Dynamics of spatial and temporal population structure of Pyricularia oryzae in Taiwan.

BACKGROUND: To gain a better understanding of how Pyricularia oryzae population shifts is important for selecting suitable resistance genes for rice breeding programs. However, the relationships between P. oryzae pathogenic dynamics, geographic distribution, rice varieties, and timeline are not well studied. RESULTS: Resistance genes Piz-5, Pi9(t), Pi12(t), Pi20(t), Pita-2, and Pi11 showed stable resistance to the Taiwan rice blast fungus over 8 years of observations. Furthermore, 1749 rice blast isolates were collected from 2014 to 2021 and categorized into five pathotype clusters based on their correlation analysis between the geographic sources and virulence of Lijiangxintuanheigu monogenic lines. A detailed map of their distributions in Taiwan is presented. Isolates collected from the western region of Taiwan had greater pathotype diversity than those from the east region. Isolates collected from the subtropical region had greater diversity than those from the tropical region. Rice cultivars carrying Pik alleles were highly susceptible to pathotype L4. Cultivars with Piz-t were highly susceptible to pathotype L5, and those with Pish were highly susceptible to pathotype L1. The geographical distribution of each pathotype was distinct, and the population size of each pathotype fluctuated significantly each year. CONCLUSION: The regional mega cultivars significantly impact the evolution of Pyricularia oryzae in Taiwan within the span of 8 years. However, the annual fluctuation of pathotype populations likely correlate to the rising annual temperatures that selected pathotype clusters by their optimal growth temperature. The results will provide useful information for effective disease management, and enable the R-genes to prolong their function in the fields. © 2023 Society of Chemical Industry.

Identification of qBK2.1, a novel QTL controlling rice resistance against Fusarium fujikuroi.

BACKGROUND: Bakanae disease caused by Fusarium fujikuroi is an increasing threat to rice production. The infected plants show symptoms such as elongation, slenderness, chlorosis, a large leaf angle, and even death. Bakanae disease is traditionally managed by seed treatment. However, fungicide-resistant F. fujikuroi isolates have emerged in several Asian areas, including Taiwan. This study aimed to identify new bakanae resistance quantitative trait loci (QTLs) and provide molecular markers to assist future breeding. RESULTS: A population of F2:9 recombinant inbred lines (RILs) was derived from the cross between an elite japonica Taiwanese cultivar 'Taikeng 16 (TK16)' and an indica variety 'Budda'. 'Budda' was found highly resistant to all 24 representative isolates of the F. fujikuroi population in Taiwan. For the RIL population, 6,492 polymorphic single nucleotide polymorphisms (SNPs) spanning the rice genome were obtained by genotyping-by-sequencing (GBS) technique, and the disease severity index (DSI) was evaluated by inoculation with a highly virulent F. fujikuroi isolate Ff266. Trait-marker association analysis of 166 RILs identified two QTLs in 'Budda'. qBK2.1 (21.97-30.15 Mb) is a novel and first bakanae resistance QTL identified on chromosome 2. qBK1.8 (5.24-8.66 Mb) partially overlaps with the previously reported qBK1.3 (4.65-8.41 Mb) on chromosome 1. The log of odds (LOD) scores of qBK1.8 and qBK2.1 were 4.75 and 6.13, accounting for 4.9% and 8.1% of the total phenotypic variation, respectively. 64 RILs carrying both qBK1.8 and qBK2.1 showed lower DSI (7%) than the lines carrying only qBK1.8 (15%), only qBK2.1 (13%), or none of the two QTLs (21%). For the future application of identified QTLs, 11 KBioscience competitive allele-specific PCR (KASP) markers and 3 insertion-deletion (InDel) markers were developed. CONCLUSIONS: Compared to other important rice diseases, knowledge of bakanae resistance has been insufficient, which limited the development and deployment of resistant cultivars. The discovery of qBK2.1 has provided a new source of bakanae resistance. The resistant RILs inheriting good plant type, good taste, and high yield characteristics from 'TK16' can be used as good resistance donors. Our newly developed markers targeting qBK2.1 and qBK1.8 can also serve as an important basis for future fine-mapping and resistance breeding.

TEAD4 is a master regulator of high-risk nasopharyngeal carcinoma.

