Multi-GWAS reveals significant genomic regions for Mungbean yellow mosaic India virus resistance in urdbean (Vigna mungo (L.) across multiple environments.

KEY MESSAGE: Unraveling genetic markers for MYMIV resistance in urdbean, with 8 high-confidence marker-trait associations identified across diverse environments, provides crucial insights for combating MYMIV disease, informing future breeding strategies. Globally, yellow mosaic disease (YMD) causes significant yield losses, reaching up to 100% in favorable environments within major urdbean cultivating regions. The introgression of genomic regions conferring resistance into urdbean cultivars is crucial for combating YMD, including resistance against mungbean yellow mosaic India virus (MYMIV). To uncover the genetic basis of MYMIV resistance, we conducted a genome-wide association study (GWAS) using three multi-locus models in 100 diverse urdbean genotypes cultivated across six individual and two combined environments. Leveraging 4538 high-quality single nucleotide polymorphism (SNP) markers, we identified 28 unique significant marker-trait associations (MTAs) for MYMIV resistance, with 8 MTAs considered of high confidence due to detection across multiple GWAS models and/or environments. Notably, 4 out of 28 MTAs were found in proximity to previously reported genomic regions associated with MYMIV resistance in urdbean and mungbean, strengthening our findings and indicating consistent genomic regions for MYMIV resistance. Among the eight highly significant MTAs, one localized on chromosome 6 adjacent to previously identified quantitative trait loci for MYMIV resistance, while the remaining seven were novel. These MTAs contain several genes implicated in disease resistance, including four common ones consistently found across all eight MTAs: receptor-like serine-threonine kinases, E3 ubiquitin-protein ligase, pentatricopeptide repeat, and ankyrin repeats. Previous studies have linked these genes to defense against viral infections across different crops, suggesting their potential for further basic research involving cloning and utilization in breeding programs. This study represents the first GWAS investigation aimed at identifying resistance against MYMIV in urdbean germplasm.

Do diverse wheat genotypes unleash their biochemical arsenal differentially to conquer cold stress? A comprehensive study in the Western Himalayas.

Wheat is one of the most important cereal crops in the world. Cold stress is a major constraint in production of wheat grown in cold climate regions. In this study, we conducted a comprehensive assessment of cold stress tolerance in wheat genotypes through field screening, cell membrane stability through electrolyte leakage assay and biochemical profiling. A core set comprising 4560 genotypes was evaluated for two years (2021-2022), revealing substantial genetic variation for cold stress tolerance. Most genotypes exhibited moderate tolerance, while a smaller proportion showed susceptibility to cold stress. Based on the cold screening data in the field, a mini-core set of 350 genotypes was selected for membrane stability analysis using electrical conductivity assays. Significant differences were observed in membrane stability among the genotypes, indicating the presence of genetic variation for this trait. Furthermore, a mini-core set was narrowed down to 50 diverse candidate genotypes that were subsequently profiled for various biochemicals, including reactive oxygen species (ROS) like lipid peroxidation (MDA) and hydrogen peroxide (H2 02 ), osmoprotectant (proline) and enzymatic antioxidants including ascorbate peroxidase (APX), superoxide dismutase (SOD), guaiacol peroxidase (GPX), and catalase (CAT). Correlation analysis of the biochemicals revealed negative associations between antioxidants and reactive oxygen species (ROS), highlighting their role in mitigating oxidative damage under cold stress. This study enhances our understanding of the physiological and biochemical mechanisms underlying cold stress tolerance in wheat. The identified genotypes with superior cold stress tolerance can serve as valuable genetic resources for wheat breeding.

Genome-wide association study unravels genomic regions associated with chlorophyll fluorescence parameters in wheat (Triticum aestivum L.) under different sowing conditions.

