Seed Storability in Rice: Physiological Foundations, Molecular Mechanisms, and Applications in Breeding

Long-term storage of crop seeds is critical for the conservation of germplasm resources, ensuring food supply, and supporting sustainable production. Rice, as a major food staple, has a substantial stock for consumption and production worldwide. However, its food value and seed viability tend to decline during storage. Understanding the physiological responses and molecular mechanisms of aging tolerance forms the basis for enhancing seed storability in rice. This review outlines the latest progress in influential factors, evaluation methods, and identification indices of seed storability. It also discusses the physiological consequences, molecular mechanisms, and strategies for breeding aging-tolerant rice in detail. Finally, it highlights challenges in seed storability research that require future attention. This review offers a theoretical foundation and research direction for uncovering the mechanisms behind seed storability and breeding aging-tolerant rice.

Drought-Tolerant Rice at Molecular Breeding Eras:An Emerging Reality

Rice(Oryza sativa L.)stands as the most significantly influential food crop in the developing world,with its total production and yield stability affected by environmental stress.Drought stress impacts about 45%of the world’s rice area,affecting plants at molecular,biochemical,physiological,and phenotypic levels.The conventional breeding method,predominantly employing single pedigree selection,has been widely utilized in breeding numerous drought-tolerant rice varieties since the Green Revolution.With rapid progress in plant molecular biology,hundreds of drought-tolerant QTLs/genes have been identified and tested in rice crops under both indoor and field conditions.Several genes have been introgressed into elite germplasm to develop commercially accepted drought-tolerant varieties,resulting in the development of several drought-tolerant rice varieties through marker-assisted selection and genetically engineered approaches.This review provides up-to-date information on proof-of-concept genes and breeding methods in the molecular breeding era,offering guidance for rice breeders to develop drought-tolerant rice varieties.

Research Progress on Application of Molecular Markers in Breeding of Camellia oleifera

Camellia oleifera is an important woody oil tree species unique to China.It is known as the world s four major woody oil crops along with olive,oil palm and coconut.It is known as the‘king of oil’because of its high oil content.With the increase of people's attention to the yield of Camellia oleifera,its high yield has become the focus.In traditional breeding model,judgment is performed by phenotypic traits,but this method is single and easily affected by the environment,and can no longer meet the demand.In contrast,molecular marker breeding is not affected by the environment,and is stable and efficient and capable of accurately mapping target genes,so it has attracted much attention.In this paper,the research progress on C.oleifera germplasm resources diversity,DNA fingerprinting construction,genetic linkage map construction and QTL mapping was summarized,and the application of SSR molecular marker technique combined with association analysis in C.oleifera breeding in recent years was discussed,in order to provide new ideas for high-yield breeding of C.oleifera.

Conventional Breeding and Molecular Markers for Blast Disease Resistance in Rice (Oryza sativa L.)

