Thermally Annealed High-Aspect-Ratio ZIF-8 Nanoplates-Incorporated Mixed Matrix Membranes for Improved H2/CO2 Selectivity.

The main challenge in the preparation of MOF-based mixed matrix membranes is to construct a good interface morphology to improve the gas separation performance and stability of the membranes. Herein, high-aspect-ratio ZIF-8 nanoplates for H2/CO2 separation membranes were synthesized by direct template conversion. The ZIF-8 nanoplates were prepared with the commercial Matrimid polymer to form MMMs by the flat scraping method. The homogeneous dispersion of high-aspect-ratio nanoplates in the membrane and the good compatibility between the filler and the matrix caused by the thermal annealing operation improve the gas separation performance and mechanical properties of MMMs. The H2/CO2 selectivity of MMMs loaded with 30 wt % ZIF-8 nanoplates increased to 10.3, and the H2 permeability was 330.1 Barrer. This synthesis method can be extended to prepare various ZIF nanoplates with elevated aspect ratios to obtain excellent performance fillers for gas separation of MMMs. In addition, the thermal annealing operation allows more efficient gas separation in polymer membranes and is a feasible way to design excellent and stable MMMs.

Development of a high quantum yield probe for detection of mitochondrial G-quadruplexes in live cells based on fluorescence lifetime imaging microscopy.

Mitochondrial G-quadruplexes are components that are potentially involved in regulating mitochondrial function and play crucial roles in the replication and transcription of mitochondrial genes. Consequently, it is imperative to develop probes that can detect mitochondrial G-quadruplexes to understand their functions and mechanisms. In this study, a triphenylamine fluorescent probe, TPPE, which has excellent cytocompatibility and does not affect the natural state of G-quadruplexes, was designed and demonstrated to localize primarily to the mitochondria. Owing to the unique binding mode between TPPE and G-quadruplexes, TPPE was able to distinguish G-quadruplexes from other substances due to the higher fluorescence lifetime and quantum yield. On the basis of the photon counts determined via fluorescence lifetime imaging microscopy, we analyzed the differences in the numbers of mitochondrial G-quadruplexes in various cell lines. We observed reductions in the number of mitochondrial G-quadruplexes during apoptosis, ferroptosis and glycolysis inhibition. This study shows the great potential of using TPPE to track and analyze mitochondrial G-quadruplexes and presents a novel perspective in the development of probes to detect mitochondrial G-quadruplexes in live cells.

Exploration of electrochemical behavior of Sb-based porous carbon composites anode for sodium-ion batteries.

Sb-based materials are considered as promising anode materials for sodium-ion batteries (SIBs) due to their excellent sodium storage capacities and suitable potentials. However, the Sb-based anodes usually suffer from intense volume expansion and severe pulverization during the alloying-dealloying process, resulting in poor cycling performance. Herein, a composite anode with Sb/Sb2O3 nanoparticles embedded in N-doped porous carbon is prepared by the gas-solid dual template method. The volume change of the anode material is mitigated by the carbon layer enwrapping and the confinement of the porous structure. Nitrogen doping provides abundant sodium storage sites, thus enhancing the storage capacity of sodium ion. Furthermore, to gain the accurate kinetic interpretation of the electrochemical process, an ex-situ transmission electron microscope (TEM) characterization combined with distribution of relaxation times (DRT) is conducted. The Sb/Sb2O3@NPC-1.0 demonstrates excellent electrochemical performance, achieving 340.3 mAh g-1 at 1A g-1, and maintains a capacity of 86.7 % after 1000 cycles. This work paves the way for the practical application of SIBs with high-performance and long-life Sb-based anodes.

An MgO passivation layer and hydrotalcite derived spinel Co2AlO4 synergically promote photoelectrochemical water oxidation conducted using BiVO4-based photoanodes.