KEY MESSAGE: Genome-wide association study identified 205 significant marker-trait associations for chlorophyll fluorescence parameters in wheat. Candidate gene mining, in silico expression, and promoter analyses revealed the potential candidate genes associated with the studied parameters. The present study investigated the effect of varied sowing conditions (viz., early, timely, and late) on different chlorophyll fluorescence parameters in diverse wheat germplasm set comprising of 198 lines over two cropping seasons (2020-2021 and 2021-2022). Further, a genome-wide association study was conducted to identify potential genomic regions associated with these parameters. The results revealed significant impacts of sowing conditions on all fluorescence parameters, with the maximum and minimum effects on FI (26.64%) and FV/FM (2.12%), respectively. Among the 205 marker-trait associations (MTAs) identified, 11 high-confidence MTAs were chosen, exhibiting substantial effects on multiple fluorescence parameters, and each explaining more than 10% of the phenotypic variation. Through gene mining of genomic regions encompassing high-confidence MTAs, we identified a total of 626 unique gene models. In silico expression analysis revealed 42 genes with an expression value exceeding 2 TPM. Among them, 10 genes were identified as potential candidate genes with functional relevance to enhanced photosynthetic efficiency. These genes mainly encoded for the following important proteins/products-ankyrin repeat protein, 2Fe-2S ferredoxin-type iron-sulfur-binding domain, NADH-ubiquinone reductase complex-1 MLRQ subunit, oxidoreductase FAD/NAD(P)-binding, photosystem-I PsaF, and protein kinases. Promoter analysis revealed the presence of light-responsive (viz., GT1-motif, TCCC-motif, I-box, GT1-motif, TCT-motif, and SP-1) and stress-responsive (viz., ABRE, AuxRR-core, GARE-motif, and ARE) cis-regulatory elements, which may be involved in the regulation of identified putative candidate genes. Findings from this study could directly help wheat breeders in selecting lines with favorable alleles for chlorophyll fluorescence, while the identified markers will facilitate marker-assisted selection of potential genomic regions for improved photosynthesis.

Identification of Novel QTLs/Defense Genes in Spring Wheat Germplasm Panel for Seedling and Adult Plant Resistance to Stem Rust and Their Validation Through KASP Marker Assays.

Stem rust is one of the major diseases threatening wheat production globally. To identify novel resistance quantitative trait loci (QTLs), we performed 35K Axiom Array SNP genotyping assays on an association mapping panel of 400 germplasm accessions, including Indian landraces, in conjunction with phenotyping for stem rust at seedling and adult plant stages. Association analyses using three genome wide association study (GWAS) models (CMLM, MLMM, and FarmCPU) revealed 20 reliable QTLs for seedling and adult plant resistance. Among these 20 QTLs, five QTLs were found consistent with three models, i.e., four QTLs on chromosome 2AL, 2BL, 2DL, and 3BL for seedling resistance and one QTL on chromosome 7DS for adult plant resistance. Further, we identified a total of 21 potential candidate genes underlying QTLs using gene ontology analysis, including a leucine rich repeat receptor (LRR) and P-loop nucleoside triphosphate hydrolase, which have a role in pathogen recognition and disease resistance. Furthermore, four QTLs (Qsr.nbpgr-3B_11, QSr.nbpgr-6AS_11, QSr.nbpgr-2AL_117-6, and QSr.nbpgr-7BS_APR) were validated through KASP located on chromosomes 3B, 6A, 2A, and 7B. Out of these QTLs, QSr.nbpgr-7BS_APR was identified as a novel QTL for stem rust resistance which has been found effective in both seedling as well as the adult plant stages. Identified novel genomic regions and validated QTLs have the potential to be deployed in wheat improvement programs to develop disease resistant varieties for stem rust and can diversify the genetic basis of resistance.

Validation of Novel spot blotch disease resistance alleles identified in unexplored wheat (Triticum aestivum L.) germplasm lines through KASP markers.

