Integrative approach for precise genotyping and transcriptomics of a salt tolerant introgression line in rice

Rice is the most salt sensitive cereal crop and its cultivation is particularly threatened by salt stress. This study reports the development of salt tolerant introgressed lines (ILs) derived from crosses between the salt tolerant indica rice variety FL478, which harbors the Saltol QTL, and the salt-sensitive japonica elite cultivar PL12. Although the introgression of the Saltol QTL has been widely used to improve salinity tolerance, the molecular basis underlying the salinity tolerance conferred by Saltol remains poorly understood. Equally, the impact of introgressions from a Saltol donor parent on the global transcriptome of ILs is largely unknown. Here, genotyping-by-sequencing (GBS) and Kompetitive allele specific PCR (KASP) genotyping, in combination with step-wise phenotypic selection in hydroponic culture, were used for the identification of salt-tolerant ILs. Transcriptome-based genotyping allowed the fine mapping of indica genetic introgressions in the best performing IL line (IL22). A total of 1,595 genes were identified in indica regions in IL22, which mainly located in large introgressions at Chromosomes 1 and 3. In addition to OsHKT1;5, an important number of genes potentially contributing to salt stress tolerance were identified in indica segments of IL22. Comparative transcript profiling also revealed important transcriptional reprograming in IL22 plants both under non-stress and salt-stress conditions, indicating an impact on the transcriptome of the japonica background by the indica introgressed genes and vice versa. Interactions among indica and japonica genes would provide novel regulatory networks contributing to salt stress tolerance in introgression rice lines

Integrative approach for precise genotyping and transcriptomics of a salt tolerant introgression line in rice

Trabajo presentado al 18th International Symposium on Rice Functional Genomics (ISRFG), celebrado en Barcelona del 3 al 5 de noviembre de 2021.Peer reviewe

Data_Sheet_2_Integrative Approach for Precise Genotyping and Transcriptomics of Salt Tolerant Introgression Rice Lines.docx

3 pages. -- Supplementary Methods: Transcriptome analysis by RNA-Seq and identification of introgressed indica regionsRice is the most salt sensitive cereal crop and its cultivation is particularly threatened by salt stress, which is currently worsened due to climate change. This study reports the development of salt tolerant introgression lines (ILs) derived from crosses between the salt tolerant indica rice variety FL478, which harbors the Saltol quantitative trait loci (QTL), and the salt-sensitive japonica elite cultivar OLESA. Genotyping-by-sequencing (GBS) and Kompetitive allele specific PCR (KASPar) genotyping, in combination with step-wise phenotypic selection in hydroponic culture, were used for the identification of salt-tolerant ILs. Transcriptome-based genotyping allowed the fine mapping of indica genetic introgressions in the best performing IL (IL22). A total of 1,595 genes were identified in indica regions of IL22, which mainly located in large introgressions at Chromosomes 1 and 3. In addition to OsHKT1;5, an important number of genes were identified in the introgressed indica segments of IL22 whose expression was confirmed [e.g., genes involved in ion transport, callose synthesis, transcriptional regulation of gene expression, hormone signaling and reactive oxygen species (ROS) accumulation]. These genes might well contribute to salt stress tolerance in IL22 plants. Furthermore, comparative transcript profiling revealed that indica introgressions caused important alterations in the background gene expression of IL22 plants (japonica cultivar) compared with its salt-sensitive parent, both under non-stress and salt-stress conditions. In response to salt treatment, only 8.6% of the salt-responsive genes were found to be commonly up- or down-regulated in IL22 and OLESA plants, supporting massive transcriptional reprogramming of gene expression caused by indica introgressions into the recipient genome. Interactions among indica and japonica genes might provide novel regulatory networks contributing to salt stress tolerance in introgression rice lines. Collectively, this study illustrates the usefulness of transcriptomics in the characterization of new rice lines obtained in breeding programs in rice.Peer reviewe

Data_Sheet_1_Integrative Approach for Precise Genotyping and Transcriptomics of Salt Tolerant Introgression Rice Lines.PDF

