phenotype,these genes are divided into three categories:panicle branch and lateral spikelets,multifloret spikelets,and panicle type.We review these genes,describe their genetic regulatory network,and propose a strategy for using them in rice breeding.These findings on rice panicle architecture may facilitate related studies in other crops.

Studies on the Photosynthetic Characteristics andAssimilate's Accumulation and Transformation inHeavy Panicle Type of Rice

Using 18 indica rice varieties with different panicle weight, the photosynthetic characteristics and assimilate's accumulation and transformation in heavy panicle type of rice(HPT)were studied. The results showed that the net photosynthetic rate of the flag leaf in HPT after heading was obviously higher than that in medium panicle type(MPT)and light panicle type(LPT). The reason for the high net photosynthetic rate in HPT was the increase of Rubisco activities and chlorophyll content, and keeping high assimilate ability to CO2 under high and low light intensity, high temperature and low CO2 content, and light midday depression and wide adaptability to environmental conditions. The high net photosynthetic rate of HPT might be also the results of its excellent stomatal characteristics and higher total quantity of stomatal opening degrees(stomatal density X stomatal opening degrees). There was a large amount of dry matter production after heading and obvious high assimilate's transformation to panicle in HPT.

Genetic Analysis and Mapping of an Enclosed Panicle Mutant Locus esp1 in Rice (Oryza sativa L.)

A mutant was isolated from the M2 of 60Co-T ray mutagenized male-fertility restorer line Zao-R974 in rice. The mutant showed pleiotropic phenotypes including dwarfism, delayed heading time, short and partially enclosed panicles, short uppermost internode, decreased grain and secondary branch numbers per panicle, and partially degenerated spikelets. The mutant was named as espl （enclosed shorter panicle 1）. Genetic analysis indicated that the mutant phenotype was controlled by a recessive locus. Spraying exogenous GA~ did not rescue the panicle enclosure. Using an F2 and a BC, population of the cross between espl and a japonica cultivar Nipponbare, we mapped the ESP1 locus to a region of-260 kb on chromosome 11. This result provides a basis for further map-based cloning of the ESP1 locus.

Fine Mapping and Cloning of the Grain Number Per-Panicle Gene (Gnp4) on Chromosome 4 in Rice (Oryza sativa L.)

Grain number per-panicle is one of the most important components for rice yield. Spikelets on the primary and secondary branches determine the grain number per-panicle in rice. In this study, we identified a natural mutant, gnp4, lack of lateral spikelet on the secondary branches in the field condition. In addition, the Gnp4 and Lax1-1 double mutant showed dramatically reduced secondary branches and spikelets in panicle at reproductive stage, and tillers at vegetative stage. By map-based cloning approach, and using four F2 segregating populations, the Gnp4 gene was finally mapped to a 10.7-kb region on the long arm of chromosome 4 in rice. In this region, only one gene was predicted, and genomic DNA sequencing of the 10.7-kb region showed no nucleotide differences between the mutant and wild type. Interestingly, we found that the methylation level of several cytosines in the promoter CpG islands region of the predicted gene in gnp4 were different from the wild type. Thus, we propose that the DNA methylation changes at these sites may induce to decrease expression level of Gnp4, consequently, resulting in phenotypic variation.

Mining Applicable Elite Alleles of Growth Duration, Plant Height and Panicle Number per Plant by Conditional QTL Mapping in Japonica Rice

Unconditional and conditional QTL mapping were conducted for growth duration (GD), plant height (PH) and effective panicle number per plant (PN) using a recombinant inbred line (RIL) population derived from a cross between two japonica rice varieties Xiushui 79 and C Bao. The RIL population consisted of 254 lines was planted in two environments, Nanjing and Sihong, Jiangsu Province, China. Results showed that additive effects were major in all of QTLs for GD, PH and PN detected by the two methods, and the epistatic effects explained a small proportion of phenotypic variation. No interactions were detected between additive QTL and environment, and between epistatic QTL pairs and environment. After growth duration was adjusted to an identical level, RM80-160bp was detected as an applicable elite allele for PN, with an additive effect of 0.71. When effective panicle number per plant was adjusted to an identical level, RM448-240bp was detected as an applicable elite allele for GD, with an additive effect of 4.64. After plant height was adjusted to an identical level, RM80-160bp was detected as an applicable elite allele for PN, with an additive effect of 0.62, and RM448-240bp was detected as an applicable elite allele for GD, with an additive effect of 3.89. These applicable elite alleles could be used to improve target traits without influencing the other two traits.