BACKGROUND: During the last few decades, the diverse sources of resistance, several genes and QTLs for spot blotch resistance have been identified. However, a large set of germplasm lines are still unexplored that have the potential to develop highly resistant wheat cultivars for the target environments. Therefore, the identification of new sources of resistance to spot blotch is essential for breeding programmes to develop spot blotch resistant cultivars and sustain wheat production. The association mapping panel of 294 diverse bread wheat accessions was used to explore new sources of spot blotch disease resistance and to identify genomic regions using genome wide association analysis (GWAS). The genotypes were tested in replicated trials for spot blotch disease at three major hot spots in India (Varanasi in UP, Pusa in Bihar, and Cooch Behar in West Bengal). The area under the disease progress curve (AUDPC) was calculated to assess the level of resistance in each genotype. RESULTS: A total of 19 highly and 76 moderately resistant lines were identified. Three accessions (EC664204, IC534306 and IC535188) were nearly immune to spot blotch disease. The genotyping of all accessions resulted in a total of 16,787 high-quality polymorphic SNPs. The GWAS was performed using a Compressed Mixed Linear Model (CMLM) and a Mixed Linear Model (MLM). A total of seven significant MTAs, common in both the models and consistent across the environment, were further validated to develop KASP markers. Four MTAs (AX-94710084, AX-94865722, AX-95135556, and AX-94529408) on three chromosomes (2AL, 2BL, and 3BL) have been successfully validated through the KASP marker. CONCLUSIONS: The new source of resistance was identified from unexplored germplasm lines. The genomic regions identified through GWAS were validated through KASP markers. The marker information and the highly resistant sources are valuable resources to rapidly develop immune or near immune wheat varieties.

Mechanisms of E. coli chemotaxis signaling pathways visualized using cryoET and computational approaches.

Chemotaxis signaling pathways enable bacteria to sense and respond to their chemical environment and, in some species, are critical for lifestyle processes such as biofilm formation and pathogenesis. The signal transduction underlying chemotaxis behavior is mediated by large, highly ordered protein complexes known as chemosensory arrays. For nearly two decades, cryo-electron tomography (cryoET) has been used to image chemosensory arrays, providing an increasingly detailed understanding of their structure and function. In this mini-review, we provide an overview of the use of cryoET to study chemosensory arrays, including imaging strategies, key results, and outstanding questions. We further discuss the application of molecular modeling and simulation techniques to complement structure determination efforts and provide insight into signaling mechanisms. We close the review with a brief outlook, highlighting promising future directions for the field.

A large-effect QTL introgressed from ricebean imparts resistance to Mungbean yellow mosaic India virus in blackgram (Vigna mungo (L.) Hepper).

KEY MESSAGE: Here, we report identification of a large effect QTL conferring Mungbean yellow mosaic India virus resistance introgressed from ricebean in blackgram variety Mash114. The tightly linked KASP markers would assist in marker-assisted-transfer of this region into Vigna species infected by MYMIV. Until recently, precise location of genes and marker-assisted selection was long thought in legumes such as blackgram due to lack of dense molecular maps. However, advances in next-generation sequencing based on high-throughput genotyping technologies such as QTL-seq have revolutionized trait mapping in marker-orphan crops. Using QTL-seq approach, we have identified a large-effect QTL for resistance to Mungbean yellow mosaic India virus (MYMIV) in blackgram variety Mash114. MYMIV is devastating disease responsible for huge yield losses in blackgram, greengram and other legumes. Mash114 showed consistent and high level of resistance to MYMIV since last nine years. Whole genome re-sequencing of MYMIV-resistant and susceptible bulks derived from RILs of cross KUG253 X Mash114 identified a large-effect QTL (qMYMIV6.1.1) spanning 3.4 Mb on chromosome 6 explaining 70% of total phenotypic variation. This region was further identified as an inter-specific introgression from ricebean. Linkage mapping using KASP markers developed from potent candidate genes involved in virus resistance identified the 500 kb genomic region equaling 1.9 cM on genetic map linked with MYMIV. The three KASP markers closely associated with MYMIV originated from serine threonine kinase, UBE2D2 and BAK1/BRI1-ASSOCIATED RECEPTOR KINASE genes. These KASPs can be used for marker-assisted transfer of introgressed segment into suitable backgrounds of Vigna species.

Marker-assisted introgression of genes into rye translocation leads to the improvement in bread making quality of wheat (Triticum aestivum L.).