13 pages. -- Supplementary Figure 1. Breeding scheme used in the marked-assisted backcross introgression of the Saltol QTL from FL478 (indica) into the background of the rice variety OLESA (temperate japonica rice). -- Supplementary Figure 2. Polymorphism obtained with the SKC10 SSR marker visualized by agarose gel analysis. (A) Saltol QTL region showing the SKC10 SSR marker and relevant salt-related genes positions. (B) PCR products obtained from the Saltol donor (FL478), the recurrent (OLESA) parent and 4 representative introgression lines derived from FL478 x OLESA crosses (BC2F1). C-, negative control, He, heterozygous, Ho, homozygous. Primers are indicated in Supplementary Table 2. -- Supplementary Figure 3. Graphical representation of the genotypes of the Saltol-introgressed rice lines (BC3F3). Genotyping was carried out by KASPar analysis. SNPs are indicated in columns according to their chromosomal location (in mega base-pairs, Mb). Introgression lines (IL1 to IL31) are clustered in four groups (I to IV) depending on the BC3F1 parent from which they derive. The Saltol QTL location (and length) is indicated in the upper part. Homozygous donor (FL478) and recurrent (OLESA) alleles are depicted in blue and white, respectively. The KASPar markers used in this study are listed in Supplementary Tables 1 and 2. -- Supplementary Figure 4. SES score of parental lines (FL478, OLESA) hydroponically grown in modified Yoshida solution containing different NaCl concentrations (60 mM, 80 mM and 100 mM) for 14 days. Box plots show the distribution of SES scores in each line and condition (15 plants/genotype each experiment; T-test, * P < 0.05). Values above each box indicate the mean SES score . -- Supplementary Figure 5. Characterization of salt tolerant introgression lines. (A) Standard evaluation system (SES) scores of visual salt injury of the 30 ILs. Evaluation was performed after 14 days of salt treatment (80 mM NaCl). SES scores are shown as the percentage of plants at each score value. 1, highly tolerant; 3, tolerant; 5, moderately tolerant; 7, sensitive; 9, highly sensitive. ILs are clustered in four groups (I to IV) depending on the BC3F1 parent used. ILs were evaluated in successive rounds, with 5 plants and 10 plants in control and salt conditions respectively in each experiment, and most salt-sensitive ILs were discarded in the following assays. A total of six independent experiments were carried out with the most salt-tolerant ILs. (B) Representative images of IL22 and IL13 plants and parental lines in control and salt conditions after 14 days of treatment. -- Supplementary Figure 6. Plant growth of parental lines (FL478, OLESA) and IL22 plants hydroponically grown in modified Yoshida solution containing 80 mM NaCl. Control plants were not supplemented with NaCl. The leaf number of each genotype at different times of salt treatment is indicated. At least 6 plants per genotype and condition were assayed. -- Supplementary Figure 7. Samples analysed by RNASeq, and comparisons of data sets from each genotype (IL22, OLESA) and condition (control, salt-treated). -- Supplementary Figure 8. Singular enrichment analysis of introgressed indica genes (chromosome 1, blocks 1 and 2, and chromosome 3) using AgriGO (Tian et al., 2017). For a full list of gene IDs, see Supplementary Table 5. -- Supplementary Figure 9. Singular enrichment analysis of japonica genes up-regulated in IL22 plants at 24 h of salt treatment (80 mM NaCl) using AgriGO (Tian et al., 2017). For a full list of gene IDs, see Supplementary Table 8. -- Supplementary Figure 10. Singular enrichment analysis of japonica genes up-regulated in OLESA plants at 24 h of salt treatment (80 mM NaCl) using AgriGO (Tian et al., 2017). For a full list of gene IDs, see Supplementary Table 8. -- Supplementary Figure 11. Singular enrichment analysis of japonica genes down-regulated in IL22 plants at 24 h of salt treatment (80 mM NaCl) using AgriGO (Tian et al., 2017). For a full list of gene IDs, see Supplementary Table 8. -- Supplementary Figure 12. Singular enrichment analysis of japonica genes down-regulated in OLESA plants at 24 h of salt treatment (80 mM NaCl) using AgriGO (Tian et al., 2017). For a full list of gene IDs, see Supplementary Table 8. -- Supplementary Figure 13. Mapman analysis of japonica genes up- and down-regulated in IL22 and OLESA plants at 24 h of salt treatment (80 mM NaCl). Regulation overview, stress and transport schemes are shown. Color scale (yellow to blue) represents the log2 fold change of salt vs. control conditions.Rice is the most salt sensitive cereal crop and its cultivation is particularly threatened by salt stress, which is currently worsened due to climate change. This study reports the development of salt tolerant introgression lines (ILs) derived from crosses between the salt tolerant indica rice variety FL478, which harbors the Saltol quantitative trait loci (QTL), and the salt-sensitive japonica elite cultivar OLESA. Genotyping-by-sequencing (GBS) and Kompetitive allele specific PCR (KASPar) genotyping, in combination with step-wise phenotypic selection in hydroponic culture, were used for the identification of salt-tolerant ILs. Transcriptome-based genotyping allowed the fine mapping of indica genetic introgressions in the best performing IL (IL22). A total of 1,595 genes were identified in indica regions of IL22, which mainly located in large introgressions at Chromosomes 1 and 3. In addition to OsHKT1;5, an important number of genes were identified in the introgressed indica segments of IL22 whose expression was confirmed [e.g., genes involved in ion transport, callose synthesis, transcriptional regulation of gene expression, hormone signaling and reactive oxygen species (ROS) accumulation]. These genes might well contribute to salt stress tolerance in IL22 plants. Furthermore, comparative transcript profiling revealed that indica introgressions caused important alterations in the background gene expression of IL22 plants (japonica cultivar) compared with its salt-sensitive parent, both under non-stress and salt-stress conditions. In response to salt treatment, only 8.6% of the salt-responsive genes were found to be commonly up- or down-regulated in IL22 and OLESA plants, supporting massive transcriptional reprogramming of gene expression caused by indica introgressions into the recipient genome. Interactions among indica and japonica genes might provide novel regulatory networks contributing to salt stress tolerance in introgression rice lines. Collectively, this study illustrates the usefulness of transcriptomics in the characterization of new rice lines obtained in breeding programs in rice.Peer reviewe