Monogenic lines,which carried 23 genes for blast resistance were tested and used donors to transfer resistance genes by crossing method.The results under blast nursery revealed that 9 genes from 23 genes were susceptible to highly susceptible under the three locations(Sakha,Gemmeza,and Zarzoura in Egypt);Pia,Pik,Pik-p,Piz-t,Pita,Pi b,Pi,Pi 19 and Pi 20.While,the genes Pii,Pik-s,Pik-h,Pi z,Piz-5,Pi sh,Pi 3,Pi 1,Pi 5,Pi 7,Pi 9,Pi 12,Pikm and Pita-2 were highly resistant at the same locations.Clustering analysis confirmed the results,which divided into two groups;the first one included all the susceptible genes,while the second one included the resistance genes.In the greenhouse test,the reaction pattern of five races produced 100%resistance under artificial inoculation with eight genes showing complete resistance to all isolates.The completely resistant genes:Pii,Pik-s,Piz,Piz-5(=bi2)(t),Pita(=Pi4)(t),Pita,Pi b and Pi1 as well as clustering analysis confirmed the results.In the F1 crosses,the results showed all the 25 crosses were resistant for leaf blast disease under field conditions.While,the results in F2 population showed seven crosses with segregation ratio of 15(R):1(S),two cross gave segregated ratio of 3 R:1 S and one gave 13:3.For the identification of blast resistance genes in the parental lines,the marker K3959,linked to Pik-s gene and the variety IRBLKS-F5 carry this gene,which was from the monogenic line.The results showed that four genotypes;Sakha 105,Sakha 103,Sakha 106 and IRBLKS-F5 were carrying Pik-s gene,while was absent in the Sakha 101,Sakha 104,IRBL5-M,IRBL9-W,IRBLTACP1 and IRBL9-W(R)genotypes.As for Pi 5 gene,the results showed that it was present in Sakha 103 and Sakha 104 varieties and absent in the rest of the genotypes.In addition,Pita-Pita-2 gene was found in the three Egyptian genotypes(Sakha 105,Sakha 101 and Sakha 104)plus IRBLTACP1 monogenetic.In F2 generation,six populations were used to study the inheritance of blast resistance and specific primers to confirm the ratio and identify the resistance genes.However,the ratios in molecular markers were the same of the ratio under field evaluation in the most population studies.These findings would facilitate in breeding programs for gene pyramiding and gene accumulation to produce durable resistance for blast using those genotypes.

Rice Heat Tolerance Breeding: A Comprehensive Review and Forward Gaze

The yield potential of rice is seriously affected by heat stress due to climate change. Since rice is a staple food globally, it is imperative to develop heat-resistant rice varieties. Thus, a thorough understanding of the complex molecular mechanisms underlying heat tolerance and the impact of high temperatures on various critical stages of the crop is needed. Adoption of both conventional and innovative breeding strategies offers a long-term advantage over other methods, such as agronomic practices, to counter heat stress. In this review, we summarize the effects of heat stress, regulatory pathways for heat tolerance, phenotyping strategies, and various breeding methods available for developing heat-tolerant rice. We offer perspectives and knowledge to guide future research endeavors aimed at enhancing the ability of rice to withstand heat stress and ultimately benefit humanity.

Pre-Breeding Genetic Diversity Assessment of Tomato(Solanum lycopersicum L.)Cultivars Based on Molecular,Morphological and Physicochemical Parameters

Appropriate knowledge of the parental cultivars is a pre-requisite for a successful breeding program.This study characterized fruit yield,quality attributes,and molecular variations of ten tomato cultivars during three consecutive generations under greenhouse conditions.Peto 86,Castle Rock,and Red Star cultivars showed the highest fruit yield(kg/plant),total phenolic compounds(TPC),and sap acidity.Principal component analysis categorized the evaluated fruit yield into three groups based on their quality attributes.A robust positive correlation appeared among traits inside each group.A positive correlation was likewise noticed between the first and the second groups.However,a negative correlation was detected between the first,the second and the third group.Molecular profiling,using seven inter-simple sequence repeat(ISSR)primers,produced 60 loci,including 49 polymorphic loci.The molecular analysis also pinpointed the highest genetic similarity(0.92)between P73 and Moneymaker,while the lowest genetic similarity(0.46)was observed between Castle Rock and Moneymaker.The cultivars P73 and Moneymaker showed the lowest genetic distance(2.24),while the highest genetic distance(5.92)was observed between Super Marmand and Peto86,on the one hand,and between Castle Rock and Moneymaker,on the other hand.The chemical analysis of fruit sap indicated the highest levels of TPC,total flavonoids,anthocyanin,ascorbic acid and total soluble solids in Peto 86 and Castle Rock cultivars.Phylogeny analysis of tomato cultivars based on morphological and molecular attributes indicated four distinct clades.Peto 86,Castle Rock,and Red star cultivars can be recommended for the tomato hybridization breeding programs in the future,with other tomato cultivars as potentially high-yielding parents.

Corrigendum to“Migration pattern of a population of Barn Swallows(Hirundo rustica)breeding in East Asian tropical region”[Avian Res.15(2024)100192]

The authors regret that the caption of Fig.4 should be replaced as below.