Introgression of genes from related species can be a powerful way to genetically improve crop yields, but selection for one trait can come at the cost to others. Wheat varieties with translocation of the short arm of chromosome 1 from the B genome of wheat (1BS) with the short arm of chromosome 1 from rye (1RS) are popular globally for their positive effect on yield and stress resistance. Unfortunately, this translocation (1BL.1RS) is also associated with poor bread making quality, mainly due to the presence of Sec-1 on its proximal end, encoding secalin proteins, and the absence of Glu-B3/Gli-B1-linked loci on its distal end, encoding low molecular weight glutenin subunits (LMW-GS). The present study aims to replace these two important loci on the 1RS arm with the wheat 1BS loci, in two popular Indian wheat varieties, PBW550 and DBW17, to improve their bread-making quality. Two donor lines in the cultivar Pavon background with absence of the Sec-1 locus and presence of the Glu-B3/Gli-B1 locus, respectively, were crossed and backcrossed with these two selected wheat varieties. In the advancing generations, marker assisted foreground selection was done for Sec-1- and Glu-B3/Gli-B1+ loci while recurrent parent recovery was done with the help of SSR markers. BC2F5 and BC2F6 near isosgenic lines (NILs) with absence of Sec-1 and presence of Glu-B3/Gli-B1 loci were evaluated for two years in replicated yield trials. As a result of this selection, thirty promising lines were generated that demonstrated improved bread making quality but also balanced with improved yield-related traits compared to the parental strains. The study demonstrates the benefits of using marker-assisted selection to replace a few loci with negative effects within larger alien translocations for crop improvement.

Bread wheat with enhanced grain carotenoid content: a novel option for wheat biofortification.

Colored wheat has piqued the interest of breeders and consumers alike. The chromosomal segment from 7E of Thinopyrum ponticum, which carries a leaf rust resistant gene, Lr19, has been rarely employed in wheat breeding operations due to its association with the Y gene, which gives a yellow tint to the flour. By prioritizing nutritional content over color preferences, consumer acceptance has undergone a paradigm change. Through marker-assisted backcross breeding, we introduced an alien segment harboring the Y (PsyE1) gene into a high yielding commercial bread wheat (HD 2967) background to generate rust resistant carotenoid biofortified bread wheat. Agro-morphological characterization was also performed on a subset of developed 70 lines having enhanced grain carotene content. In the introgression lines, carotenoid profiling using HPLC analysis demonstrated a considerable increase in ß-carotene levels (up to 12 ppm). Thus, the developed germplasm caters the threat to nutritional security and can be utilized to produce carotenoid fortified wheat. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01338-0.

Pyramiding of genes for grain protein content, grain quality, and rust resistance in eleven Indian bread wheat cultivars: a multi-institutional effort.

Improvement of grain protein content (GPC), loaf volume, and resistance to rusts was achieved in 11 Indian wheat cultivars that are widely grown in four different agro-climatic zones of India. This involved use of marker-assisted backcross breeding (MABB) for introgression and pyramiding of the following genes: (i) the high GPC gene Gpc-B1; (ii) HMW glutenin subunits 5 + 10 at Glu-D1 loci, and (iii) rust resistance genes, Yr36, Yr15, Lr24, and Sr24. GPC increased by 0.8 to 3.3%, although high GPC was generally associated with yield penalty. Further selection among high GPC lines allowed identification of progenies with higher GPC associated with improvement in 1000-grain weight and grain yield in the backgrounds of the following four cultivars: NI5439, UP2338, UP2382, and HUW468. The high GPC progenies (derived from NI5439) were also improved for grain quality using HMW glutenin subunits 5 + 10 at Glu-D1 loci. Similarly, progenies combining high GPC and rust resistance were obtained in the backgrounds of following five cultivars: Lok1, HD2967, PBW550, PBW621, and DBW1. The improved pre-bred lines developed following multi-institutional effort should prove a valuable source for the development of cultivars with improved nutritional quality and rust resistance in the ongoing wheat breeding programmes. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01277-w.

Juvenile heat stress tolerance in Triticum durum-Aegilops tauschii derived synthetics: a way forward for wheat improvement.