MxCo3-xO4 co-catalysed photoanodes with high potential for improvement in PEC water-oxidizing properties are reported. However, it is difficult to control the recombination of photogenerated carriers at the interface between the catalyst and cocatalyst. Here, an ultra-thin MgO passivation layer was introduced into the MxCo3-xO4/BiVO4 coupling system to construct a ternary composite photoanode Co2AlO4/MgO/BiVO4. The photocurrent density of the electrode is 3.52 mA cm-2, which is 3.2 times that of BiVO4 (at 1.23 V vs. RHE). The photocurrent is practically increased by 0.86 mA cm-2 and 1.56 mA cm-2 in comparison with that of Co2AlO4/BiVO4 and MgO/BiVO4 electrodes, respectively. Meanwhile, the Co2AlO4/MgO/BiVO4 electrode has the highest charge separation efficiency, the lowest charge transfer resistance (Rct) and best stability. The excellent PEC performance could be attributed to the inhibitive effect provided by the MgO passivation layer that efficaciously suppresses the electron-hole recombination at the interface and drives the hole transfer outward, which is induced by Co2AlO4 to capture the electrode/electrolyte interface for efficient water oxidation reaction. In order to understand the origin of this improvement, first-principles calculations with density functional theory (DFT) were performed. The theoretical investigation converges to our experimental results. This work proposes a novel idea for restraining the recombination of photogenerated carriers between interfaces and the rational design of efficient photoanodes.

Identification of genomic regions controlling spikelet degeneration under FRIZZLE PANICLE (FZP) defect genetic background in rice.

The FZP gene plays a critical role in the formation of lateral branches and spikelets in rice panicle architecture. This study investigates the qSBN7 allele, a hypomorphic variant of FZP, and its influence on panicle architectures in different genetic backgrounds. We evaluated two backcross inbred lines (BILs), BC5_TCS10sbn and BC3_TCS10sbn, each possessing the homozygous qSBN7 allele but demonstrating differing degrees of spikelet degeneration. Our analysis revealed that BC5_TCS10sbn had markedly low FZP expression, which corresponded with an increase in axillary branches and severe spikelet degeneration. Conversely, BC3_TCS10sbn exhibited significantly elevated FZP expression, leading to fewer secondary and tertiary branches, and consequently decreased spikelet degeneration. Compared to BC5_TCS10sbn, BC3_TCS10sbn carries three additional chromosomal substitution segments from its donor parent, IR65598-112-2. All three segments significantly enhance the expression of FZP and reduce the occurrence of tertiary branch and spikelet degeneration. These findings enhance our understanding of the mechanisms regulating FZP and aid rice breeding efforts.

Non-monotone Exponential Time (NEXT) Model for the Longitudinal Trend of a Continuous Outcome in Clinical Trials.

The dose-response curve has been studied extensively for decades. However, most of these methods ignore intermediate measurements of the response variable and only use the measurement at the endpoint. In early phase trials, it is crucial to utilize all available data due to the smaller sample size. Simulation studies have shown that the longitudinal dose-response surface model provides a more precise parameter estimation compared to the traditional dose response using only data from the primary time point. However, the current longitudinal models with parametric assumptions assume the treatment effect increases monotonically over time, which may be controversial to reality. We propose a parametric non-monotone exponential time (NEXT) model, an enhanced longitudinal dose-response model with greater flexibility, capable of accommodating non-monotonic treatment effects and making predictions for longer-term efficacy. In addition, the estimator for the time to maximum treatment effect and its asymptotic distribution have been derived from NEXT. Extensive simulation studies using known data-generating models and using real clinical data showed the NEXT model outperformed the existing monotone longitudinal models.

Artichoke (Cynara scolymus L.) water extract alleviates palmitate-induced insulin resistance in HepG2 hepatocytes via the activation of IRS1/PI3K/AKT/FoxO1 and GSK-3ß signaling pathway.