Differential cross section measurements for the production of a W boson in association with jets in proton–proton collisions at √s = 7 TeV

Measurements are reported of differential cross sections for the production of a W boson, which decays into a muon and a neutrino, in association with jets, as a function of several variables, including the transverse momenta (pT) and pseudorapidities of the four leading jets, the scalar sum of jet transverse momenta (HT), and the difference in azimuthal angle between the directions of each jet and the muon. The data sample of pp collisions at a centre-of-mass energy of 7 TeV was collected with the CMS detector at the LHC and corresponds to an integrated luminosity of 5.0 fb[superscript −1]. The measured cross sections are compared to predictions from Monte Carlo generators, MadGraph + pythia and sherpa, and to next-to-leading-order calculations from BlackHat + sherpa. The differential cross sections are found to be in agreement with the predictions, apart from the pT distributions of the leading jets at high pT values, the distributions of the HT at high-HT and low jet multiplicity, and the distribution of the difference in azimuthal angle between the leading jet and the muon at low values.United States. Dept. of EnergyNational Science Foundation (U.S.)Alfred P. Sloan Foundatio

Optimasi Portofolio Resiko Menggunakan Model Markowitz MVO Dikaitkan dengan Keterbatasan Manusia dalam Memprediksi Masa Depan dalam Perspektif Al-Qur`an