BACKGROUND: Exponentially increasing population and everchanging climatic conditions are two major concerns for global food security. Early sowing in the second fortnight of October is an emerging trend with farmers in Indo Gangetic Plains to avoid yield losses from terminal heat stress. This also benefits the use of residual soil moisture of rice crop, conserving about one irrigation. But most of the available wheat cultivars are not well adapted to early-season sowing. METHODS AND RESULTS: Two in-house developed SHWs, syn14128 and syn14170, were screened for juvenile heat stress. Seedling length, biochemical parameters, and expression of amylase gene immediately after heat shock (HS) of 45 °C for 12 h and 20 h, and 24 h indicated significantly lower malondialdehyde, hydrogen peroxide, and higher free radical scavenging activities. Syn14170 reported higher total soluble sugar (TSS) under both HS periods, while syn14128 had a sustainable TSS content and amylase activity under HS as well as the recovery period. CONCLUSIONS: Both the SHWs had lower oxidative damage along with high free radical scavenging under heat stress. The higher expression of amy4 along with sustainable TSS after heat stress in syn14128 indicated it as a potential source of juvenile heat stress tolerance. Variable response of SHWs to different biochemical parameters under heat stress opens future perspectives to explore the enzymatic pathways underlying these responses.

Elucidation of underlying molecular mechanism of 5-Fluorouracil chemoresistance and its restoration using fish oil in experimental colon carcinoma.

Latest strategies for cancer treatment primarily focus on the use of chemosensitizers to enhance therapeutic outcome. N-3 PUFAs have emerged as the strongest candidate for the prevention of colorectal cancer (CRC). Our previous studies have demonstrated that fish oil (FO) rich in n-3 PUFAs not only increased therapeutic potential of 5-Fluorouracil(5-FU) in colon cancer but also ameliorated its toxicity. Henceforth, the present study is designed to elucidate mechanistic insights of FO as a chemosensitizer to circumvent drug resistance in experimental colon carcinoma. The colon cancer was induced by 1,2-dimethylhydrazine(DMH)/dextran sulfate sodium(DSS) in male Balb/c mice and these animals were treated with 5-FU(12.5 mg/kg b.w.), FO(0.2 ml), or 5-FU + FO(12.5 mg/kg b.w + 0.2 ml) orally for 14 days. The molecular mechanism of overcoming 5-FU resistance using FO in colon cancer was delineated by estimating expression of cancer stem cell markers using flowcytometric method and drug transporters by immunohistochemistry and immunoblotting. Additionally, distribution profile of 5-FU and its cytotoxic metabolite, 5-FdUMP at target(colon), and non-target sites (serum, kidney, liver, spleen) was assessed using high-performance liquid chromatography(HPLC) method. The observations revealed that expression of CSCs markers was remarkably reduced after using fish oil along with 5-FU in carcinogen-treated animals. Interestingly, the use of FO alongwith 5-FU also significantly declined the expression of drug transporters (ABCB1,ABCC5) and consequently resulted in an increased cellular uptake of 5-FU and its metabolite, 5-FdUMP at target site (colon). It could be possibly associated with change in permeability of cell membrane owing to the alteration in membrane fluidity. The present study revealed the mechanistic insights of FO as a MDR revertant which successfully restored 5-FU-mediated chemoresistance in experimental colon carcinoma.

A robust KASP marker for selection of four pairs of linked leaf rust and stripe rust resistance genes introgressed on chromosome arm 5DS from different wheat genomes.

Stripe rust and leaf rust are among the most devastating diseases of wheat, limiting its production globally. Wheat wild relatives harbour genetic diversity for new genes and alleles for all major wheat diseases. However, the use of this genetic variation from wild progenitor and non-progenitor species has been limited in the breeding programs. Reasons include limited recombination of donor and recipient genomes and the lack of tertiary gene pool markers. Here, we describe the development of a SNP based marker from the flow-sorted and sequenced Aegilops umbellulata chromosome 5U which can be used for marker assisted selection of four pair of alien leaf rust and stripe rust resistance genes. Lr57-Yr40_CAPS16 marker was reported earlier to be linked with alien leaf and stripe rust resistance genes introgressed on wheat chromosome 5DS. Due to its dominant nature and laborious to work with, a new SNP-based KASP marker, XTa5DS-2754099_kasp23, was developed from the same CAPS marker contig. XTa5DS-2754099_kasp23 was tested in Aegilops umbellulata, Ae. geniculata, Ae. peregrina and Ae. caudata derived alien introgression lines, which harbour four pairs of linked leaf and stripe rust genes; Lr76-Yr70, Lr57-Yr40, LrP- YrP, LrAc-YrAc, respectively. This KASP marker was found to be effective for the selection of the aforesaid four pairs of leaf rust and stripe rust resistance genes. Further, we tested and validated XTa5DS-2754099_kasp23 on commercial varieties and advanced breeding lines from four countries (India, Egypt, Australia and UK) including hexaploid and durum wheat. Our results provide evidence that KASP marker, XTa5DS-2754099_kasp23 can be used in marker-assisted selection of the four pairs of rust resistance alien genes in wheat breeding programmes.