BACKGROUND: Artichoke (Cynara scolymus L.) is a typical element of a traditional Mediterranean diet and has potential health advantages for insulin resistance (IR) and type 2 diabetes mellitus (T2DM). This study aims to evaluate the effect and underlying mechanism of artichoke water extract (AWE) on palmitate (PA)-induced IR in human hepatocellular carcinoma (HepG2) cells. METHODS: The effect of AWE on cell viability was determined using CCK8 assay. Cellular glucose uptake, glucose consumption, glucose production, and glycogen content were assessed after AWE treatment. The gene expression and protein levels were examined by real-time polymerase chain reaction (qRT-PCR) and western blotting. RESULTS: The results showed that AWE dose-dependently increased cell viability in IR HepG2 cells (P < 0.01). AWE treatment significantly promoted glucose uptake and consumption, decreased glucose production, and increased the cellular glycogen content in IR HepG2 cells (P < 0.01). Mechanistically, AWE elevated the phosphorylation and total protein levels of major insulin signaling molecules in IR HepG2 cells, which resulted in a decrease in the expression of phosphoenolpyruvate carboxykinase (PEPCK) and glucose-6-phosphatase (G6Pase) and the inhibition of glycogen synthase (GS) phosphorylation in IR HepG2 cells. Furthermore, the protective effect of AWE on IR HepG2 cells might be ascribed to the inhibition of the endoplasmic reticulum (ER) stress. CONCLUSION: We conclude that AWE may improve glucose metabolism by regulating IRS1/PI3K/AKT/FoxO1 and GSK-3ß signaling associated with the inhibition of ER stress in IR HepG2 cells induced by PA.

Cross-Attention Based Multi-Resolution Feature Fusion Model for Self-Supervised Cervical OCT Image Classification.

Cervical cancer seriously endangers the health of the female reproductive system and even risks women's life in severe cases. Optical coherence tomography (OCT) is a non-invasive, real-time, high-resolution imaging technology for cervical tissues. However, since the interpretation of cervical OCT images is a knowledge-intensive, time-consuming task, it is tough to acquire a large number of high-quality labeled images quickly, which is a big challenge for supervised learning. In this study, we introduce the vision Transformer (ViT) architecture, which has recently achieved impressive results in natural image analysis, into the classification task of cervical OCT images. Our work aims to develop a computer-aided diagnosis (CADx) approach based on a self-supervised ViT-based model to classify cervical OCT images effectively. We leverage masked autoencoders (MAE) to perform self-supervised pre-training on cervical OCT images, so the proposed classification model has a better transfer learning ability. In the fine-tuning process, the ViT-based classification model extracts multi-scale features from OCT images of different resolutions and fuses them with the cross-attention module. The ten-fold cross-validation results on an OCT image dataset from a multi-center clinical study of 733 patients in China indicate that our model achieved an AUC value of 0.9963 ± 0.0069 with a 95.89 ± 3.30% sensitivity and 98.23 ± 1.36 % specificity, outperforming some state-of-the-art classification models based on Transformers and convolutional neural networks (CNNs) in the binary classification task of detecting high-risk cervical diseases, including high-grade squamous intraepithelial lesion (HSIL) and cervical cancer. Furthermore, our model with the cross-shaped voting strategy achieved a sensitivity of 92.06% and specificity of 95.56% on an external validation dataset containing 288 three-dimensional (3D) OCT volumes from 118 Chinese patients in a different new hospital. This result met or exceeded the average of four medical experts who have used OCT for over one year. In addition to promising classification performance, our model has a remarkable ability to detect and visualize local lesions using the attention map of the standard ViT model, providing good interpretability for gynecologists to locate and diagnose possible cervical diseases.

Theoretical evaluation of the effect of bimetallic Au-based alloy catalysts on initial N2 electroreduction pathways.

Theoretical studies on the effect of bimetallic Au-based alloy catalysts on initial N2 electroreduction pathways at the present simulated electrode/aqueous interfaces based on DFT calculations are conducted in this work. The calculated results indicate that the alloying of Au with the transition metals Ni, Pd, Pt, Ru and Ta can facilitate the activation of N2 molecules in the presence of the electrode/aqueous interface, which may be derived from the kinetic overpotential of the outer Helmholtz plane. The N2 reduction pathway may be adsorption strength-dependent on N2, in which the incorporation of transition metals with a strong chemical affinity for N2 molecules may lead to a dissociative mechanism via the initial NN bond cleavage pathway, whereas the incorporation of transition metals with medium N2 binding strength may make N2 reduction proceed by the associative mechanism via the initial N2H formation pathway. The barriers of the initial N2 electroreduction into N2H species can be notably decreased after alloying Au with Ni, Pd, Pt, Ru and Ta compared with that on the Au electrode and the lowest N2H formation barriers can be obtained in these bimetallic Au-based alloy surfaces with an atomic ratio of 1 : 1, suggesting the strongest electrocatalytic activity. Further changing the atomic ratio leads to a notably increased formation barrier of N2H species, which can be explained by the Sabatier principle. It is concluded that the incorporation of Ni, Pd, Pt and Ru into Au can remarkably enhance the electrocatalytic activity since the HER barriers are notably higher than those of N2H formation, whereas the alloying of Au with Ta may not be able to effectively improve the N2 reduction performance due to the uninhibited HER. The present theoretical evaluations provide a promising method to design efficient bimetallic alloy electrocatalysts for N2 electroreduction into NH3 products.

