Multiomics-assisted characterization of rice-Yellow Stem Borer interaction provides genomic and mechanistic insights into stem borer resistance in rice.

KEY MESSAGE: By deploying a multi-omics approach, we unraveled the mechanisms that might help rice to combat Yellow Stem Borer infestation, thus providing insights and scope for developing YSB resistant rice varieties. Yellow Stem Borer (YSB), Scirpophaga incertulas (Walker) (Lepidoptera: Crambidae), is a major pest of rice, that can lead to 20-60% loss in rice production. Effective management of YSB infestation is challenged by the non-availability of adequate sources of resistance and poor understanding of resistance mechanisms, thus necessitating studies for generating resources to breed YSB resistant rice and to understand rice-YSB interaction. In this study, by using bulk-segregant analysis in combination with next-generation sequencing, Quantitative Trait Loci (QTL) intervals in five rice chromosomes were mapped that could be associated with YSB resistance at the vegetative phase in a resistant rice line named SM92. Further, multiple SNP markers that showed significant association with YSB resistance in rice chromosomes 1, 5, 10, and 12 were developed. RNA-sequencing of the susceptible and resistant lines revealed several genes present in the candidate QTL intervals to be differentially regulated upon YSB infestation. Comparative transcriptome analysis revealed a putative candidate gene that was predicted to encode an alpha-amylase inhibitor. Analysis of the transcriptome and metabolite profiles further revealed a possible link between phenylpropanoid metabolism and YSB resistance. Taken together, our study provides deeper insights into rice-YSB interaction and enhances the understanding of YSB resistance mechanism. Importantly, a promising breeding line and markers for YSB resistance have been developed that can potentially aid in marker-assisted breeding of YSB resistance among elite rice cultivars.

Improvement of bacterial blight resistance of the high yielding, fine-grain, rice variety, Gangavati sona through marker-assisted backcross breeding.

Gangavati sona (GS) is a high-yielding, fine-grain rice variety widely grown in the Tungabhadra command area in Karnataka, India; however, it is susceptible to bacterial blight (BB). Therefore, the present study was conducted to improve the GS variety for BB resistance. Three BB-resistant genes (xa5, xa13, and Xa21) were introgressed into the genetic background of susceptible cultivar GS through marker-assisted backcrossing (MABB) by using Improved samba Mahsuri (ISM), a popular, high-yielding, bacterial blight resistant rice variety as a donor parent. Foreground selection was carried out using gene-specific markers, viz., xa5FM (xa5), xa13prom (xa13), and pTA248 (Xa21), while background selection was carried out using well-distributed 64 polymorphic microsatellite markers. The true heterozygote F1 was used as the male parent for backcrossing with GS to obtain BC1F1. The process was repeated in BC1F1 generation, and a BC2F1 plant (IGS-5-11-5) possessing all three target genes along with maximum recurrent parent genome (RPG) recovery (86.7%) was selfed to obtain BC2F2s. At BC2F2, a single triple gene homozygote plant (IGS-5-11-5-33) with 92.6% RPG recovery was identified and advanced to BC2F5 by a pedigree method. At BC2F5, the seven best entries were selected, possessing all three resistance genes with high resistance levels against bacterial blight, yield level, and grain quality features equivalent to better than GS. The improved versions of GS will immensely benefit the farmers whose fields are endemic to BB.

DRR Dhan 58, a Seedling Stage Salinity Tolerant NIL of Improved Samba Mahsuri Shows Superior Performance in Multi-location Trials.