Genomic insights into evolution of extensive drug resistance in Stenotrophomonas maltophilia complex.

We report first complete genomic investigation of extensive drug resistance (XDR) in a nosocomial Stenotrophomonas maltophilia complex strain that is resistant to mainstream drugs (trimethoprim/sulfamethoxazole and levofloxacin). Comprehensive genomic investigation revealed its exclusive fourteen dynamic regions and highly enriched resistome comprising of two sulfonamide resistance genes on two diverse super-integrons of chromosomal origin. In addition, both these integrons harbour array of antibiotic resistance and commonly used disinfectant's resistance genes linked to ISCR elements. Isolation of a novel XDR strain from Indian tertiary care unit belonging to novel ST with diverse array of resistance genes on ISCR linked super-integrons indicates extent and nature of selection pressure in hospitals. Since, repetitive elements have major role in their spread and due to limitations of draft genomes, there is an urgent need to employ complete genome-based investigation for tracking the emergence of XDR at global level and designing strategies of antimicrobial stewardship and disinfection. IMPORTANCE: Hospital settings in India have one of the highest usages of antimicrobials and a heavy patient load. We hereby report a novel clinical isolate of S. maltophilia complex with two super-integrons that harbour array of antimicrobial resistance genes along with biocide and heavy metal resistance genes. Further, the presence of ISCR type of transposable elements on both the integrons indicates their propensity to transfer resistome while their chromosomal origin suggests possibilities for further genomic/phenotypic complexities according to selection pressure. Such complex mobile cassettes in a novel strain is a potential threat to global health care. Hence, to understand the evolution of opportunistic nosocomial pathogen, there is an urgent need to employ cost-effective long read technologies to keep vigilance on novel and XDR pathogens in populous countries. There is also need for surveillance of the usage of disinfectants and other antimicrobials for environmental hygiene and linked/rapid co-evolution of XDR in nosocomial pathogens. Repositories: Complete genome sequence of Stenotrophomonas maltophilia SM866: CP031058.

Can ACGME Milestones predict surgical specialty board passage: an example in Obstetrics and Gynecology.

BACKGROUND: Multiple tools including Accreditation Council for Graduate Medical Education (ACGME) standardized milestones can be utilized to assess trainee and residency program performance. However, little is known regarding the objective validation of these tools in predicting written board passage. METHODS: In this retrospective study, data was gathered on n = 45 Wayne State University Obstetrics and Gynecology program graduates over the five-year period ending July 2018. United States Medical Licensing Examination (USMLE) scores, Council on Resident Education in Obstetrics and Gynecology (CREOG) in-training scores and ACGME milestones were used to predict American Board of Obstetrics and Gynecology (ABOG) board passage success on first attempt. Significance was set at p < 0.05. RESULTS: Written board passage was associated with average CREOGs (p = 0.01) and milestones (p = 0.008) while USMLE1 was not significantly associated (p = 0.055). USMLE1 <217 (Positive predictive value (PPV) = 96%). CREOGs <197 (PPV = 100%) and milestones <3.25 (PPV = 100%), particularly practice-based learning and systems-based practice milestones were most strongly correlated with board failure. Using a combination of these two milestones, it is possible to correctly predict board passage using our model (PPV = 86%). DISCUSSION: This study is the first validating the utility of milestones in a surgical specialty by demonstrating their ability to predict board passage. Residents with CREOGs or milestones below thresholds are at risk for board failure and may warrant early intervention.

Cloning, expression analysis and In silico characterization of HSP101: a potential player conferring heat stress in Aegilops speltoides (Tausch) Gren.