Cervical optical coherence tomography image classification based on contrastive self-supervised texture learning.

BACKGROUND: Cervical cancer (CC) seriously affects the health of the female reproductive system. Optical coherence tomography (OCT) emerged as a noninvasive, high-resolution imaging technology for cervical disease detection. However, OCT image annotation is knowledge-intensive and time-consuming, which impedes the training process of deep-learning-based classification models. PURPOSE: This study aims to develop a computer-aided diagnosis (CADx) approach to classifying in-vivo cervical OCT images based on self-supervised learning. METHODS: In addition to high-level semantic features extracted by a convolutional neural network (CNN), the proposed CADx approach designs a contrastive texture learning strategy to leverage unlabeled cervical OCT images' texture features. We conducted 10-fold cross-validation on the OCT image dataset from a multicenter clinical study on 733 patients from China. RESULTS: In a binary classification task for detecting high-risk diseases, including high-grade squamous intraepithelial lesion and CC, our method achieved an area-under-the-curve value of 0.9798 ± 0.0157 with a sensitivity of 91.17% ± 4.99% and a specificity of 93.96% ± 4.72% for OCT image patches; also, it outperformed two out of four medical experts on the test set. Furthermore, our method achieved 91.53% sensitivity and 97.37% specificity on an external validation dataset containing 287 three-dimensional OCT volumes from 118 Chinese patients in a new hospital using a cross-shaped threshold voting strategy. CONCLUSIONS: The proposed contrastive-learning-based CADx method outperformed the end-to-end CNN models and provided better interpretability based on texture features, which holds great potential to be used in the clinical protocol of "see-and-treat."

New Insights on Volatile Components of Vanilla planifolia Cultivated in Taiwan.

Vanilla (Vanilla planifolia) is a precious natural flavoring that is commonly used throughout the world. In the past, all vanilla used in Taiwan was imported; however, recent breakthroughs in cultivation and processing technology have allowed Taiwan to produce its own supply of vanilla. In this study, headspace solid-phase microextraction (HS-SPME) combined with GC-FID and GC-MS was used to analyze the volatile components of vanilla from different origins produced in Taiwan under different cultivation and processing conditions. The results of our study revealed that when comparing different harvest maturities, the composition diversity and total volatile content were both higher when the pods were matured for more than 38 weeks. When comparing different killing conditions, we observed that the highest vanillin percentage was present after vanilla pods were killed three times in 65 °C treatments for 1 min each. From the experiment examining the addition of different strains, the PCA results revealed that the volatiles of vanilla that was processed with Dekkera bruxellensis and Bacillus subtilis was clearly distinguished from which obtained by processing with the other strains. Vanilla processed with B. subtilis contained 2-ethyl-1-hexanol, and this was not detected in other vanillas. Finally, when comparing the vanillin percentage from seven different regions in Taiwan, vanilla percentage from Taitung and Taoyuan Longtan were the highest.

Asymbiotic germination of Vanilla planifolia in relation to the timing of seed collection and seed pretreatments.