The molecular basis underlying nasopharyngeal carcinoma (NPC) remains unclear. Recent progress in transcriptional regulatory network analysis helps identify the master regulator (MR) proteins that transcriptionally define malignant tumor phenotypes. Here, we investigated transcription factor-target interactions and identified TEA domain transcription factor 4 (TEAD4) as an MR of high-risk NPC. Precisely, TEAD4 promoted NPC migration, invasion and cisplatin resistance, depending on its autopalmitoylation. Mechanistically, YTHDF2 (YTH domain family 2) recognized WTAP (Wilms tumor 1-associating protein)-mediated TEAD4 m6A methylation to facilitate its stability and led to aberrant up-regulation of TEAD4. Up-regulated TEAD4 further drove NPC progression by transcriptionally activating BZW2 (basic leucine zipper and W2 domains 2) to induce the oncogenic AKT pathway. Moreover, the transcriptional activity of TEAD4 was independent of its canonical coactivators YAP/TAZ. Clinically, TEAD4 serves as an independent predictor of unfavorable prognosis and cisplatin response in NPC. Our data revealed the crucial role of TEAD4 in driving tumor malignancy, thus, may provide therapeutic vulnerability in NPC.

The Bph45 Gene Confers Resistance against Brown Planthopper in Rice by Reducing the Production of Limonene.

Brown planthopper (BPH), a monophagous phloem feeder, consumes a large amount of photoassimilates in rice and causes wilting. A near-isogenic line 'TNG71-Bph45' was developed from the Oryza sativa japonica variety 'Tainung 71 (TNG71) carrying a dominant BPH-resistance locus derived from Oryza nivara (IRGC 102165) near the centromere of chromosome 4. We compared the NIL (TNG71-Bph45) and the recurrent parent to explore how the Bph45 gene confers BPH resistance. We found that TNG71-Bph45 is less attractive to BPH at least partially because it produces less limonene. Chiral analysis revealed that the major form of limonene in both rice lines was the L-form. However, both L- and D-limonene attracted BPH when applied exogenously to TNG71-Bph45 rice. The transcript amounts of limonene synthase were significantly higher in TNG71 than in TNG71-Bph45 and were induced by BPH infestation only in the former. Introgression of the Bph45 gene into another japonica variety, Tainan 11, also resulted in a low limonene content. Moreover, several dominantly acting BPH resistance genes introduced into the BPH-sensitive IR24 line compromised its limonene-producing ability and concurrently decreased its attractiveness to BPH. These observations suggest that reducing limonene production may be a common resistance strategy against BPH in rice.

Uncovering the Genetic of Cadmium Accumulation in the Rice 3K Panel.

Because Cadmium (Cd) is harmful to humans, and most non-smokers are exposed to Cd mainly through rice consumption, low-Cd rice breeding is urgently needed. It might not be possible to apply variation created using gene editing technology to breeding directly, so it is important to explore genetic variation in this trait in a natural population. In this study, variation in 4 genes was identified among 3024 accessions from the International Rice Research Institute 3000 Rice Genome Project (IRRI 3K-RGP) and 71 other important varieties, and the relationships between the variants and plant Cd accumulation were validated with hydroponic and pot experiments. Variants in OsNRAMP1, OsNRAMP5, OsLCD, and OsHMA3 were grouped into two, four, three, and two haplotypes, respectively. Fourteen combinations of these haplotypes, which were referred to as Cd-mobile types, were found in the collection. Of these, type 14 was shown to have the greatest potential for low-Cd accumulation, and functional markers for this type were designed. The results of this study provide an important resource for low-Cd rice breeding and highlight an effective strategy for pre-breeding programs.

Controlling the lodging risk of rice based on a plant height dynamic model.