Novel umami peptides from two Termitomyces mushrooms and molecular docking to the taste receptor T1R1/T1R3

Wild edible Termitomyces mushrooms are popular in Southwest China and umami is important flavor qualities of edible mushrooms.This study aimed to understand the umami taste of Termitomyces intermedius and Termitomyces aff.bulborhizus.Ten umami peptides from aqueous extracts were separated using a Sephadex G-15 gel filtration chromatography.The intense umami fraction was evaluated by both sensory evaluation and electronic tongue.They were identified as KLNDAQAPK,DSTDEKFLR,VGKGAHLSGEH,MLKKKKLA,SLGFGGPPGY,TVATFSSSTKPDD,AMDDDEADLLLLAM,VEDEDEKPKEK,SPEEKKEEET and PEGADKPNK.Seven peptides,except VEDEDEKPKEK,SPEEKKEEET and PEGADKPNK were selectively synthesized to verify their taste characteristics.All these 10 peptides had umami or salt taste.The 10 peptides were conducted by molecular docking to study their interaction with identified peptides and the umami taste receptor T1R1/T1R3.All these 10 peptides perfectly docked the active residues in the T1R3 subunit.Our results provide theoretical basis for the umami taste and address the umami mechanism of two wild edible Termitomyces mushrooms.

Molecular Mechanism and Molecular Design of Lubricating Oil Antioxidants

To overcome the limitations of traditional experimental“trial and error”methods in lubricant additive design,a new molecular design method based on molecular structure parameters is established here.The molecular mechanism of the antioxidant reaction of hindered phenol,diphenylamine,and alkyl sulfide are studied via molecular simulations.Calculation results show that the strong electron-donating ability and high hydrogen-donating activity of the antioxidant molecule and the low hydrogen-abstracting activity of free radicals formed after dehydrogenation are the internal molecular causes of the shielding of phenol and diphenylamine from scavenging peroxy free radicals,and the strong electron-donating ability is the internal molecular cause of the high activity of thioether in decomposing alkyl hydrogen peroxide.Based on this antioxidant molecular mechanism,a molecular design rule of antioxidant is proposed,namely“high EHOMO,large Q(S),low bond dissociation energy BDE(O—H)and BDE(N—H)”.Two new antioxidants,PAS-I and PAS-II,are designed and prepared by chemical bonding of hindered phenol,diphenylamine,and sulfur atoms.Experimental results show that these antioxidants both have excellent antioxidant effects in lubricating oil,and that PAS-II is the superior antioxidant,consistent with theoretical predictions.

Creating large EMS populations for functional genomics and breeding in wheat

Wheat germplasm is a fundamental resource for basic research,applied studies,and wheat breeding,which can be enriched normally by several paths,such as collecting natural lines,accumulating breeding lines,and introducing mutagenesis materials.Ethyl methane sulfonate(EMS)is an alkylating agent that can effectively introduce genetic variations in a wide variety of plant species.In this study,we created a million-scale EMS population(MEP)that started with the Chinese wheat cultivars‘Luyan 128’,‘Jimai 38’,‘Jimai 44’,and‘Shannong 30’.In the M1 generation,the MEP had numerous phenotypical variations,such as>3,000 chlorophyll-deficient mutants,2,519 compact spikes,and 1,692 male sterile spikes.There were also rare mutations,including 30 independent tillers each with double heads.Some M1 variations of chlorophyll-deficiency and compact spikes were inheritable,appearing in the M2 or M3 generations.To advance the entire MEP to higher generations,we adopted a single-seed descendent(SSD)approach.All other seed composites of M2 were used to screen other agronomically important traits,such as the tolerance to herbicide quizalofop-P-methyl.The MEP is available for collaborative projects,and provides a valuable toolbox for wheat genetics and breeding for sustainable agriculture.

Germplasm and molecular breeding in horticultural crops

Horticulture is an important part of agricultural planting and production, which is of great significance for enriching human nutrition and beautifying and transforming the human living environment. At present, the area of horticultural crops in China is about 40 million ha, accounting for about onefourth of the national crop planting area, while the production of primary agricultural products is 1 billion tons, and the output value accounts for more than half of the total output value of the planting industry.