BACKGROUND: Vanilla planifolia is an important tropical orchid for production of natural vanilla flavor. Traditionally, V. planifolia is propagated by stem cuttings, which produces identical genotype that are sensitive to virulent pathogens. However, propagation with seed germination of V. planifolia is intricate and unstable because the seed coat is extremely hard with strong hydrophobic nature. A better understanding of seed development, especially the formation of impermeable seed coat would provide insights into seed propagation and conservation of genetic resources of Vanilla. RESULTS: We found that soaking mature seeds in 4% sodium hypochlorite solution from 75 to 90 min significantly increased germination. For the culture of immature seeds, the seed collection at 45 days after pollination (DAP) had the highest germination percentage. We then investigated the anatomical features during seed development that associated with the effect of seed pretreatment on raising seed germination percentage. The 45-DAP immature seeds have developed globular embryos and the thickened non-lignified cell wall at the outermost layer of the outer seed coat. Seeds at 60 DAP and subsequent stages germinated poorly. As the seed approached maturity, the cell wall of the outermost layer of the outer seed coat became lignified and finally compressed into a thick envelope at maturity. On toluidine blue O staining, the wall of outer seed coat stained greenish blue, indicating the presence of phenolic compounds. As well, on Nile red staining, a cuticular substance was detected in the surface wall of the embryo proper and the innermost wall of the inner seed coat. CONCLUSION: We report a reliable protocol for seed pretreatment of mature seeds and for immature seeds culture based on a defined time schedule of V. plantifolia seed development. The window for successful germination of culturing immature seed was short. The quick accumulation of lignin, phenolics and/or phytomelanins in the seed coat may seriously inhibit seed germination after 45 DAP. As seeds matured, the thickened and lignified seed coat formed an impermeable envelope surrounding the embryo, which may play an important role in inducing dormancy. Further studies covering different maturity of green capsules are required to understand the optimal seed maturity and germination of seeds.

Genetic Control of Reproductive Traits in Tomatoes Under High Temperature.

Global climate change is increasing the range of temperatures that crop plants must face during their life cycle, giving negative effects to yields. In this changing scenario, understanding the genetic control of plant responses to a range of increasing temperature conditions is a prerequisite to developing cultivars with increased resilience. The current work reports the identification of Quantitative Trait Loci (QTL) involved in reproductive traits affected by temperature, such as the flower number (FLN) and fruit number (FRN) per truss and percentage of fruit set (FRS), stigma exsertion (SE), pollen viability (PV) and the incidence of the physiological disorder tipburn (TB). These traits were investigated in 168 Recombinant Inbred Lines (RIL) and 52 Introgression Lines (IL) derived from the cross between Solanum lycopersicum var. "MoneyMaker" and S. pimpinellifolium accession TO-937. Mapping populations were cultivated under increased temperature regimen conditions: T1 (25°C day/21°C night), T2 (30°C day/25°C night) and T3 (35°C day/30°C night). The increase in temperature drastically affected several reproductive traits, for example, FRS in Moneymaker was reduced between 75 and 87% at T2 and T3 when compared to T1, while several RILs showed a reduction of less than 50%. QTL analysis allowed the identification of genomic regions affecting these traits at different temperatures regimens. A total of 22 QTLs involved in reproductive traits at different temperatures were identified by multi-environmental QTL analysis and eight involved in pollen viability traits. Most QTLs were temperature specific, except QTLs on chromosomes 1, 2, 4, 6, and 12. Moreover, a QTL located in chromosome 7 was identified for low incidence of TP in the RIL population, which was confirmed in ILs with introgressions on chromosome 7. Furthermore, ILs with introgressions in chromosomes 1 and 12 had good FRN and FRS in T3 in replicated trials. These results represent a catalog of QTLs and pre-breeding materials that could be used as the starting point for deciphering the genetic control of the genetic response of reproductive traits at different temperatures and paving the road for developing new cultivars adapted to climate change.

A Novel Variation in the FRIZZLE PANICLE (FZP) Gene Promoter Improves Grain Number and Yield in Rice.

Secondary branch number per panicle plays a crucial role in regulating grain number and yield in rice. Here, we report the positional cloning and functional characterization for SECONDARY BRANCH NUMBER7 (qSBN7), a quantitative trait locus affecting secondary branch per panicle and grain number. Our research revealed that the causative variants of qSBN7 are located in the distal promoter region of FRIZZLE PANICLE (FZP), a gene previously associated with the repression of axillary meristem development in rice spikelets. qSBN7 is a novel allele of FZP that causes an ∼56% decrease in its transcriptional level, leading to increased secondary branch and grain number, and reduced grain length. Field evaluations showed that qSBN7 increased grain yield by 10.9% in a temperate japonica variety, TN13, likely due to its positive effect on sink capacity. Our findings suggest that incorporation of qSBN7 can increase yield potential and improve the breeding of elite rice varieties.

