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

A multitype sticky particle construction of Wasserstein stable semigroups solving one-dimensional diagonal hyperbolic systems with large monotonic data

International audienceThis article is dedicated to the study of diagonal hyperbolic systems in one space dimension, with cumulative distribution functions, or more generally nonconstant monotonic bounded functions, as initial data. Under a uniform strict hyperbolicity assumption on the characteristic fields, we construct a multitype version of the sticky particle dynamics and obtain existence of global weak solutions by compactness. We then derive a $L^p$ stability estimate on the particle system uniform in the number of particles. This allows to construct nonlinear semigroups solving the system in the sense of Bianchini and Bressan [Ann. of Math. (2), 2005]. We also obtain that these semigroup solutions satisfy a stability estimate in Wasserstein distances of all orders, which encompasses the classical $L^1$ estimate and generalises to diagonal systems the results by Bolley, Brenier and Loeper [J. Hyperbolic Differ. Equ., 2005] in the scalar case. Our results are obtained without any smallness assumption on the variation of the data, and only require the characteristic fields to be Lipschitz continuous and the system to be uniformly strictly hyperbolic

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

Klebsiella pneumoniae related community-acquired acute lower respiratory infections in CAMBODIA: clinical characteristics and treatment

<p>Abstract</p> <p>Background</p> <p>In many Asian countries, <it>Klebsiella pneumoniae </it>(KP) is the second pathogen responsible for community-acquired pneumonia. Yet, very little is known about <it>KP </it>etiology in ALRI in Cambodia, a country that has one of the weakest medical infrastructures in the region. We present here the first clinico-radiological description of <it>KP </it>community-acquired ALRI in hospitalized Cambodian patients.</p> <p>Methods</p> <p>Through ALRI surveillance in two provincial hospitals, <it>KP </it>was isolated from sputum and blood cultures, and identified by API20E gallery from patients ≥ 5 years-old with fever and respiratory symptoms onset ≤14 days. Antibiotics susceptibility testing was provided systematically to clinicians when bacteria were isolated. We collected patients' clinical, radiological and microbiological data and their outcome 3 months after discharge. We also compared <it>KP</it>-related with other bacteria-related ALRI to determine risk factors for <it>KP </it>infection.</p> <p>Results</p> <p>From April 2007 to December 2009, 2315 ALRI patients ≥ 5 years-old were enrolled including 587 whose bacterial etiology could be assigned. Of these, 47 (8.0%) had <it>KP </it>infection; their median age was 55 years and 68.1% were females. Reported prior medication was high (42.5%). Patients' chest radiographs showed pneumonia (61.3% including 39% that were necrotizing), preexisting parenchyma lesions (29.5%) and pleural effusions alone (4.5%) and normal parenchyma (4.5%). Five patients had severe conditions on admission and one patient died during hospitalization. Of the 39 patients that were hospital discharged, 14 died including 12 within 1 month after discharge. Only 13 patients (28%) received an appropriate antibiotherapy. Extended-spectrum beta-lactamases (ESBL) - producing strains were found in 8 (17.0%) patients. Female gender (Odds ratio (OR) 2.1; <it>p </it>= 0.04) and diabetes mellitus (OR 3.1; <it>p </it>= 0.03) were independent risk factors for <it>KP</it>-related ALRI.</p> <p>Conclusions</p> <p><it>KP </it>ALRI in Cambodia has high fatality rate, are more frequently found in women, and should be considered in diabetic patients. The extremely high frequency of ESBL-producing strains in the study is alarming in the context of uncontrolled antibiotic consumption and in absence of microbiology capacity in most public-sector hospitals.</p

Autoantibodies neutralizing type I IFNs are present in ~4% of uninfected individuals over 70 years old and account for ~20% of COVID-19 deaths

Publisher Copyright: © 2021 The Authors, some rights reserved.Circulating autoantibodies (auto-Abs) neutralizing high concentrations (10 ng/ml; in plasma diluted 1:10) of IFN-alpha and/or IFN-omega are found in about 10% of patients with critical COVID-19 (coronavirus disease 2019) pneumonia but not in individuals with asymptomatic infections. We detect auto-Abs neutralizing 100-fold lower, more physiological, concentrations of IFN-alpha and/or IFN-omega (100 pg/ml; in 1:10 dilutions of plasma) in 13.6% of 3595 patients with critical COVID-19, including 21% of 374 patients >80 years, and 6.5% of 522 patients with severe COVID-19. These antibodies are also detected in 18% of the 1124 deceased patients (aged 20 days to 99 years; mean: 70 years). Moreover, another 1.3% of patients with critical COVID-19 and 0.9% of the deceased patients have auto-Abs neutralizing high concentrations of IFN-beta. We also show, in a sample of 34,159 uninfected individuals from the general population, that auto-Abs neutralizing high concentrations of IFN-alpha and/or IFN-omega are present in 0.18% of individuals between 18 and 69 years, 1.1% between 70 and 79 years, and 3.4% >80 years. Moreover, the proportion of individuals carrying auto-Abs neutralizing lower concentrations is greater in a subsample of 10,778 uninfected individuals: 1% of individuals 80 years. By contrast, auto-Abs neutralizing IFN-beta do not become more frequent with age. Auto-Abs neutralizing type I IFNs predate SARS-CoV-2 infection and sharply increase in prevalence after the age of 70 years. They account for about 20% of both critical COVID-19 cases in the over 80s and total fatal COVID-19 cases.Peer reviewe

New insights into the genetic etiology of Alzheimer's disease and related dementias

Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele