Uncovering Genomic Regions Associated With 36 Agro-Morphological Traits in Indian Spring Wheat Using GWAS

Wheat genetic improvement by integration of advanced genomic technologies is one way of improving productivity. To facilitate the breeding of economically important traits in wheat, SNP loci and underlying candidate genes associated with the 36 agro-morphological traits were studied in a diverse panel of 404 genotypes. By using Breeders’ 35K Axiom array in a comprehensive genome-wide association study covering 4364.79 cM of the wheat genome and applying a compressed mixed linear model, a total of 146 SNPs (-log10P ≥ 4) were found associated with 23 traits out of 36 traits studied explaining 3.7–47.0% of phenotypic variance. To reveal this a subset of 260 genotypes was characterized phenotypically for six quantitative traits [days to heading (DTH), days to maturity (DTM), plant height (PH), spike length (SL), awn length (Awn_L), and leaf length (Leaf_L)] under five environments. Gene annotations mined ∼38 putative candidate genes which were confirmed using tissue and stage specific gene expression data from RNA Seq. We observed strong co-localized loci for four traits (glume pubescence, SL, PH, and awn color) on chromosome 1B (24.64 cM) annotated five putative candidate genes. This study led to the discovery of hitherto unreported loci for some less explored traits (such as leaf sheath wax, awn attitude, and glume pubescence) besides the refined chromosomal regions of known loci associated with the traits. This study provides valuable information of the genetic loci and their potential genes underlying the traits such as awn characters which are being considered as important contributors toward yield enhancement

Clonal Haematopoiesis and Risk of Chronic Liver Disease

Chronic liver disease is a major public health burden worldwide1. Although different aetiologies and mechanisms of liver injury exist, progression of chronic liver disease follows a common pathway of liver inflammation, injury and fibrosis2. Here we examined the association between clonal haematopoiesis of indeterminate potential (CHIP) and chronic liver disease in 214,563 individuals from 4 independent cohorts with whole-exome sequencing data (Framingham Heart Study, Atherosclerosis Risk in Communities Study, UK Biobank and Mass General Brigham Biobank). CHIP was associated with an increased risk of prevalent and incident chronic liver disease (odds ratio = 2.01, 95% confidence interval (95% CI) [1.46, 2.79]; P \u3c 0.001). Individuals with CHIP were more likely to demonstrate liver inflammation and fibrosis detectable by magnetic resonance imaging compared to those without CHIP (odds ratio = 1.74, 95% CI [1.16, 2.60]; P = 0.007). to assess potential causality, Mendelian randomization analyses showed that genetic predisposition to CHIP was associated with a greater risk of chronic liver disease (odds ratio = 2.37, 95% CI [1.57, 3.6]; P \u3c 0.001). In a dietary model of non-alcoholic steatohepatitis, mice transplanted with Tet2-deficient haematopoietic cells demonstrated more severe liver inflammation and fibrosis. These effects were mediated by the NLRP3 inflammasome and increased levels of expression of downstream inflammatory cytokines in Tet2-deficient macrophages. In summary, clonal haematopoiesis is associated with an elevated risk of liver inflammation and chronic liver disease progression through an aberrant inflammatory response

The genetic determinants of recurrent somatic mutations in 43,693 blood genomes

Nononcogenic somatic mutations are thought to be uncommon and inconsequential. To test this, we analyzed 43,693 National Heart, Lung and Blood Institute Trans-Omics for Precision Medicine blood whole genomes from 37 cohorts and identified 7131 non-missense somatic mutations that are recurrently mutated in at least 50 individuals. These recurrent non-missense somatic mutations (RNMSMs) are not clearly explained by other clonal phenomena such as clonal hematopoiesis. RNMSM prevalence increased with age, with an average 50-year-old having 27 RNMSMs. Inherited germline variation associated with RNMSM acquisition. These variants were found in genes involved in adaptive immune function, proinflammatory cytokine production, and lymphoid lineage commitment. In addition, the presence of eight specific RNMSMs associated with blood cell traits at effect sizes comparable to Mendelian genetic mutations. Overall, we found that somatic mutations in blood are an unexpectedly common phenomenon with ancestry-specific determinants and human health consequences

Depolarization of light in a multiply scattering medium: effect of the refractive index of a scatterer