Assessment of Genetic Differentiation and Linkage Disequilibrium in Solanum pimpinellifolium Using Genome-Wide High-Density SNP Markers.

To mine new favorable alleles for tomato breeding, we investigated the feasibility of utilizing Solanum pimpinellifolium as a diverse panel of genome-wide association study through the restriction site-associated DNA sequencing technique. Previous attempts to conduct genome-wide association studies using S. pimpinellifolium were impeded by an inability to correct for population stratification and by lack of high-density markers to address the issue of rapid linkage disequilibrium decay. In the current study, a set of 24,330 SNPs was identified using 99 S. pimpinellifolium accessions from the Tomato Genetic Resource Center. Approximately 84% of PstI site-associated DNA sequencing regions were located in the euchromatic regions, resulting in the tagging of most SNPs on or near genes. Our genotypic data suggested that S. pimpinellifolium were divided into three single-ancestry subpopulations and four mixed-ancestry subpopulations. Additionally, our SNP genotypic data consistently confirmed the genetic differentiation, achieving a relatively reliable correction of population stratification. Previous studies utilized the 8K tomato SNP array, SolCAP, to investigate the genetic variation of S. pimpinellifolium and we performed a meta-analysis of these genotypes. The result suggested SolCAP array was less appropriate to profile the genetic differentiation of S. pimpinellifolium when more accessions were involved because the samples belonging to the same accession demonstrated different genome patterns. Moreover, as expected, rapid linkage disequilibrium decay was observed in S. pimpinellifolium, especially in euchromatic regions. Approximately two-thirds of the flanking SNP markers did not display linkage disequilibrium based on r2 = 0.1. However, the 18-Kb linkage disequilibrium decay indeed reveals the potential of single-gene resolution in GWAS when markers are saturated.

A Bayesian statistical analysis of stochastic phenotypic plasticity model of cancer cells.

The phenotypic plasticity of cancer cells has received special attention in recent years. Even though related models have been widely studied in terms of mathematical properties, a thorough statistical analysis on parameter estimation and model selection is still very lacking. In this study, we present a Bayesian approach which is devised to deal with the data sets containing both mean and variance information of relative frequencies of cancer stem cells (CSCs). Both Gibbs sampling and Metropolis-Hastings (MH) algorithm are used to perform point and interval estimations of cell-state transition rates between CSCs and non-CSCs. Extensive simulations demonstrate the validity of our model and algorithm. By applying this method to a published data on SW620 colon cancer cell line, the model selection favors the phenotypic plasticity model, relative to conventional hierarchical model of cancer cells. Further quantitative analysis shows that, in the presence of phenotypic equilibrium, the variance data greatly influences the time-variant pattern of the parameters. Moreover, it is found that the occurrence of self-renewal of CSCs shows a strong negative correlation with de-differentiation rate from non-CSCs to CSCs, suggesting a balancing mechanism in the heterogenous population of cancer cells.

Chromosome-level assembly, genetic and physical mapping of Phalaenopsis aphrodite genome provides new insights into species adaptation and resources for orchid breeding.

The Orchidaceae is a diverse and ecologically important plant family. Approximately 69% of all orchid species are epiphytes, which provide diverse microhabitats for many small animals and fungi in the canopy of tropical rainforests. Moreover, many orchids are of economic importance as food flavourings or ornamental plants. Phalaenopsis aphrodite, an epiphytic orchid, is a major breeding parent of many commercial orchid hybrids. We provide a high-quality chromosome-scale assembly of the P. aphrodite genome. The total length of all scaffolds is 1025.1 Mb, with N50 scaffold size of 19.7 Mb. A total of 28 902 protein-coding genes were identified. We constructed an orchid genetic linkage map, and then anchored and ordered the genomic scaffolds along the linkage groups. We also established a high-resolution pachytene karyotype of P. aphrodite and completed the assignment of linkage groups to the 19 chromosomes using fluorescence in situ hybridization. We identified an expansion in the epiphytic orchid lineage of FRS5-like subclade associated with adaptations to the life in the canopy. Phylogenetic analysis further provides new insights into the orchid lineage-specific duplications of MADS-box genes, which might have contributed to the variation in labellum and pollinium morphology and its accessory structure. To our knowledge, this is the first orchid genome to be integrated with a SNP-based genetic linkage map and validated by physical mapping. The genome and genetic map not only offer unprecedented resources for increasing breeding efficiency in horticultural orchids but also provide an important foundation for future studies in adaptation genomics of epiphytes.