Molecular mechanisms underlying microglial sensing and phagocytosis in synaptic pruning

Microglia are the main non-neuronal cells in the central nervous system that have important roles in brain development and functional connectivity of neural circuits.In brain physiology,highly dynamic microglial processes are facilitated to sense the surrounding environment and stimuli.Once the brain switches its functional states,microglia are recruited to specific sites to exert their immune functions,including the release of cytokines and phagocytosis of cellular debris.The crosstalk of microglia between neurons,neural stem cells,endothelial cells,oligodendrocytes,and astrocytes contributes to their functions in synapse pruning,neurogenesis,vascularization,myelination,and blood-brain barrier permeability.In this review,we highlight the neuron-derived“find-me,”“eat-me,”and“don't eat-me”molecular signals that drive microglia in response to changes in neuronal activity for synapse refinement during brain development.This review reveals the molecular mechanism of neuron-microglia interaction in synaptic pruning and presents novel ideas for the synaptic pruning of microglia in disease,thereby providing important clues for discovery of target drugs and development of nervous system disease treatment methods targeting synaptic dysfunction.

Analysis of CH_(4) and H_(2) Adsorption on Heterogeneous Shale Surfaces Using aMolecular Dynamics Approach

Determining the adsorption of shale gas on complex surfaces remains a challenge in molecular simulation studies.Difficulties essentially stem from the need to create a realistic shale structure model in terms of mineral heterogeneityand multiplicity.Moreover,precise characterization of the competitive adsorption of hydrogen andmethane in shale generally requires the experimental determination of the related adsorptive capacity.In thisstudy,the adsorption of adsorbates,methane(CH_(4)),and hydrogen(H_(2))on heterogeneous shale surface modelsof Kaolinite,Orthoclase,Muscovite,Mica,C_(60),and Butane has been simulated in the frame of a moleculardynamic’s numerical technique.The results show that these behaviors are influenced by pressure and potentialenergy.On increasing the pressure from 500 to 2000 psi,the sorption effect for CH_(4)significantly increasesbut shows a decline at a certain stage(if compared to H_(2)).The research findings also indicate that raw shalehas a higher capacity to adsorb CH_(4)compared to hydrogen.However,in shale,this difference is negligible.

Facile synthesis of Cu-doped manganese oxide octahedral molecular sieve for the efficient degradation of sulfamethoxazole via peroxymonosulfate activation

Advanced processes for peroxymonosulfate(PMS)-based oxidation are efficient in eliminating toxic and refractory organic pol-lutants from sewage.The activation of electron-withdrawing HSO_(5)^(-)releases reactive species,including sulfate radical(·SO_(4)^(-)),hydroxyl radical(·OH),superoxide radical(·O_(2)^(-)),and singlet oxygen(1O_(2)),which can induce the degradation of organic contaminants.In this work,we synthesized a variety of M-OMS-2 nanorods(M=Co,Ni,Cu,Fe)by doping Co^(2+),Ni^(2+),Cu^(2+),or Fe^(3+)into manganese oxide oc-tahedral molecular sieve(OMS-2)to efficiently remove sulfamethoxazole(SMX)via PMS activation.The catalytic performance of M-OMS-2 in SMX elimination via PMS activation was assessed.The nanorods obtained in decreasing order of SMX removal rate were Cu-OMS-2(96.40%),Co-OMS-2(88.00%),Ni-OMS-2(87.20%),Fe-OMS-2(35.00%),and OMS-2(33.50%).Then,the kinetics and struc-ture-activity relationship of the M-OMS-2 nanorods during the elimination of SMX were investigated.The feasible mechanism underly-ing SMX degradation by the Cu-OMS-2/PMS system was further investigated with a quenching experiment,high-resolution mass spec-troscopy,and electron paramagnetic resonance.Results showed that SMX degradation efficiency was enhanced in seawater and tap water,demonstrating the potential application of Cu-OMS-2/PMS system in sewage treatment.