BACKGROUND: Rice is a key global food crop. Rice lodging causes a reduction in plant height and crop yield, and rice is prone to lodging in the late growth stage because of panicle initiation. We used two water irrigation modes and four fertilizer application intervals to investigate the relationship between lodging and various cultivation conditions over 2 years. RESULTS: Plant height data were collected and combined with aerial images, revealing that rice lodging was closely related to the nitrogen fertilizer content. The aerial images demonstrated that lodging mainly occurred in the fields treated with a high-nitrogen fertilizer, and analysis of variance revealed that plant height was signifi-cantly affected by nitrogen fertilizer. These results demonstrated that rice plant height in the booting stage was significantly positively correlated with the lodging results (r = 0.67) and nega-tively correlated with yield (r = - 0.46). If the rice plant height in the booting stage exceeded 70.7 cm and nitrogen fertilizer was continuously applied, according to the predicted growing curve of plant height, the plant would be at risk of lodging. Results showed more rainfall accumulated in the later stage of rice growth accompanied by strong instantaneous gusts, the risk of lodging in-creased. CONCLUSION: The results provide predictions that can be applied in intelligent production and lodging risk management, and they form the basis of cultivation management and response policies for each growth period.

Insights into the genetic spatial structure of Nicaraguan weedy rice and control of its seed spread.

BACKGROUND: The genetic backgrounds and occurrence patterns of weedy rice (WR, Oryza sativa) are highly diverse, and so are the challenges facing its control among countries. WR control is difficult because it is similar to cultivated rice and manual removal is one of the few options for control. Understanding the ecology of WR will aid efforts to break its life cycle and establish long-term management strategies under both irrigated and rainfed systems. RESULTS: Nicaraguan WR (NWR) plants were genetically closer to the AUS and Indica pools in terms of to genetic distance. A map of admixture coefficients suggested a pattern of long-distance dispersal and spread of NWR across Nicaragua, which has likely been facilitated by commercial activities and sharing of harvesting equipment between border cities or important trading ports and inland regions. Moreover, the NWR plants from the soil seedbank in irrigated regions showed different habitats and lower grain number per panicle compared with plants spread by seed-mediated contamination. In addition, grain indexes showed that length-to-width ratio was a better indicator than awn length for distinguishing between NWR and Nicaraguan Indica cultivars. CONCLUSION: Analysis of the population structure and habitats of NWR revealed five clusters derived from seed-mediated contamination in rainfed upland regions, plants from the soil seedbank in irrigated double-cropping regions, and pollen-mediated contamination across both regions. Field weed management before harvesting and seed purification based on the length-to-width ratio can be conducted to improve the efficiency of long-term control of WR in Nicaragua. © 2022 Society of Chemical Industry.

Evaluation of the real-time fluorescence loop-mediated isothermal amplification assay for the detection of Ureaplasma urealyticum.

Ureaplasma urealyticum (UU) is commonly present in human reproductive tract, which frequently leads to genital tract infection. Hence, there is an urgent need to develop a rapid detection method for UU. In our study, a real-time fluorescence loop-mediated isothermal amplification (LAMP) assay was developed and evaluated for the detection of UU. Two primers were specifically designed based on the highly conserved regions of ureaseB genes. The reaction was carried out for 60 min in a constant temperature system using Bst DNA polymerase, and the process was monitored by real-time fluorescence signal, while polymerase chain reaction (PCR) was performed simultaneously. In real-time fluorescence LAMP reaction system, positive result was only obtained for UU among 9 bacterial strains, with detection sensitivity of 42 pg/µL (4.2 × 105 CFU/mL), and all 16 clinical samples of UU could be detected. In conclusion, real-time fluorescence LAMP is a simple, sensitive, specific and effective method compared with conventional PCR, which shows great promise in the rapid detection of UU.

Assessment of Grain Harvest Moisture Content Using Machine Learning on Smartphone Images for Optimal Harvest Timing.

Grain moisture content (GMC) is a key indicator of the appropriate harvest period of rice. Conventional testing is time-consuming and laborious, thus not to be implemented over vast areas and to enable the estimation of future changes for revealing optimal harvesting. Images of single panicles were shot with smartphones and corrected using a spectral-geometric correction board. In total, 86 panicle samples were obtained each time and then dried at 80 °C for 7 days to acquire the wet-basis GMC. In total, 517 valid samples were obtained, in which 80% was randomly used for training and 20% was used for testing to construct the image-based GMC assessment model. In total, 17 GMC surveys from a total of 201 samples were also performed from an area of 1 m2 representing on-site GMC, which enabled a multi-day GMC prediction. Eight color indices were selected using principal component analysis for building four machine learning models, including random forest, multilayer perceptron, support vector regression (SVR), and multivariate linear regression. The SVR model with a MAE of 1.23% was the most suitable for GMC of less than 40%. This study provides a real-time and cost-effective non-destructive GMC measurement using smartphones that enables on-farm prediction of harvest dates and facilitates the harvesting scheduling of agricultural machinery.

