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.

PpTCP18 is upregulated by lncRNA5 and controls branch number in peach (Prunus persica) through positive feedback regulation of strigolactone biosynthesis

Branch number is an important agronomic trait in peach(Prunus persica)trees because plant architecture affects fruit yield and quality.Although breeders can select varieties with different tree architecture,the biological mechanisms underlying architecture remain largely unclear.In this study,a pillar peach(‘Zhaoshouhong’)and a standard peach(‘Okubo’)were compared.‘Zhaoshouhong’was found to have significantly fewer secondary branches than‘Okubo’.Treatment with the synthetic strigolactone(SL)GR24 decreased branch number.Transcriptome analysis indicated that PpTCP18(a homologous gene of Arabidopsis thaliana BRC1)expression was negatively correlated with strigolactone synthesis gene expression,indicating that PpTCP18 may play an important role in peach branching.Yeast one-hybrid,electrophoretic mobility shift,dual-luciferase assays and PpTCP18-knockdown in peach leaf buds indicated that PpTCP18 could increase expression of PpLBO1,PpMAX1,and PpMAX4.Furthermore,transgenic Arabidopsis plants overexpressing PpTCP18 clearly exhibited reduced primary rosette-leaf branches.Moreover,lncRNA sequencing and transient expression analysis revealed that lncRNA5 targeted PpTCP18,significantly increasing PpTCP18 expression.These results provide insights into the mRNA and lncRNA network in the peach SL signaling pathway and indicate that PpTCP18,a transcription factor downstream of SL signaling,is involved in positive feedback regulation of SL biosynthesis.This role of PpTCP18 may represent a novel mechanism in peach branching regulation.Our study improves current understanding of the mechanisms underlying peach branching and provides theoretical support for genetic improvement of peach tree architecture.

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.

Stochastic Model of Dengue: Analysing the Probability of Extinction and LLN

In this article, we develop and analyze a continuous-time Markov chain (CTMC) model to study the resurgence of dengue. We also explore the large population asymptotic behavior of probabilistic model of dengue using the law of large numbers (LLN). Initially, we calculate and estimate the probabilities of dengue extinction and major outbreak occurrence using multi-type Galton-Watson branching processes. Subsequently, we apply the LLN to examine the convergence of the stochastic model towards the deterministic model. Finally, theoretical numerical simulations are conducted exploration to validate our findings. Under identical conditions, our numerical results demonstrate that dengue could vanish in the stochastic model while persisting in the deterministic model. The highlighting of the law of large numbers through numerical simulations indicates from what population size a deterministic model should be considered preferable.

TCD5 Enhances the Photosynthesis Capacity,Increases the Panicle Number and the Yield in Rice

Improvement of photosynthetic efficiency is a major approach to increase crop yield potential.Previously,we cloned a gene encoding the chloroplast-located putative monooxygenase TCD5,which is essential in plastid development under low temperature in rice(Oryza sativa L.).In this study,the effects of TCD5 on the photosynthesis and the yields were investigated in rice.Two sets of genetic materials with three levels of TCD5 expression,including tcd5 mutant or TCD5 RNAi transgenic lines and TCD5 over-expression transgenic lines in Jiahua1 and Nipponbare backgrounds,were used in the field trails of multi-locations and multi-years.TCD5 positively affected the panicle number and the yield at dosage.Compared with the wild-types,the panicle numbers were 12.4%-14.6%less in tcd5 mutant and 8.3%-38.6%less in TCD5 RNAi lines,but 26.2%-61.8%more in TCD5 over-expression lines.The grain yields per plant were 9.1%-18.4%less in tcd5 mutant and 14.3%-56.7%less in TCD5 RNAi lines,but 6.9%-56.5%more in TCD5 over-expression lines.The measurements of net photosynthetic rate indicated that mutation or knock down of TCD5 decreased the net photosynthetic rate by 10.4%and 15.6%,respectively,while increasing it by 8.9%and 8.7%in the TCD5 over-expression lines in Jiahua1 and Nipponbare backgrounds,respectively.Accordingly,the measurements of chlorophyll fluorescence parameters showed that the electron transport rate and quantum yield decreased in tcd5 mutant or TCD5 RNAi lines but increased in TCD5 overexpression lines,both in Jiahua1 and Nipponbare backgrounds.IP-MS screening revealed that TCD5 interacts with 29 chloroplast proteins involved in chlorophyll synthesis,photo-reactions of the photosynthesis,carbon assimilation and metabolism,energy metabolism,redox balance,protein synthesis and transportation.Two TCD5 interacted proteins,D1 and FBA were effective targets for improving photosynthesis.These results suggest a potentially new strategy for increasing rice yield by enhancing photosynthesis.