BACKGROUND: Improved Samba Mahsuri (ISM) is an elite, high-yielding, bacterial blight resistant, fine-grained rice variety with low glycaemic index. It is highly sensitive to salt stress, particularly at seedling stage, which significantly reduces its yield potential in coastal areas. A salinity tolerant QTL, Saltol, associated with seedling stage tolerance was previously mapped on chromosome 1 (10.6-11.5 Mb) from the Indian landrace, Pokkali and is effective in different genetic backgrounds. The objective of this study was to enhance salinity tolerance of ISM by incorporating the Saltol QTL through marker-assisted backcross breeding using the breeding line, FL478 (Pokkali/IR29). RESULTS: Foreground selection was carried out at each generation using five Saltol-specific markers and three bacterial blight resistance genes, Xa21, xa13 and xa5. Background selection was conducted using 66 well distributed polymorphic SSR markers and at the BC3F2 generation, a single plant with maximum recurrent parent genome recovery (95.3%) was identified and advanced to the BC3F4 generation. Based on bacterial blight resistance, seedling stage salinity tolerance and resemblance to ISM, four advanced breeding lines were selected for testing in replicated experiments near Hyderabad, India. A promising near-isogenic line, DRR Dhan 58, was evaluated in multi-location trials-coastal salinity and it showed significant salinity tolerance, resistance to bacterial blight disease, high yield and excellent grain quality during the 2019 and 2020 trials. DRR Dhan 58 was 95.1% similar to ISM based on genotyping with the 90 K SNP chip. Whole genome resequencing analysis of Pokkali and FL478 which were salinity tolerant checks, ISM and DRR Dhan 58 showed a high degree of relatedness with respect to the candidate gene loci for Saltol and OsSKC1 (Shoot K+ Concentration 1). CONCLUSION: DRR Dhan 58, possessing Saltol and three bacterial blight resistance genes (Xa21, xa13 and xa5) in the genetic background of the Indian mega-variety of rice, Samba Mahsuri, was developed for potential cultivation in areas prone to seedling stage salinity, as well as areas with endemic bacterial blight disease. This entry had a 24% yield advantage over the recurrent parent ISM under coastal saline conditions in multi-location trials and was recently released for commercial cultivation in India.

Marker assisted improvement of low soil phosphorus tolerance in the bacterial blight resistant, fine-grain type rice variety, Improved Samba Mahsuri.

Improved-Samba-Mahsuri (ISM), a high-yielding, popular bacterial blight resistant (possessing Xa21, xa13, and xa5), fine-grain type, low glycemic index rice variety is highly sensitive to low soil phosphorus (P). We have deployed marker-assisted backcross breeding (MABB) approach for targeted transfer of Pup1, a major QTL associated with low soil P tolerance, using Swarna as a donor. A new co-dominant marker, K20-1-1, which is specific for Pup1 was designed and used for foreground selection along with functional markers specific for the bacterial blight resistance genes, Xa21, xa13, and xa5. A set of 66 polymorphic SSR marker were used for the background selection along with a pair of flanking markers for the recombination selection in backcross derived progenies and in BC2F2 generation, 12 plants, which are homozygous for Pup1, all the three bacterial blight resistance genes and possessing agro-morphological traits equivalent to or better than ISM were selected and selfed to produce BC2F3s. They were evaluated in plots with low soil P and normal soil P at ICAR-IIRR, Hyderabad for their low soil P tolerance, and bacterial blight resistance and superior lines were advanced to BC2F6. One of the lines, when tested at multiple locations in India was found promising under both normal as well as low soil P conditions.

Zinc Biofortified Rice Varieties: Challenges, Possibilities, and Progress in India.

Zinc malnutrition is a major issue in developing countries where polished rice is a staple food. With the existing significant genetic variability for high zinc in polished rice, the development of biofortified rice varieties was targeted in India with support from HarvestPlus, Department of Biotechnology, and Indian Council of Agricultural Research of Government of India. Indian Institute of Rice Research (IIRR) facilitates rice varietal release through All India Coordinated Rice Improvement Project (AICRIP) and also supports rice biofortification program in India. Various germplasm sets of several national institutions were characterized at IIRR for their zinc content in brown rice using energy-dispersive X-ray fluorescence spectroscopy indicating the range of zinc to be 7.3 to 52.7 mg/kg. Evaluation of different mapping populations involving wild germplasm, landraces, and varieties for their zinc content showed the feasibility of favorable recombination of high zinc content and yield. Ninety-nine genotypes from germplasm and 344 lines from mapping populations showed zinc content of ≥28 mg/kg in polished rice meeting the target zinc content set by HarvestPlus. Through AICRIP biofortification trial constituted since 2013, 170 test entries were nominated by various national institutions until 2017, and four biofortified rice varieties were released. Only the test entry with target zinc content, yield, and quality parameters is promoted to the next year; thus, each test entry is evaluated for 3 years across 17 to 27 locations for their performance. Multilocation studies of two mapping populations and AICRIP biofortification trials indicated the zinc content to be highly influenced by environment. The bioavailability of a released biofortified rice variety, viz., DRR Dhan 45 was found to twice that of control IR64. The technology efficacy of the four released varieties developed through conventional breeding ranged from 48 to 75% with zinc intake of 38 to be 47% and 46 to 57% of the RDA for male and female, respectively. The observations from the characterization of germplasm and mapping populations for zinc content and development of national evaluation system for the release of biofortified rice varieties have been discussed in the context of the five criteria set by biofortification program.