Explore the genetics of weedy traits using rice 3K database.

BACKGROUND: Weedy rice, a conspecific weedy counterpart of the cultivated rice (Oryza sativa L.), has been problematic in rice-production area worldwide. Although we started to know about the origin of some weedy traits for some rice-growing regions, an overall assessment of weedy trait-related loci was not yet available. On the other hand, the advances in sequencing technologies, together with community efforts, have made publicly available a large amount of genomic data. Given the availability of public data and the need of "weedy" allele mining for a better management of weedy rice, the objective of the present study was to explore the genetic architecture of weedy traits based on publicly available data, mainly from the 3000 Rice Genome Project (3K-RGP). RESULTS: Based on the results of population structure analysis, we have selected 1378 individuals from four sub-populations (aus, indica, temperate japonica, tropical japonica) without admixed genomic composition for genome-wide association analysis (GWAS). Five traits were investigated: awn color, seed shattering, seed threshability, seed coat color, and seedling height. GWAS was conducted for each sub-population × trait combination and we have identified 66 population-specific trait-associated SNPs. Eleven significant SNPs fell into an annotated gene and four other SNPs were close to a putative candidate gene (± 25 kb). SNPs located in or close to Rc were particularly predictive of the occurrence of seed coat color and our results showed that different sub-populations required different SNPs for a better seed coat color prediction. We compared the data of 3K-RGP to a publicly available weedy rice dataset. The profile of allele frequency, phenotype-genotype segregation of target SNP, as well as GWAS results for the presence and absence of awns diverged between the two sets of data. CONCLUSIONS: The genotype of trait-associated SNPs identified in this study, especially those located in or close to Rc, can be developed to diagnostic SNPs to trace the origin of weedy trait occurred in the field. The difference of results from the two publicly available datasets used in this study emphasized the importance of laboratory experiments to confirm the allele mining results based on publicly available data.

Assessment of Rice Developmental Stage Using Time Series UAV Imagery for Variable Irrigation Management.

Rice is one of the three major crops in the world and is the major crop in Asia. Climate change and water resource shortages may result in decreases in rice yields and possible food shortage crises. In this study, water-saving farming management was tested, and IOT field water level monitoring was used to regulate water inflow automatically. Plant height (PH) is an important phenotype to be used to determine difference in rice growth periods and yields using water-saving irrigation. An unmanned aerial vehicle (UAV) with an RGB camera captured sequential images of rice fields to estimate rice PH compared with PH measured on site for estimating rice growth stages. The test results, with two crop harvests in 2019, revealed that with adequate image calibration, the correlation coefficient between UAV-PH and field-PH was higher than 0.98, indicating that UAV images can accurately determine rice PH in the field and rice growth phase. The study demonstrated that water-saving farming is effective, decreasing water usage for the first and second crops of 2019 by 53.5% and 21.7%, respectively, without influencing the growth period and final yield. Coupled with an automated irrigation system, rice farming can be adaptive to water shortage situations.

Transcriptome Analysis of Early Defenses in Rice against Fusarium fujikuroi.