We report the results of a study carried out to investigate the influence of the refractive index and size parameter of a scatterer on the depolarization of linearly and circularly polarized light in a turbid medium. The results show that for a given refractive index of the surrounding medium, the influence of the refractive index of the scatterer on the depolarization of both linearly and circularly polarized light is rather weak for samples with smaller-sized scatterers (Rayleigh scatterers, radius a « λ, anisotropy parameter g < or=0.2). For a given value of optical thickness (τ=μs×d, μs being the scattering coefficient, d the physical thickness), the depolarization of circularly polarized light was observed to be higher than that of linearly polarized light for these samples. In contrast, for samples prepared using larger-sized scatterers (Mie scatterers, a > or=λ, g > or= 0.7), linearly polarized light was observed to depolarize much faster than circularly polarized light when the refractive index of scatterers was large (n=1.59) but no appreciable difference in depolarization of linearly and circularly polarized light was observed when the refractive index of scatterers had a lower value (n=1.37). Further, for scattering samples having Mie scatterers, for comparable values of τ and g, depolarization of polarized light was much higher for samples with scatterers of lower refractive index

Comparative Study on the Outcome of Primary Skin Closure Versus Delayed Primary Skin Closure in Case of Emergency Laparotomies

Introduction: One of the most common complications that one can encounter is the surgical site infection (SSI) after any surgical procedures especially after exploratory laparotomy for perforative peritonitis. A surgical wound is considered as infected when there is purulent drainage from the wound. The purpose of the present study was to compare the primary wound closure technique and delayed primary wound closure technique with regard to the rate of wound infection and other complications which are usually associated with the infection like wound dehiscence, stitch sinuses, incisional hernias and duration of hospital stay. Materials and Methodology: 120 participants were randomly divided into two groups with 60 subjects each for primary wound closure and delayed primary wound closure. Data was coded and entered in Microsoft Excel sheet and the data analysis was done using SPSS-17. Association between qualitative variables will be analysed using Chi-square test. Associations between quantitative variables were analysed using independent sample t-test. Non parametric tests were if whenever necessary. When a p value of less than 0.05 is considered as statistically significant.&nbsp

Not Available

Not AvailableMicroRNA are 20–24 nt, non-coding, single stranded molecule regulating traits and stress response. Tissue and time specifc expression limits its detection, thus is major challenge in their discovery. Wheat has limited 119 miRNAs in MiRBase due to limitation of conservation based methodology where old and new miRNA genes gets excluded. This is due to origin of hexaploid wheat by three successive hybridization, older AA, BB and younger DD subgenome. Species specifc miRNA prediction (SMIRP concept) based on 152 thermodynamic features of training dataset using support vector machine learning approach has improved prediction accuracy to 97.7%. This has been implemented in TamiRPred (http://webtom.cabgrid.res.in/tamirpred). We also report highest number of putative miRNA genes (4464) of wheat from whole genome sequence populated in database developed in PHP and MySQL. TamiRPred has predicted 2092 (>45.10%) additional miRNA which was not predicted by miRLocator. Predicted miRNAs have been validated by miRBase, small RNA libraries, secondary structure, degradome dataset, star miRNA and binding sites in wheat coding region. This tool can accelerate miRNA polymorphism discovery to be used in wheat trait improvement. Since it predicts chromosomewise miRNA genes with their respective physical location thus can be transferred using linked SSR markers. This prediction approach can be used as model even in other polyploid crops.Not Availabl

Not Available

Not AvailableDrought is one of the major impediments in wheat productivity. Traditional breeding and marker assisted QTL introgression had limited success. Available wheat genomic and RNA-seq data can decipher novel drought tolerance mechanisms with putative candidate gene and marker discovery. Drought is frst sensed by root tissue but limited information is available about how roots respond to drought stress. In this view, two contrasting genotypes, namely, NI5439 41 (drought tolerant) and WL711 (drought susceptible) were used to generate ~78.2 GB data for the responses of wheat roots to drought. A total of 45139 DEGs, 13820 TF, 288 miRNAs, 640 pathways and 435829 putative markers were obtained. Study reveals use of such data in QTL to QTN refnement by analysis on two model drought-responsive QTLs on chromosome 3B in wheat roots possessing 18 diferentially regulated genes with 190 sequence variants (173 SNPs and 17 InDels). Gene regulatory networks showed 69 hub-genes integrating ABA dependent and independent pathways controlling sensing of drought, root growth, uptake regulation, purine metabolism, thiamine metabolism and antibiotics pathways, stomatal closure and senescence. Eleven SSR markers were validated in a panel of 18 diverse wheat varieties. For efective future use of fndings, web genomic resources were developed. We report RNA-Seq approach on wheat roots describing the drought response mechanisms under feld drought conditions along with genomic resources, warranted in endeavour of wheat productivityNot Availabl