Heat shock protein (HSP101) function as molecular chaperones and confer thermotolerance to plants. In the present investigation, identification, comprehensive expression analysis, phylogeny and protein modelling of HSP101 gene has been done in Aegilops speltoides accession Pau3583. In the present study, we cloned and in silico characterized a HSP101C gene designated as AsHSP101C-Pau3583. AsHSP101C-Pau3583 is 4180 bp long with seven exons and six introns and encoded a polypeptide of 910 amino acids predicted by FGENESH. We have identified 58 SNPs between the AsHSP101C-Pau3583 and reference gene sequence extracted from Ae. speltoides TGAC assembly. Real-time RT-PCR analysis of expression levels of HSP101 gene in two wheat genotypes under heat stress revealed that gene namely HSP101C was up-regulated in Aegilops speltoides acc. Pau3583 by > fourfold in comparison to Triticum aestivum cv. PBW343 under heat stress signifies that it plays a role in conferring heat tolerance. Sequence comparison and phylogenetic analysis of AsHSP101C-Pau3583 with seven wheat homologs Triticum aestivum, Aegilops speltoides (TGAC), Triticum durum cv Cappelli, Triticum durum cv Strongfield, Triticum monococcum, Aegilops tauschii and Triticum urartu showed significant similarities with highly conserved coding regions and functional domains (AAA, AAA + 2, ClpB domains), suggesting the conserved function of HSP101C in different species. The illustration of the protein models of HSP101C in homologs provided information for the ATP-binding motifs within the nucleotide binding domains (NBD), specific for the chaperone activity. These findings are important and identified SNPs could be used for designing markers for ensuring the transfer of AsHSP101C-Pau3583 gene into hexaploid wheat and its role in heat tolerance. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-01005-2.

Understanding COVID-19 transmission, health impacts and mitigation: timely social distancing is the key.

COVID-19 is a highly infectious disease caused by SARS-CoV-2, first identified in China and spread globally, resulting into pandemic. Transmission of virus takes place either directly through close contact with infected individual (symptomatic/asymptomatic) or indirectly by touching contaminated surfaces. Virus survives on the surfaces from few hours to days. It enters the human body through nose, eyes or mouth. Other sources of contamination are faeces, blood, food, water, semen etc. Parameters such as temperature/relative humidity also play an important role in transmission. As the disease is evolving, so are the number of cases. Proper planning and restriction are helping in influencing the trajectory of the transmission. Various measures are undertaken to prevent infection such as maintaining hygiene, using facemasks, isolation/quarantine, social/physical distancing, in extreme cases lockdown (restricted movement except essential services) in hot spot areas or throughout the country. Countries that introduced various mitigation measures had experienced control in transmission of COVID-19. Python programming is conducted for change point analysis (CPA) using Bayesian probability approach for understanding the impact of restrictions and mitigation methods in terms of either increase or stagnation in number of COVID-19 cases for eight countries. From analysis it is concluded that countries which acted late in bringing in the social distancing measures are suffering in terms of high number of cases with USA, leading among eight countries analysed. The CPA week in comparison with date of lockdown and first reported case strongly correlates (Pearson's r = - 0.86 to - 0.97) to cases, cases per unit area and cases per unit population, indicating earlier the mitigation strategy, lesser the number of cases. The overall paper will help the decision makers in understanding the possible steps for mitigation, more so in developing countries where the fight against COVID-19 seems to have just begun.

Aegilops umbellulata introgression carrying leaf rust and stripe rust resistance genes Lr76 and Yr70 located to 9.47-Mb region on 5DS telomeric end through a combination of chromosome sorting and sequencing.