BACKGROUND: Bakanae is a seedborne disease caused by Fusarium fujikuroi. Rice seedlings emerging from infected seeds can show diverse symptoms such as elongated and slender stem and leaves, pale coloring, a large leaf angle, stunted growth and even death. Little is known about rice defense mechanisms at early stages of disease development. RESULTS: This study focused on investigating early defenses against F. fujikuroi in a susceptible cultivar, Zerawchanica karatals (ZK), and a resistant cultivar, Tainung 67 (TNG67). Quantitative PCR revealed that F. fujikuroi colonizes the root and stem but not leaf tissues. Illumina sequencing was conducted to analyze the stem transcriptomes of F. fujikuroi-inoculated and mock-inoculated ZK and TNG67 plants collected at 7 days post inoculation (dpi). More differentially expressed genes (DEGs) were identified in ZK (n = 169) than TNG67 (n = 118), and gene ontology terms related to transcription factor activity and phosphorylation were specifically enriched in ZK DEGs. Among the complex phytohormone biosynthesis and signaling pathways, only DEGs involved in the jasmonic acid (JA) signaling pathway were identified. Fourteen DEGs encoding pattern-recognition receptors, transcription factors, and JA signaling pathway components were validated by performing quantitative reverse transcription PCR analysis of individual plants. Significant repression of jasmonate ZIM-domain (JAZ) genes (OsJAZ9, OsJAZ10, and OsJAZ13) at 3 dpi and 7 dpi in both cultivars, indicated the activation of JA signaling during early interactions between rice and F. fujikuroi. Differential expression was not detected for salicylic acid marker genes encoding phenylalanine ammonia-lyase 1 and non-expressor of pathogenesis-related genes 1. Moreover, while MeJA did not affect the viability of F. fujikuroi, MeJA treatment of rice seeds (prior to or after inoculation) alleviated and delayed bakanae disease development in susceptible ZK. CONCLUSIONS: Different from previous transcriptome studies, which analyzed the leaves of infected plants, this study provides insights into defense-related gene expression patterns in F. fujikuroi-colonized rice stem tissues. Twelve out of the 14 selected DEGs were for the first time shown to be associated with disease resistance, and JA-mediated resistance was identified as a crucial component of rice defense against F. fujikuroi. Detailed mechanisms underlying the JA-mediated bakanae resistance and the novel defense-related DEGs are worthy of further investigation.

Invasion and Colonization Pattern of Fusarium fujikuroi in Rice.

Bakanae disease in rice can cause abnormal elongation of the stem and leaves, development of adventitious roots, a larger leaf angle, and even death. Little is known about the infection, colonization, and distribution of Fusarium fujikuroi in rice plants across different growth stages. In this study, microscopic observation and quantitative real-time PCR were combined to investigate the pathogenesis of bakanae, using artificially inoculated seedlings of a susceptible rice cultivar, Zerawchanica karatals (ZK), a resistant cultivar, Tainung 67 (TNG67), naturally infected adult field plants (cultivars Kaohsiung 139, Taikeng 2, and Tainan 11), and an F. fujikuroi isolate expressing green fluorescent protein. In rice seedlings, F. fujikuroi hyphae were found to directly penetrate the epidermis of basal stems and roots, then extend inter- and intracellularly to invade the vascular bundles. Occlusion of vascular bundles and radial hyphal expansion from vascular bundles to surrounding parenchyma were observed in adult plants. Analysis of consecutive 3-cm segments of the whole plant revealed that F. fujikuroi was largely confined to the embryo, basal stem, and basal roots in seedlings, and distributed unevenly in the lower aerial parts (including nodes and internodes) of adult plants. The elongation and development of adventitious roots did not necessarily correlate with the amount of F. fujikuroi in diseased plants. Treatment of rice seeds with gibberellic acid-3 (GA3) at 0.5 mg/liter resulted in significantly more elongation of ZK than TNG67 seedlings, suggesting that the susceptibility of ZK to bakanae is associated with its higher sensitivity to GA3.

Phylogenetic origin and dispersal pattern of Taiwan weedy rice.

BACKGROUND: Knowledge of the genetic diversity and spatial structure of Taiwan weedy red rice (WRR) populations, which adapted in a transplanting system, will facilitate the design of effective methods to control this weed by tracing its origins and dispersal patterns in a given region. RESULTS: Taiwan WRR is genetically most similar to Taiwan indica cultivars and landraces according to genetic distance. The inbreeding coefficient of the Taiwan WRR population is greater than 0.8, which is similar to the inbred cultivars. The ancestry coefficients map suggests a dispersal pattern of long-distance and seed-mediated contamination across Taiwan, often from warmer, earlier-planted regions to cooler, later-planted regions. Parentage analysis of Taiwan WRR revealed that mostly early indica landraces and indica cultivars were present in the genetic pool; in rare cases temperate japonica was present. Based on the above results, the phylogenetic origin of most Taiwan weedy rice appears to be from hybrid progenies of old cultivated red rice accessions crossed with 'DGWG'. The inbreeding coefficient trend of the six TWR clusters suggests a temporal shift from 'old' indica landraces with red bran (high inbreeding coefficient) to modern indica varieties (low inbreeding coefficient). CONCLUSION: Although there were sustained efforts to remove these old red rice accessions from paddy fields before 1945, some farmers continued to use low purity seed. This practice, along with volunteer cultivation of these old varieties in the second cropping season, apparently has facilitated the long-distance, seed-mediated contamination of rice seed, and the increase in weedy rice seed in paddy soil. © 2019 Society of Chemical Industry.