Risk portfolio on modern finance has become increasingly technical, requiring the use of sophisticated mathematical tools in both research and practice. Since companies cannot insure themselves completely against risk, as human incompetence in predicting the future precisely that written in Al-Quran surah Luqman verse 34, they have to manage it to yield an optimal portfolio. The objective here is to minimize the variance among all portfolios, or alternatively, to maximize expected return among all portfolios that has at least a certain expected return. Furthermore, this study focuses on optimizing risk portfolio so called Markowitz MVO (Mean-Variance Optimization). Some theoretical frameworks for analysis are arithmetic mean, geometric mean, variance, covariance, linear programming, and quadratic programming. Moreover, finding a minimum variance portfolio produces a convex quadratic programming, that is minimizing the objective function ðð¥with constraintsð ð 𥠥 ðandð´ð¥ = ð. The outcome of this research is the solution of optimal risk portofolio in some investments that could be finished smoothly using MATLAB R2007b software together with its graphic analysis

Impacts of the Tropical Pacific/Indian Oceans on the Seasonal Cycle of the West African Monsoon

The current consensus is that drought has developed in the Sahel during the second half of the twentieth century as a result of remote effects of oceanic anomalies amplified by local land–atmosphere interactions. This paper focuses on the impacts of oceanic anomalies upon West African climate and specifically aims to identify those from SST anomalies in the Pacific/Indian Oceans during spring and summer seasons, when they were significant. Idealized sensitivity experiments are performed with four atmospheric general circulation models (AGCMs). The prescribed SST patterns used in the AGCMs are based on the leading mode of covariability between SST anomalies over the Pacific/Indian Oceans and summer rainfall over West Africa. The results show that such oceanic anomalies in the Pacific/Indian Ocean lead to a northward shift of an anomalous dry belt from the Gulf of Guinea to the Sahel as the season advances. In the Sahel, the magnitude of rainfall anomalies is comparable to that obtained by other authors using SST anomalies confined to the proximity of the Atlantic Ocean. The mechanism connecting the Pacific/Indian SST anomalies with West African rainfall has a strong seasonal cycle. In spring (May and June), anomalous subsidence develops over both the Maritime Continent and the equatorial Atlantic in response to the enhanced equatorial heating. Precipitation increases over continental West Africa in association with stronger zonal convergence of moisture. In addition, precipitation decreases over the Gulf of Guinea. During the monsoon peak (July and August), the SST anomalies move westward over the equatorial Pacific and the two regions where subsidence occurred earlier in the seasons merge over West Africa. The monsoon weakens and rainfall decreases over the Sahel, especially in August.Peer reviewe

Penilaian Kinerja Keuangan Koperasi di Kabupaten Pelalawan

This paper describe development and financial performance of cooperative in District Pelalawan among 2007 - 2008. Studies on primary and secondary cooperative in 12 sub-districts. Method in this stady use performance measuring of productivity, efficiency, growth, liquidity, and solvability of cooperative. Productivity of cooperative in Pelalawan was highly but efficiency still low. Profit and income were highly, even liquidity of cooperative very high, and solvability was good

Juxtaposing BTE and ATE – on the role of the European insurance industry in funding civil litigation

One of the ways in which legal services are financed, and indeed shaped, is through private insurance arrangement. Two contrasting types of legal expenses insurance contracts (LEI) seem to dominate in Europe: before the event (BTE) and after the event (ATE) legal expenses insurance. Notwithstanding institutional differences between different legal systems, BTE and ATE insurance arrangements may be instrumental if government policy is geared towards strengthening a market-oriented system of financing access to justice for individuals and business. At the same time, emphasizing the role of a private industry as a keeper of the gates to justice raises issues of accountability and transparency, not readily reconcilable with demands of competition. Moreover, multiple actors (clients, lawyers, courts, insurers) are involved, causing behavioural dynamics which are not easily predicted or influenced. Against this background, this paper looks into BTE and ATE arrangements by analysing the particularities of BTE and ATE arrangements currently available in some European jurisdictions and by painting a picture of their respective markets and legal contexts. This allows for some reflection on the performance of BTE and ATE providers as both financiers and keepers. Two issues emerge from the analysis that are worthy of some further reflection. Firstly, there is the problematic long-term sustainability of some ATE products. Secondly, the challenges faced by policymakers that would like to nudge consumers into voluntarily taking out BTE LEI