Identification of rice landraces with promising yield and the associated genomic regions under low nitrogen.

With the priority of the low input sustainable rice cultivation for environment friendly agriculture, NUE of rice becomes the need of the hour. A set of 472 rice genotypes comprising landraces and breeding lines were evaluated for two seasons under field conditions with low and recommended nitrogen and >100 landraces were identified with relative higher yield under low nitrogen. Donors were identified for higher N uptake, N translocation into grains and grain yield under low N. Grains on secondary branches, N content in grain and yield appears to be the selection criterion under low N. Through association mapping, using minimum marker set of 50 rice SSR markers, 12 genomic regions were identified for yield and yield associated traits under low nitrogen. Four associated genomic regions on chromosomes 5, 7 and 10 were fine mapped and QTL for yield under low N were identified from the marker delimited regions. Three candidate genes viz., 2-oxoglutarate /malate translocator (Os05g0208000), alanine aminotransferase (Os07g0617800) and pyridoxal phosphate-dependent transferase (Os10g0189600) from QTL regions showed enhanced expression in the genotypes with promising yield under low N. Marker assisted selection using SSR markers associated with three candidate genes identified two stable breeding lines confirmed through multi-location evaluation.

Clinical variables associated with indeterminate QuantiFERON®-TB Gold assay results: role of pre-incubation delay.

SETTING: The QuantiFERON®-TB Gold (QFT) assay is an interferon-gamma release assay used for the clinical diagnosis of latent tuberculous infection. Relatively high rates of indeterminate results are a significant downside of the test. OBJECTIVE: To evaluate clinical variables associated with lower QFT-indeterminate rates after reducing pre-incubation delay. DESIGN: In 2016, a new protocol of on-site incubation of QFT samples, followed by analysis at the outside laboratory, was implemented, resulting in much shorter pre-incubation delay of the samples. We retrospectively identified 3583 patients who underwent QFT before and after implementation of the new protocol. Patient records were scrutinized and QFT results were evaluated with respect to associated clinical conditions. RESULTS: The patients were analyzed by dividing them into two cohorts based on maximum pre-incubation time (standard vs. immediate). Monthly indeterminate results dropped from 12.7% ± 0.02 in the standard cohort to 5.5% ± 0.03 in the immediate cohort (P < 0.001). A significant reduction in relative indeterminate rates was found in the immediate cohort patients with immunocompromised state, autoimmune conditions, liver disease and hypoalbuminemia. No difference was identified in patients with malignancies and renal failure. CONCLUSION: Limiting the pre-incubation time to 1 h maximum significantly improved QFT performance, especially in patients from certain clinical categories.

Performance of rapid SOFIA Influenza A+B test compared to Luminex x-TAG respiratory viral panel assay in the diagnosis of influenza A, B, and subtype H3.

Influenza is an acute respiratory illness caused by influenza A or B viruses that occur in outbreaks, mainly during the winter season. Rapid laboratory diagnosis of influenza can help guide the clinical management of suspected patients effectively. Clinical sensitivities and specificities of the rapid influenza diagnostic tests have varied considerably in the literature. Most of these studies are evaluated using previously frozen or stored specimens that had previously tested positive. This study compares the performance of the rapid SOFIA Influenza A+B test to nucleic acid multiplex test x-TAG respiratory viral panel (RVP) assay in freshly collected nasal aspirates and measured simultaneously by both assays. Retrospective data from 1649 nasal aspirates (September 2014 to May 2015) collected from adults as well as from children tested simultaneously by both rapid SOFIA Influenza A+B FIA immunofluorescence (Quidel, San Diego, CA) and qualitative nucleic acid multiplex RVP assay X-TAG Luminex technology (Luminex, Austin, Texas, USA) were analyzed. Concordance, and analytical sensitivity and specificity were evaluated for influenza A, subtypes H1 and H3, and influenza B. Prevalence for influenza A by RVP was 15%, for subtype H3 it was 11.2%, and for influenza B, 2.9%. None of the aspirates were positive for influenza A subtype H1. SOFIA Influenza rapid test demonstrated good specificity and low sensitivity compared with a nucleic acid test for influenza A, subtype H3, and for influenza B. SOFIA Influenza A + B test performed well in providing a rapid diagnosis, however, confirmatory molecular testing is recommended for negative test results. Re-evaluation of test performance should be periodically carried out during outbreaks with the emergence and circulation of new influenza strains.