Genome-wide association mapping of gene loci affecting disease resistance in the rice-Fusarium fujikuroi pathosystem.

BACKGROUND: Rice bakanae disease has emerged as a new threat to rice production. In recent years, an increase in the occurrence and severity of bakanae disease has been reported in several areas in Asia. Although bakanae disease affects rice yield and quality, little is known about the genetics of bakanae resistance in rice. The lack of large-scale screens for bakanae resistance in rice germplasm has also limited the development and deployment of resistant varieties. RESULTS: A genome-wide association study (GWAS) was conducted to identify genes/loci conferring bakanae resistance in rice. A total of 231 diverse accessions from Rice Diversity Panel 1 (RDP1) were inoculated with a highly virulent Taiwanese Fusarium fujikuroi isolate and assessed for resistance using two parameters: (1) disease severity index based on visual rating and (2) colonization rate determined by reisolation of F. fujikuroi from the basal stems of infected rice seedlings. We identified 14 quantitative trait loci (QTLs) (10 for disease severity and 4 for colonization rate), including 1 mapped for both parameters. A total of 206 candidate genes were identified within the 14 QTLs, including genes encoding leucine-rich repeat (LRR)-containing and NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4) proteins, hormone-related genes, transcription factor genes, ubiquitination-related genes, and oxidase/oxidoreductase genes. In addition, a candidate QTL (qBK1.7) that co-localized with the previously identified QTLs qBK1 and qFfR1, was verified by linkage analysis using a population of 132 recombinant inbred lines derived from IR64 x Nipponbare. GWAS delineated qBK1.7 to a region of 8239 bp containing three genes. Full-length sequencing across qBK1.7 in 20 rice accessions revealed that the coding regions of two LRR-containing genes Os01g0601625 and Os01g0601675 may be associated with bakanae resistance. CONCLUSIONS: This study facilitates the exploitation of bakanae resistance resources in RDP1. The information on the resistance performance of 231 rice accessions and 14 candidate QTLs will aid efforts to breed resistance to bakanae and uncover resistance mechanisms. Quantification of the level of F. fujikuroi colonization in addition to the conventional rating of visual symptoms offers new insights into the genetics of bakanae resistance.

A Statistical Procedure for Genome-Wide Detection of QTL Hotspots Using Public Databases with Application to Rice.

Genome-wide detection of quantitative trait loci (QTL) hotspots underlying variation in many molecular and phenotypic traits has been a key step in various biological studies since the QTL hotspots are highly informative and can be linked to the genes for the quantitative traits. Several statistical methods have been proposed to detect QTL hotspots. These hotspot detection methods rely heavily on permutation tests performed on summarized QTL data or individual-level data (with genotypes and phenotypes) from the genetical genomics experiments. In this article, we propose a statistical procedure for QTL hotspot detection by using the summarized QTL (interval) data collected in public web-accessible databases. First, a simple statistical method based on the uniform distribution is derived to convert the QTL interval data into the expected QTL frequency (EQF) matrix. And then, to account for the correlation structure among traits, the QTL for correlated traits are grouped together into the same categories to form a reduced EQF matrix. Furthermore, a permutation algorithm on the EQF elements or on the QTL intervals is developed to compute a sliding scale of EQF thresholds, ranging from strict to liberal, for assessing the significance of QTL hotspots. With grouping, much stricter thresholds can be obtained to avoid the detection of spurious hotspots. Real example analysis and simulation study are carried out to illustrate our procedure, evaluate the performances and compare with other methods. It shows that our procedure can control the genome-wide error rates at the target levels, provide appropriate thresholds for correlated data and is comparable to the methods using individual-level data in hotspot detection. Depending on the thresholds used, more than 100 hotspots are detected in GRAMENE rice database. We also perform a genome-wide comparative analysis of the detected hotspots and the known genes collected in the Rice Q-TARO database. The comparative analysis reveals that the hotspots and genes are conformable in the sense that they co-localize closely and are functionally related to relevant traits. Our statistical procedure can provide a framework for exploring the networks among QTL hotspots, genes and quantitative traits in biological studies. The R codes that produce both numerical and graphical outputs of QTL hotspot detection in the genome are available on the worldwide web http://www.stat.sinica.edu.tw/chkao/.