Exploring the taste presentation and receptor perception mechanism of salty peptides from Stropharia rugosoannulata based on molecular dynamics and thermodynamics simulation

The taste presentation and receptor perception mechanism of the salty peptide of Stropharia rugosoannulata were predicted and verified using peptide omics and molecular interaction techniques.The combination of aspartic acid(D)and glutamic acid(E),or peptide fragments composed of arginine(R),constitute the characteristic taste structural basis of salty peptides of S.rugosoannulata.The taste intensity of the salty peptide positively correlates with its concentration within a specific concentration range(0.25–1.0 mg/mL).The receptor more easily recognizes the first amino acid residue at the N-terminal of salty peptides and the aspartic acid residue in the peptides.GLU513,ASP707,and VAL508 are the critical amino acid residues for the receptor to recognize salty peptides.TRPV1 is specifically the receptor for recognizing salty peptides.Hydrogen bonds and electrostatic interactions are the main driving forces for the interactions between salty peptides and TRPV1 receptors.KSWDDFFTR has the most potent binding capacity with the receptor and has tremendous potential for application in sodium salt substitution.This study confirmed the taste receptor that specifically recognizes salty peptides,analyzed the receptor-peptide binding interaction,and provided a new idea for understanding the taste receptor perception of salty peptides.

Risk stratification for radioactive iodine refractoriness using molecular alterations in distant metastatic differentiated thyroid cancer

Objective: Patients with radioactive iodine-refractory differentiated thyroid cancer(RAIR-DTC) are often diagnosed with delay and constrained to limited treatment options. The correlation between RAI refractoriness and the underlying genetic characteristics has not been extensively studied.Methods: Adult patients with distant metastatic DTC were enrolled and assigned to undergo next-generation sequencing of a customized 26-gene panel(Thyro Lead). Patients were classified into RAIR-DTC or non-RAIR groups to determine the differences in clinicopathological and molecular characteristics. Molecular risk stratification(MRS) was constructed based on the association between molecular alterations identified and RAI refractoriness, and the results were classified as high, intermediate or low MRS.Results: A total of 220 patients with distant metastases were included, 63.2% of whom were identified as RAIRDTC. Genetic alterations were identified in 90% of all the patients, with BRAF(59.7% vs. 17.3%), TERT promoter(43.9% vs. 7.4%), and TP53 mutations(11.5% vs. 3.7%) being more prevalent in the RAIR-DTC group than in the non-RAIR group, except for RET fusions(15.8% vs. 39.5%), which had the opposite pattern. BRAF and TERT promoter are independent predictors of RAIR-DTC, accounting for 67.6% of patients with RAIR-DTC. MRS was strongly associated with RAI refractoriness(P<0.001), with an odds ratio(OR) of high to low MRS of 7.52 [95%confidence interval(95% CI), 3.96-14.28;P<0.001] and an OR of intermediate to low MRS of 3.20(95% CI,1.01-10.14;P=0.041).Conclusions: Molecular alterations were associated with RAI refractoriness, with BRAF and TERT promoter mutations being the predominant contributors, followed by TP53 and DICER1 mutations. MRS might serve as a valuable tool for both prognosticating clinical outcomes and directing precision-based therapeutic interventions.

Development of in situ characterization techniques in molecular beam epitaxy

Ex situ characterization techniques in molecular beam epitaxy(MBE)have inherent limitations,such as being prone to sample contamination and unstable surfaces during sample transfer from the MBE chamber.In recent years,the need for improved accuracy and reliability in measurement has driven the increasing adoption of in situ characterization techniques.These techniques,such as reflection high-energy electron diffraction,scanning tunneling microscopy,and X-ray photoelectron spectroscopy,allow direct observation of film growth processes in real time without exposing the sample to air,hence offering insights into the growth mechanisms of epitaxial films with controlled properties.By combining multiple in situ characterization techniques with MBE,researchers can better understand film growth processes,realizing novel materials with customized properties and extensive applications.This review aims to overview the benefits and achievements of in situ characterization techniques in MBE and their applications for material science research.In addition,through further analysis of these techniques regarding their challenges and potential solutions,particularly highlighting the assistance of machine learning to correlate in situ characterization with other material information,we hope to provide a guideline for future efforts in the development of novel monitoring and control schemes for MBE growth processes with improved material properties.