Pharmacological concentrations of recombinant factor VIIa restore hemostasis independent of tissue factor in antibody-induced hemophilia mice.

UNLABELLED: ESSENTIALS: The role of tissue factor (TF) in recombinant factor VIIa (rFVIIa) therapy in hemophilia is unclear. An acquired mouse hemophilia model with very low or normal levels of human TF was used in the study. rFVIIa is equally effective in correcting the bleeding in mice expressing low or normal levels of TF. Pharmacological doses of rFVIIa restore hemostasis in hemophilia independent of TF. BACKGROUND: Recombinant factor VIIa (rFVIIa) has been used widely for treating hemophilia patients with inhibitory autoantibodies against factor VIII or IX. Its mechanism of action is not entirely known. A majority of in vitro studies suggested that pharmacological concentrations of rFVIIa restore hemostasis in hemophilia in a phospholipid-dependent manner, independent of tissue factor (TF). However, a few studies suggested that a TF-dependent mechanism has a primary role in correction of bleeding by rFVIIa in hemophilia patients. Here, we investigated the potential contribution of TF in rFVIIa-induced hemostasis in hemophilia employing a model system of FVIII antibody-induced hemophilia in TF transgenic mice. METHODS: Mice expressing low levels of human TF (LTF mice), mice expressing relatively high levels of human TF (HTF mice) and wild-type mice (WT mice) had neutralizing anti-FVIII antibodies administered in order to induce hemophilia in these mice. The mice were then treated with varying concentrations of rFVIIa. rFVIIa-induced hemostasis was evaluated with the saphenous vein bleeding model. RESULTS: Administration of FVIII inhibitory antibodies induced the hemophilic bleeding phenotype in all three genotypes. rFVIIa administration rescued the bleeding phenotype in all three genotypes. No significant differences were observed in rFVIIa-induced correction of bleeding between LTF and HTF mice that had FVIII antibodies administered. CONCLUSIONS: Our results provide strong evidence supporting the suggestion that the hemostatic effect of pharmacological doses of rFVIIa stems from a TF-independent mechanism.

Effect of salinity and use of stress indices of morphological and physiological traits at the seedling stage in rice.

Rice (Oryza sativa L.) is the most important cereal crop and a major staple food for majority of the human populations worldwide. Rice crop is sensitive to salinity. In spite of large number of studies on salinity tolerance of rice, our knowledge on the overall effect of salinity on rice seedling growth is limited. Improvement in salt tolerance of crop plants remains indescribable, largely due to the fact that salinity is a complex trait which affects almost every aspect of the physiology, biochemistry and genomics of plants. The present investigation was conducted to establish the relationship between various morphological, physiological traits and stress indices. A set of 131 rice accessions was evaluated in two levels namely, non-stress (EC ~ 1.2 dS/m) and saline stress (EC ~ 10 dS/m) in hydroponics at seedling stage. Root length and shoot lengths were reduced by 52 and 50%, respectively in saline stress compared to non-stress conditions. There was a significant correlation between various morphological and physiological parameters in non-saline in addition to saline stress as well as non-stress. The effect of the increased Na+ concentration in the medium is detrimental to root length and shoot length as observed by reduction in root length and a concomitant reduction in shoot length. Increased concentration of Na+ led to augmented Na+/K+ ratio with increased stress in the medium and decreased expression of traits. A significant positive correlation (r=0.60) was noticed between stress tolerance index (STI) of root and shoot length. The stress susceptibility index (SSI) for root length was expressed significant positive correlation with SSI for shoot length (r=0.43). SSI for K+ content was registered significant negative correlation with STI for Na+ content (r=-0.43). The three accessions namely, IC 545004, IC 545486 and IC 545215 were found to be the best performers adjudged on the morphological and physiological criteria in saline stress situation. These three rice accessions could be used as a donor parent or for genotypic studies in future breeding programs.