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.

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.

Mining Elite Alleles of Growth Duration and Productive Panicle Number per Plant by Association Mapping with Conditional Phenotypic Value in Japonica Rice

To provide genetic information and materials for breeding hybrid japonica rice with wide adaptability and strong competitive advantage of yield, elite alleles and their carrier varieties of growth duration （GD） and productive panicle number per plant （PN） were detected. A natural population composed of 94 japonica varieties was phenotyped for the GD, PN and plant height （PH） in two environments. The conditional phenotypic data were transferred by the linear model method in software QGAStation 1.0, and association mapping based on the unconditional and conditional phenotype values of GD and PN was analyzed by using general linear model in software TASSEL. A total of 34 simple sequence repeat （SSR） marker loci associated with GD and PN were detected in the two environments. Among them, 15 were associated with GD, and 19 were associated with PN. Four elite alleles of RM8095-120bp, RM7102-176bp, RM72-170bp and RM72-178bp were associated with GD, and their carrier varieties were Hongmangshajing, Nipponbare, Hongmangshajing and Nannongjing 62401, respectively. These elite alleles from the carrier varieties can shorten GD by 2.03-9.93 d when they were introduced into improved materials. RM72-182bp associated with PN was an elite allele, and its carrier variety was Xiaoqingzhong. It can increase PN by three when introduced into improved materials. Moreover, these elite alleles can be used to improve target traits without influencing another two traits.

Comparison of QTL for Grain Number per Panicle in Three Populations Sharing 3 Parents and Fine Mapping of Gn1c

Complex traits, such as yield components, are inherited in a quantitative manner and typically controlled by quantitative trait loci (QTL). Grain number per panicle (GN) is an important component of yield in rice and

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.

Dissection of the genetic architecture for tassel branch number by QTL analysis in two related populations in maize

Tassel branch number （TBN） is the principal component of maize tassel inflorescence architecture and is a typical quan- titative trait controlled by multiple genes. The main objective of this research was to detect quantitative trait loci （QTLs） for TBN. The maize inbred line SICAU1212 was used as the common parent to develop BC1S1 and recombinant inbred line （RIL） populations with inbred lines 3237 and B73, respectively. The two related populations consisted of 123 and 238 lines, respectively. Each population was grown and phenotyped for TBN in two environments. Eleven QTLs were detected in the BC1S1 population, located on chromosomes 2, 3, 5, and 7, accounted for 4.45-26.58% of the phenotypic variation. Two QTLs （qB11Jtbn2-1, qB12Ctbn2-1, qBJtbn2-1; q11JBtbn5-1, qB12Ctbn5-1, qBJtbn5-1） that accounted for more than 10% of the phenotypic variation were identified. Three QTLs located on chromosomes 2, 3 and 5, exhibited stable expres- sion in the two environments. Ten QTLs were detected in the RIL population, located on chromosomes 2, 3, 5, 8, and 10, accounted for 2.69-13.58% of the TBN variation. One QTL （qR14Dtbn2-2） explained 〉10% of the phenotypic variation. One common QTL （qB12Ctbn2-2, qR14Dtbn2-2, qRJtbn2-2） was detected between the two related populations. Three pairs of epistatic effects were identified between two loci with or without additive effects and accounted for 1.19-4.26% of the phenotypic variance. These results demonstrated that TBN variation was mainly caused by major effects, minor effects and slightly modified by epistatic effects. Thus, identification of QTL for TBN may help elucidate the genetic basis of TBN and also facilitate map-based cloning and marker-assisted selection （MAS） in maize breeding programs.

ON THE BASIC REPRODUCTION NUMBER OF GENERAL BRANCHING PROCESSES

Under a very general condition （TNC condition） we show that the spectral radius of the kernel of a general branching process is a threshold parameter and hence plays a role as the basic reproduction number in usual CMJ processes. We discuss also some properties of the extinction probability and the generating operator of general branching processes. As an application in epidemics, in the final section we suggest a generalization of SIR model which can describe infectious diseases transmission in an inhomogeneous population.