Genetic mapping of the qSBN7 locus, a QTL controlling secondary branch number per panicle in rice.

Secondary branch number (SBN) is an important component affecting spikelet number per panicle (SPP) and yield in rice. During recurrent backcross breeding, four BC2F4 populations derived from the high-yield donor parent IR65598-112-2 and the recurrent parent Tainan 13 (a local japonica cultivar) showed discontinuous variations of SPP and SBN within populations. Genetic analysis of 92 BC2F4 individuals suggested that both SPP and SBN are controlled by a single recessive allele. Two parents and 37 BC2F4 individuals showing high- and low-SBN type phenotypes were analyzed by restriction-site associated DNA sequencing (RAD-seq). Based on 2,522 reliable SNPs, the qSBN7 was mapped to a distal region of the long arm of chromosome 7. Trait-marker association analysis with an additional 166 high-SBN type BC2F4 individuals and 8 newly developed cleaved amplified polymorphic sequence markers further delimited the qSBN7 locus to a 601.4-kb region between the markers SNP2788 and SNP2849. Phenotype evaluation of two BC2F5 backcross inbred lines revealed that qSBN7 increased SPP by 83.2% and SBN by 61.0%. The qSBN7 of IR65598-112-2 could be used for improving reproductive sink capacity in rice.

Reassessment of QTLs for late blight resistance in the tomato accession L3708 using a restriction site associated DNA (RAD) linkage map and highly aggressive isolates of Phytophthora infestans.

Tomato late blight caused by the oomycete pathogen Phytophthora infestans (Mont.) de Bary is a major threat to tomato production in cool and wet environments. Intensified outbreaks of late blight have been observed globally from the 1980s, and are associated with migration of new and more aggressive populations of P. infestans in the field. The objective of this study was to reassess late blight resistance in the wild tomato accession L3708 (Solanum pimpinellifolium L.) against pathogens of different aggressiveness. An F2:3 genetic mapping population was developed using L3708 as the paternal parent. Two isolates of P. infestans, Pi39A and Pi733, were used for inoculation. Pi733 is a highly aggressive genotype that defeats three known late blight resistance genes, Ph-1, Ph-2, and Ph-5t in tomato. In contrast, Pi39A is a less aggressive genotype that defeats only Ph-1. Restriction site Associated DNA Sequencing (RAD-Seq) technology was used to massively sequence 90 bp nucleotides adjacent to both sides of PstI restriction enzyme cutting sites in the genome for all individuals in the genetic mapping population. The RAD-seq data were used to construct a genetic linkage map containing 440 single nucleotide polymorphism markers. Quantitative trait locus (QTL) analysis identified a new disease-resistant QTL specific to Pi733 on chromosome 2. The Ph-3 gene located on chromosome 9 could be detected whichever isolates were used. This study demonstrated the feasibility and efficiency of RAD-Seq technology for conducting a QTL mapping experiment using an F2:3 mapping population, which allowed the identification of a new late blight resistant QTL in tomato.

High-resolution genetic mapping and candidate gene identification of the SLP1 locus that controls glume development in rice.

Stunted lemma palea 1 (slp1) is a rice mutant that displays dwarfism, shortened inflorescence lengths, severely degenerated lemmas/paleas, and sterility. The SLP1 locus was mapped between markers RM447 and D275 in the distal region of the long arm of chromosome 8, using the F2 progeny derived from the cross between the Slp1/slp1 mutant (Oryza sativa subsp. japonica) and the variety Taichung Native 1 (TN1, O. sativa subsp. indica). The SLP1 locus was further delimited to a 46.4-kb genomic region containing three putative genes: OsSPL16, OsMADS45, and OsMADS37. Comparisons of the sequence variations and expression levels of the three candidate genes between wild-type plants and homozygous slp1 mutants suggested that a missense mutation in the sixth amino acid of the OsSPL16 protein was likely responsible for the slp1 mutant phenotypes.