Factor VIIa binding to endothelial cell protein C receptor protects vascular barrier integrity in vivo.

BACKGROUND: Recent studies have shown that factor VIIa binds to endothelial cell protein C receptor(EPCR), a cellular receptor for protein C and activated protein C. At present, the physiologic significance of FVIIa interaction with EPCR in vivo remains unclear. OBJECTIVE: To investigate whether exogenously administered FVIIa, by binding to EPCR, induces a barrier protective effect in vivo. METHODS: Lipopolysaccharide(LPS)-induced vascular leakage in the lung and kidney,and vascular endothelial growth factor (VEGF)-induced vascular leakage in the skin, were used to evaluate the FVIIa-induced barrier protective effect. Wild-type, EPCR-deficient, EPCR-overexpressing and hemophilia A mice were used in the studies. RESULTS: Administration ofFVIIa reduced LPS-induced vascular leakage in the lung and kidney; the FVIIa-induced barrier protective effect was attenuated in EPCR-deficient mice. The extent of VEGF-induced vascular leakage in the skin was highly dependent on EPCR expression levels. Therapeutic concentrations of FVIIa attenuated VEGF-induced vascular leakage in control mice but not in EPCR-deficient mice.Blockade of FVIIa binding to EPCR with a blocking mAb completely attenuated the FVIIa-induced barrier protective effect. Similarly, administration of protease activated receptor 1 antagonist blocked the FVIIa induced barrier protective effect. Hemophilic mice showed increased vascular permeability, and administration of therapeutic concentrations of FVIIa improved barrier integrity in these mice. CONCLUSIONS: This is the first study to demonstrate that FVIIa binding to EPCR leads to a barrier protective effect in vivo. This finding may have clinical relevance, as it indicates additional advantages of using FVIIa in treating hemophilic patients.

Analysis of tissue factor expression in various cell model systems: cryptic vs. active.

BACKGROUND: Tissue factor (TF) encryption plays an important role in regulating TF coagulant activity. Potential differences in experimental cell model systems and strategies hampered our understanding of the TF encryption mechanisms. OBJECTIVE: To characterize the procoagulant activity status of TF in different cell types, and to determine whether increased TF procoagulant activity following the activation stems from transformation of the cryptic TF to the active form. METHODS: Simultaneous kinetic analyses of TF-FVIIa activation of FX and FVIIa binding to cell surface TF were performed under identical experimental conditions in fibroblast (WI-38), cancer cell (MDA-231), endothelial cell (HUVEC) and monocytic cell (THP-1) model systems. These data were then utilized to estimate TF coagulant-specific activity and percentages of active and cryptic TF present in these cell types. RESULTS: MDA-231 and WI-38 cells express 10 to 100 times more TF on their cell surfaces compared with perturbed HUVEC and THP-1 cells. TF-specific activity on cell surfaces of MDA-231, WI-38 and THP-1 cells was very similar. Nearly 80-90% of the TF in MDA-231, WI-38 and THP-1 cells was cryptic. A plasma concentration of FVII would be sufficient to bind both active and cryptic TF on cell surfaces. Increased TF activity following cell activation stems from decryption of cryptic TF rather than increasing the coagulant activity of the active TF. CONCLUSIONS: Our data demonstrate that TF encryption is not limited to a specific cell type, and unlike previously thought, the majority of the TF expressed in cancer cells is not constitutively procoagulant.

Endothelial cell protein C receptor-mediated redistribution and tissue-level accumulation of factor VIIa.