Mapping quantitative trait loci for fruit traits and powdery mildew resistance in melon (Cucumis melo).

BACKGROUND: Fruit characters affect consumer preferences and the market value of melons is determined by fruit quality. Most fruit quality-related traits are controlled by multiple genes, and are influenced by environmental factors. Furthermore, powdery mildew is another limiting factor in melon production. To develop new melon cultivars with disease resistance and high quality fruits using the molecular marker-assisted breeding strategy, identification of quantitative trait loci for fruit quality and disease resistance is required. RESULTS: The F2 populations from the cross of TARI-08874 (Cucumis melo ssp. melo) and 'Bai-li-gua' (C. melo ssp. agrestis) were used to map the quantitative trait loci (QTLs) for fruit-related traits and powdery mildew resistance in two trials. All traits were significantly different (P < 0.05) between parents. The generated linkage map consisted of twelve major linkage groups (LGs), spanning 626.1 cM in total, with an average distance of 8.3 cM between flanking markers. Nineteen QTLs were detected for seven melon traits, among which ten QTLs were localized to the same positions as the corresponding QTLs described in other studies. Four of these QTLs were detected in both trials. The results of identified QTLs in this study suggested that fruit size in the tested populations were mainly determined by fruit diameter and flesh thickness. All of the major QTLs for fruit diameter and flesh thickness were identified on LG5 and LG11. Four QTLs identified responsible for netting width of fruit rind were co-localized with the QTLs for netting density, suggesting similar genetic mechanisms affecting these two traits. Additionally, only one major QTL for powdery mildew resistance was detected on LG2, and it was closely linked to a simple sequence repeat (SSR) marker CMBR120 which was identified in a previous study. CONCLUSION: Because the netting feature is a crucial factor for external appearance of fruits in Asia market, we focus on mining the genetic information of fruit netting. This is the first report of QTL mapping to netting width. Furthermore, new QTLs were identified for netting density (qND4, qND6, and qND7) and netting width (qNW2, qNW4, qNW6, and qNW7) successfully. In addition, novel QTLs for fruit diameter (qFD5), flesh thickness (qFT11) were also detected.

Influence of baseline and worsening renal function on efficacy of spironolactone in patients With severe heart failure: insights from RALES (Randomized Aldactone Evaluation Study).

OBJECTIVES: This study investigated the influence of baseline and worsening renal function (WRF) on the efficacy of spironolactone in patients with severe heart failure (HF). BACKGROUND: Renal dysfunction or decline in renal function is a known predictor of adverse outcome in patients with HF, and treatment decisions are often on the basis of measures of renal function. METHODS: We used data from the RALES (Randomized Aldactone Evaluation Study) in 1,658 patients with New York Heart Association functional class III or IV HF and an ejection fraction <35%. Participants were randomized to spironolactone 25 mg, which could be titrated to 50 mg, or placebo daily. Renal function (estimated glomerular filtration rate [eGFR]) was estimated by the Modification of Diet in Renal Disease equation. Worsening renal function was defined as a 30% reduction in eGFR from baseline to 12 weeks post-randomization. RESULTS: Individuals with reduced baseline eGFR exhibited similar relative risk reductions in all-cause death and the combined endpoint of death or hospital stays for HF as those with a baseline eGFR >60 ml/min/1.73 m(2) and greater absolute risk reduction compared with those with a higher baseline eGFR (10.3% vs. 6.4%). Moreover, WRF (17% vs. 7% for spironolactone and placebo groups, p < 0.001) was associated with an increased adjusted risk of death in the placebo group (hazard ratio: 1.9, 95% confidence interval: 1.3 to 2.6) but not in those randomized to spironolactone (hazard ratio: 1.1, 95% confidence interval: 0.79 to 1.5, p interaction = 0.009). The risk of hyperkalemia and renal failure was higher in those with worse baseline renal function and those with WRF, particularly in the spironolactone arm, but the substantial net benefit of spironolactone therapy remained. CONCLUSIONS: The absolute benefit of spironolactone was greatest in patients with reduced eGFR. Worsening renal function was associated with a negative prognosis, yet the mortality benefit of spironolactone was maintained.