Advances in Understanding Cadmium Stress and Breeding of Cadmium-Tolerant Crops

Cadmium(Cd) pollution has emerged as a critical global environmental concern, due to its significant toxicity, environmental persistence, and the pervasiveness of contamination. Significantly, the bioaccumulation of Cd in agricultural crops constitutes a primary vector for its entry into the human diet. This issue warrants urgent attention from both the scientific community and policymakers to develop and implement effective mitigation strategies. This review delves into the physiological impacts of Cd stress on plants, including the suppression of photosynthetic activity, amplification of oxidative stress, and disruptions in mineral nutrient homeostasis. Additionally, the resistance mechanisms deployed by plants in response to Cd stress have been explored, and the prospective contributions of molecular breeding strategies in augmenting crop tolerance to Cd and minimizing its bioaccumulation have been assessed. By integrating and analyzing these findings, we seek to inform future research trajectories and proffer strategic approaches to enhance agricultural sustainability, safeguard human health, and protect environmental integrity.

Topgrafting as a tool in operational Scots pine breeding

Effective breeding requires multiplying desired genotypes,keeping them at a convenient location to perform crosses more efficiently,and building orchards to generate material for reforestation.While some of these aims can be achieved by conventional grafting involving only rootstock and scion,topgrafting is known to deliver all in a shorter time span.In this study,Scots pine scions were grafted onto the upper and lower tree crowns in two clonal archives with the aim of inducing early female and male strobili produc-tion,respectively.Their survival rates and strobili production were analyzed with generalized linear mixed models.Sur-vival was low(14%)to moderate(41%),and mainly affected by the topgraft genotype,interstock genotype,crown posi-tion and weather conditions in connection with the grafting procedure.Survival was not affected by the cardinal position in the crown(south or north).Male flowering was ample three years after grafting and reached 56%in the first year among live scions,increasing to 62 and 59%in consecutive years.Female flowering was scarce and was 9%at first,later increasing to 26 and 20%of living scions but was strongly affected by the topgraft genotype.In one subset of scions,female flowering was observed 1 year after grafting.Overall,flowering success was mainly affected by the topgraft and interstock genotypes,and secondary growth of scions.This is one of few reports on topgrafting in functional Scots pine clonal archives.

Breeding and Seed Reproduction Techniques of a New Tetraploid Common Buckwheat Variety‘Pintianqiao 3’

[Objectives]This study was conducted to actively carry out the breeding of new tetraploid common buckwheat varieties and its supporting breeding techniques.[Methods]Pintianqiao 3 is a new tetraploid common buckwheat variety developed by College of Agriculture of Shanxi Agricultural University and Agricultural Genetic Resources Center of Shanxi Agricultural University,using‘Pintianqiao 1’as the parent,through mutation treatment with 0.2%colchicine aqueous solution,grain selection,plant selection,isolation and identification,variety comparison,regional test and field investigation.The variety has chromosomes 2n=4X=32,and shows a spring sowing period of 101 d and a summer sowing period of 80 d,large flowers and seeds(with a 1000-grain weight of 41.4 g),and good resistance to lodging.[Results]From 2021 to 2022,Pintianqiao 3 participated in the independent joint regional test of common buckwheat varieties in Shanxi Province,and the average yield in 10 test positions was 1.8 kg,equivalent to 1800 kg/hm^(2),which was 8.4%higher than the control.It passed the field investigation conducted by Shanxi provincial expert group for identification of non-major crop varieties in Dongyang and Kelan experimental sites on September 2-3,2022.On January 4,2024,it passed the preliminary examination of Shanxi Provincial Crop Variety Approval Committee.The seed reproduction technique of Pintianqiao 3 including land selection,preparation before sowing,sowing,field management and timely harvesting has been developed.[Conclusions]This study provides technical support for the demonstration and popularization of this new variety.