BACKGROUND: Recent studies show that activated factor VII (FVIIa) binds to the endothelial cell protein C receptor (EPCR) on the vascular endothelium; however, the importance of this interaction in hemostasis or pathophysiology is unknown. OBJECTIVE: The aim of the present study was to investigate the role of the FVIIa interaction with EPCR on the endothelium in mediating FVIIa transport from the circulation to extravascular tissues. METHODS: Wild-type, EPCR-deficient or ECPR-over-expressing mice were injected with human recombinant (r)FVIIa (120 µg kg(-1) body weight) via the tail vein. At varying time intervals after rFVIIa administration, blood and various tissues were collected to measure FVIIa antigen and activity levels. Tissue sections were analyzed by immunohistochemistry for FVIIa and EPCR. RESULTS: The data reveal that, after intravenous (i.v.) injection, rFVIIa rapidly disappears from the blood and associates with the endothelium in an EPCR-dependent manner. Immunohistochemical analyses revealed that the association of FVIIa with the endothelium was maximal at 30 min and thereafter progressively declined. The FVIIa association with the endothelium was undetectable at time points exceeding 24 h post-FVIIa administration. The levels of rFVIIa accumulated in tissue correlate with expression levels of EPCR in mice and FVIIa associated with tissues remained functionally active for periods of at least 7 days. CONCLUSIONS: The observation that an EPCR-dependent association of FVIIa with the endothelium is most pronounced soon after rFVIIa administration and subsequently declines temporally, combined with the retention of functionally active FVIIa in tissue homogenates for extended periods, indicates that FVIIa binding to EPCR on the endothelium facilitates the transport of FVIIa from circulation to extravascular tissues where TF resides.

Regulation of tissue factor coagulant activity on cell surfaces.

Tissue factor (TF) is a transmembrane glycoprotein and an essential component of the factor VIIa-TF enzymatic complex that triggers activation of the coagulation cascade. Formation of TF-FVIIa complexes on cell surfaces not only trigger the coagulation cascade but also transduce cell signaling via activation of protease-activated receptors. Tissue factor is expressed constitutively on cell surfaces of a variety of extravascular cell types, including fibroblasts and pericytes in and surrounding blood vessel walls and epithelial cells, but is generally absent on cells that come into contact with blood directly. However, TF expression could be induced in some blood cells, such as monocytes and endothelial cells, following an injury or pathological stimuli. Tissue factor is essential for hemostasis, but aberrant expression of TF leads to thrombosis. Therefore, a proper regulation of TF activity is critical for the maintenance of hemostatic balance and health in general. TF-FVIIa coagulant activity at the cell surface is influenced not only by TF protein expression levels but also independently by a variety of mechanisms, including alterations in membrane phospholipid composition and cholesterol content, thiol-dependent modifications of TF allosteric disulfide bonds, and other post-translational modifications of TF. In this article, we critically review the key literature on mechanisms by which TF coagulant activity is regulated at the cell surface in the absence of changes in TF protein levels with specific emphasis on recently published data and provide the authors' perspective on the subject.

Glycosylation of tissue factor is not essential for its transport or functions.

BACKGROUND: Glycosylation plays an important role in protein function. The importance of glycosylation for tissue factor (TF) function is unclear. OBJECTIVE: The aim of the present study is to investigate the importance of TF glycosylation in transport to the cell surface and its coagulant and signaling functions. METHODS: Endothelial cells and peripheral blood mononuclear cells (PBMC) were treated with tunicamycin to inhibit N-linked glycosylation. Site-specific mutagenesis of one or more potential N-linked glycosylation sites in TF was used to generate TF mutants lacking glycans. TF expression at the cell surface was determined in binding assays using (125)I-FVIIa or (125)I-TF mAb and confocal microscopy. TF coagulant activity was measured by factor (F) Xa generation assay, and TF signaling function was assessed by measuring cleavage of protease activated receptor 2 (PAR2) and activation of p44/42 MAPK. RESULTS: Tunicamycin treatment reduced TF activity at the endothelial cell surface; however, this reduction was found to be the result of decreased TF protein production in tunicamycin-treated cells. Tunicamycin treatment had no significant effect on TF activity or antigen levels in PBMC. No significant differences were observed in TF protein expression and procoagulant activity among cells transfected to express either wild-type TF or TF mutants. A fully non-glycosylated TF is shown to bind FVIIa and interact with FX with the same efficiency as that of wild-type TF. Non-glycosylated TF is also capable of supporting FVIIa cleavage of PAR2 and PAR2-dependent p44/42 MAPK activation. CONCLUSIONS: Glycosylation is not essential for TF transport and coagulant or signaling functions.