Identification and characterization of a no-grain mutant(nog1)in foxtail millet

Increasing crop grain yields is an urgent global priority due to population growth,shrinking arable land,and severe climate change in recent years(Tang et al.2023).Unraveling the process of panicle development is crucial for enhancing the grain yield of cereal crops.In the development of rice panicles,the inflorescence meristem(IM)gives rise to two types of lateral branch meristems(BMs):primary branch meristem(pBM)and secondary branch meristem(sBM).The pBM generates sBM and spikelet meristems(SMs),and the sBM further differentiates into more SMs(Zhang and Yuan 2014).

Mapping of QTLs Controlling Panicle Length and Effective Panicle Number of Rice

Panicle length and effective panicle number of rice are closely related to yield. In this experiment, indica V20B as female parent was crossed with javanica CPSLO17 as male parent, recombinant inbred line （RIL） populations were obtained by single seed descent method, and with the RIL populations as mapping populations, QTL mapping and analysis were performed to the two panicle traits, panicle length and effective panicle. A high-density genetic map was constructed with SLAF labels, interval mapping was performed by software Map QTL5 under the threshold of 3.9, and 7 QTLs were detected on 3 chromosomes in total. Among the 7 QTLs, 5 QTLs controlling panicle length （qPLI-1, qPL1-2, qPL6-1, qPI_6-2 and qPL6-3） were located on chromosomes 1 and 6, respectively, and showed the contribution rates of 6.41%, 22.22%, 6.15%, 12.24% and 13.01%, respectively, their effect-increasing loci were mainly from CPSLO17, and qPL1-1 is a new QTL; and 2 QTLs controlling effective panicle number （qPN1 and qPN4） were located on chromosomes 1 and 4, respectively, and exhibited the contribution rates of 13.15% and 8.18%, respectively, and the effect-increasing loci were from parent V2OB. The marking of these loci lays a foundation for further cloning of genes controlling panicle length and effective panicle number and molecular marker-assisted selection.

Exploration and Validation of the Potential Downstream Genes Underlying ipa1-2D Locus for Rice Panicle Branching

In recent years,some super hybrid rice varieties were bred with strong culms and large panicles,which are mainly contributed by the ipa1-2D locus.A gain-of-function allele of OsSPL14 is the ipa1-2D and it can greatly increase the panicle primary branch number.However,the key downstream genes mediating this trait variation are not fully explored.In this study,we developed high-quality near-isogenic lines(NILs)with a difference of only 30 kb chromosomal segment covering the ipa1-2D locus.Using the NILs,we explored the impact of ipa1-2D on five sequential stages of early inflorescence development,and found that the locus can greatly enhance the initiation of primary branch meristems.A transcriptomic analysis was performed to unveil the downstream molecular network of ipa1-2D,and 87 genes were found differentially expressed,many of which are involved in metabolism and catalysis processes.In addition,transgenic lines of overexpression and RNA interference were generated to shape different levels of OsSPL14.They were also used to validate the expression variation explored by transcriptome.Based on the gene annotation,twelve potential downstream targets of ipa1-2D were selected,and their expression variation was confirmed by qRT-PCR analysis both in NILs and transgenic lines.This research expands the molecular network underlying ipa1-2D and provides novel gene information which might be involved in the control of panicle branching.We discussed the potential function of identified genes and highlighted their values for future function exploration and breeding application.

Influence of the Number of Reserved Fruit on Fruit-bearing Branch of Early-maturing Citrus unshiu Marc. on Fruit Growth and Development

In order to provide theoretical references for early-maturing Citrus unshiu Marc. in terms of fruit thinning, timely fertilization and harvesting, as wel as for for-mulation of of Early-maturing Citrus unshiu Marc. Cultivation Technique Standards in Guizhou Province, the dynamic changes of fruit longitudinal diameter and trans-verse diameter of 11-year-old and 12-year-old early maturing Citrus unshiu Marc. were tested in two consecutive years and the effects of single-fruit bearing branch on fruit growth and development were compared. The results showed annual varia-tion of longitudinal and transverse diameter of the fruit in Guizhou grew faster at the beginning and then slowed down gradual y, maintaining a slow-growth period after October; the growth curve final y was flat in mature stage. General y, the growth and development stage of fruit showed four growth peaks, showing an in-creasing S-shape curve and fruit net increase also had four growth peaks with a double S-shape curve. Specifical y, longitudinal diameters growth alternated with transverse diameter growth and the former proved much stronger. In terms of ef-fects of single-fruit bearing branch on longitudinal and transverse diameter growth, the number of reserved fruits had direct effects on the growth, net increase of weight, time of growth peak, fluctuation and the number of growth peak. The growth and development, and quality of fruits in the treatments with two or three fruits re-served on single fruit-bearing branch proved better compared with the control with four left fruits. It suggested that early June and early July are the best time for fer-tilization of early-maturing Citrus unshiu Marc. in Guizhou Pprovince and would have better effect if combined with foliage spraying. The suitable harvest time is in the end of October. The preferred number of reserved fruit on single fruit-bearing branch is 2-3. In actual production, the implementation of flower and fruit thinning should also takes tree age, balance of tree vigor, strength of fruit bearing branch, alternate bearing phenomenon and other factors into consideration.