[Effect of safflower injection on endoplasmic reticulum stress-induced apoptosts in rats with hypoxic pulmonary hypertension].

OBJECTIVE: To explore the effects of safflower injection on prevention and treatment of hypoxic pulmonary hypertension and clarify the function of the endoplasmic reticulum stress apoptosis pathway during the process. METHODS: Thirty male SD rats were randomly grouped as normal control group, hypoxia-hypercapnia group and hypoxia+safflower group. The latter two groups were put in the cabin with oxygen concentration ranged from 9% to 11% and carbon dioxide concentration from 5% to 6%. The pulmonary artery pressure and the index of right ventricular hypertrophy were determined after hypoxia exposure (8 h/dx28 d). Changes in morphology of lung tissue were observed by electron microscopy. To explore the possible mechanisms, we also detected apoptosis and apoptosis-related genes/proteins in lung tissue by TUNEL reactivity and PCR and Western blot. RESULTS: Compared with the normal control group, pulmonary artery pressure and the index of right ventricular hypertrophy in hypoxia group were 45% and 33.4% higher, respectively. Tiny blood vessel wall of lungs was thickened and edema, and proliferation of collagen fibers was obvious under the electron microscope. TUNEL staining of apoptotic cells in lung tissues showed more high brightness green fluorescence (+-++), but less green fluorescence showed in the pulmonary vascular smooth muscle cell layer, and apoptosis index (AI) value was 150% higher; gene and protein expression levels of endoplasmic reticulum stress pathway were increased. Compared with hypoxia-hypercapnia group, pulmonary artery pressure and the index of right ventricular hypertrophy in the hypoxia+safflower group were 18% and 15.6% lower, respectively; collagen fibers were decreased, and smooth muscle cells and epithelial cells were got apoptotic-like changes under the electron microscope. TUNEL staining of apoptotic cells in lung tissues showed brighter green fluorescence (++-+++); the high brightness green fluorescence showed in pulmonary vascular smooth muscle cell layer, and apoptotic index (Al) value was 40% higher; gene and protein expressions of endoplasmic reticulum stress pathway were significantly upregulated. CONCLUSION: Our findings demonstrate that safflower injection could activate endoplasmic reticulum stress-induced apoptosis and especially promote apoptosis in pulmonary vascular smooth muscle cells.

[Relationship between interleukin-6 gene-572C/G polymorphism and chronic periodontitis].

OBJECTIVE: To investigate the relationship between interleukin-6 (IL-6) gene -572C/G polymorphism and the risk of chronic periodontitis disease. METHODS: IL-6-572C/G genotype polymorphism was examined in 93 patients with chronic periodontitis and 96 control subjects by PCR restriction fragment length polymorphism (PCR-RFLP) method. RESULTS: IL-6-572GG genotype and G allele were more frequent in chronic periodontitis patients than that in control subjects (P<0.05). -572CC, CG and GG genotype frequency were 52.7 % , 40.9 %, 6.4 % in chronic periodontitis patients and 67.7 %, 31.3%, 1.0 % in control subjects, respectively. -572CG + GG genotype and G allele were more frequent in patients than that in control subjects (P<0.05). Compared with CC genotype,the odds ratio for chronic periodontitis was 1.88 (95% CI: 1.04-3.40, P<0.05) for CG + GG genotype. CONCLUSIONS: The frequency of -572CG + GG genotype was higher in patients with chronic periodontitis compared with the control subjects. IL-6-572C/G polymorphism may be a genetic susceptibility factor for chronic periodontitis in Chinese Hans population.