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.

A natural allele of TAW1 contributes to high grain number and grain yield in rice

Grain number per panicle (GNP) is a complex trait controlled by quantitative trait loci (QTL),directly determining grain yield in rice.Identifying GNP-associated QTL is desirable for increasing rice yield.A rice chromosome segment substitution line (CSSL),F771,which showed increased panicle length and GNP,was identified in a set of CSSLs derived from a cross between two indica cultivars,R498 (recipient) and WY11327 (donor).Genetic analysis showed that the panicle traits in F771 were semidominant and controlled by multiple QTL.Six QTL were consistently identified by QTL-seq analysis.Among them,the major QTL q PLN10 for panicle length and GNP was localized to a 121-kb interval between markers N802 and N909 on chromosome 10.Based on quantitative real-time PCR and sequence analysis,TAWAWA1(TAW1),a known regulator of rice inflorescence architecture,was identified as the candidate gene for q PLN10.A near-isogenic line,NIL-TAW1,was developed to evaluate its effects.In comparison with the recurrent parent R498,NIL-TAW1 showed increased panicle length (14.0%),number of secondary branches (20.9%) and GNP (22.0%),and the final grain yield per plant of NIL-TAW1 was increased by18.6%.Transgenic experiments showed that an appropriate expression level of TAW1 was necessary for panicle development.Haplotype analysis suggested that the favorable F771-type (Hap 13) of TAW1was introduced from aus accessions and had great potential value in high-yield breeding both in indica and japonica varieties.Our results provide a promising genetic resource for rice grain yield improvement.

Superior grains determined by grain weight are not fully correlated with the flowering order in rice

Rice panicles are composed of many branches with two types of extreme grains,the superior and the inferior.Traditionally,it has been well accepted that earlier flowers result in superior grains and late flowers generate inferior grains.However,these correlations have never been strictly examined in practice.In order to determine the accurate relationship between superior and inferior grains and the flowering order,we localized all the seeds in a panicle in four distinct rice species and systematically documented the rice flowering order,flower locations and the final grain weight for their relationships.Our results demonstrated that the grain weight is more heavily determined by the position of the seeds than by the flowering order.Despite earlier flowering has a positive correlation with the grain weight in general,grains from flowers blooming on the second day after anthesis generally gained the highest weight.This suggests earlier flowers may not result in superior grains.Therefore,we concluded that superior and inferior grains,commonly determined by grain weight,are not fully correlated with the flowering order in rice.Following the order of the grain weight,the superior grains are generally localized at the middle parts of the primary branches,whereas inferior grains were mainly on the last two secondary branches of the lower half part of the panicle.In addition,the weight of inferior grains were affected by spikelet thinning and spraying with exogenous plant growth regulators,indicating that physiological incompetence might be the major reason for the occurrence of the inferior grains.

Discovery of and Preliminary studies on a Rapid-Leafing Rice Genotype at the Vegetative Growth Stage

The leafing rates of fourteen rice varieties were measured in a sowing-time experiment, and a rapid leafing genotype at the vegetative growth stage was discovered in an indica variety Yanhui 559. The leaf number on the main culm of Yanhui 559 was always 4-5 leaves more than that of Lemont, and the leafing rate of Yanhui 559 was significantly higher than that of Lemont based on similar growth durations from sowing to heading. Furthermore, the difference of the leafing rate was significant at the vegetative growth stage, but not distinctive at the panicle initiation stage. Genetic analysis of the leafing rates in the two backcross populations of Yanhui 559 and Lemont showed that major and quantitative genes controlled the expression of rapid leafing character. Based on results of investigation for some plants with similar growth durations in the backcrossing populations, the rapid leafing genotypes exhibited earlier tillering and more tiller numbers per plant, and its yield components including the number of panicles per plant and number of grains per panicle were superior to those of the slow leafing genotypes. Further research and application feasibility of the rapid leafing genotype in breeding were discussed.