KEY MESSAGE: Lr76 and Yr70 have been fine mapped using the sequence of flow-sorted recombinant 5D chromosome from wheat-Ae. umbellulata introgression line. The alien introgression has been delineated to 9.47-Mb region on short arm of wheat chromosome 5D. Leaf rust and stripe rust are among the most damaging diseases of wheat worldwide. Wheat cultivation based on limited number of rust resistance genes deployed over vast areas expedites the emergence of new pathotypes warranting a continuous deployment of new resistance genes. In this paper, fine mapping of Aegilops umbellulata-derived leaf rust and stripe rust resistance genes Lr76 and Yr70 is being reported. We flow sorted and paired-end sequenced 5U chromosome of Ae. umbellulata, recombinant chromosome 5D (5DIL) from wheat-Ae. umbellulata introgression line pau16057 and 5DRP of recurrent parent WL711. Chromosome 5U reads were mapped against the reference Chinese Spring chromosome 5D sequence, and alien-specific SNPs were identified. Chromosome 5DIL and 5DRP sequences were de novo assembled, and alien introgression-specific markers were designed by selecting 5U- and 5D-specific SNPs. Overall, 27 KASP markers were mapped in high-resolution population consisting of 1404 F5 RILs. The mapping population segregated for single gene each for leaf rust and stripe rust resistance. The physical order of the SNPs in pau16057 was defined by projecting the 27 SNPs against the IWGSC RefSeq v1.0 sequence. Based on this physical map, the size of Ae. umbellulata introgression was determined to be 9.47 Mb on the distal most end of the short arm of chromosome 5D. This non-recombining alien segment carries six NB-LRR encoding genes based on NLR annotation of assembled chromosome 5DIL sequence and IWGSC RefSeq v1.1 gene models. The presence of SNPs and other sequence variations in these genes between pau16057 and WL711 suggested that they are candidates for Lr76 and Yr70.

Comparative analysis of chromosome 2A molecular organization in diploid and hexaploid wheat.

Diploid A genome wheat species harbor immense genetic variability which has been targeted and proven useful in wheat improvement. Development and deployment of sequence-based markers has opened avenues for comparative analysis, gene transfer and marker assisted selection (MAS) using high throughput cost effective genotyping techniques. Chromosome 2A of wheat is known to harbor several economically important genes. The present study aimed at identification of genic sequences corresponding to full length cDNAs and mining of SSRs and ISBPs from 2A draft sequence assembly of hexaploid wheat cv. Chinese Spring for marker development. In total, 1029 primer pairs including 478 gene derived, 501 SSRs and 50 ISBPs were amplified in diploid A genome species Triticum monococcum and T. boeoticum identifying 221 polymorphic loci. Out of these, 119 markers were mapped onto a pre-existing chromosome 2A genetic map consisting of 42 mapped markers. The enriched genetic map constituted 161 mapped markers with final map length of 549.6 cM. Further, 2A genetic map of T. monococcum was anchored to the physical map of 2A of cv. Chinese Spring which revealed several rearrangements between the two species. The present study generated a highly saturated genetic map of 2A and physical anchoring of genetically mapped markers revealed a complex genetic architecture of chromosome 2A that needs to be investigated further.

Vitamin D: Its Deficiency and Effect of Supplementation on Maternal Outcome.

OBJECTIVES: Vitamin D deficiency is on a rise globally and so are the maternal complications related to it. This deficiency can be easily detected and corrected by simple oral supplementation for a better health outcome in pregnancy. METHODS: Antenatal women with no history of Vitamin D intake and first antenatal visit at our hospital between 26 to 28 weeks of gestation or after 34 weeks were tested for levels of Vitamin 25(OH)D. Deficient women (< 30 ng/ml) between 26 to 28 weeks were supplemented and tested again before delivery (Group A). Deficient women after 34 weeks who did not receive supplementation before delivery constituted Group B. Maternal outcome was noted and compared in both the groups. RESULTS: Out of the 189 Vitamin D deficient women included in the study; 105(55.5%) were enrolled in Group A and 84 (44.4%) in Group B. 24 (12.7%) women were severely deficient (<4 ng/ml), 134 (70.9%) were deficient (<20 ng/ml) and 28(14.8%) were vitamin D insufficient (20-30 ng/ml). A statistically significant reduction (<0.001) was observed in vitamin D deficient women after supplementation in group A. 5.7% women developed preeclampsia in group A as compared to 28.5% in group B (p<0.0001). Higher (13%) incidence of gestational diabetes mellitus was observed in group B as compared to group A (6.6%) though the difference was not significant. A significantly higher incidence of preterm labor was observed in group B (p=0.007). CONCLUSION: Vitamin D deficiency is correlated with a higher incidence of preeclampsia, gestational diabetes mellitus and preterm birth. Maternal screening in targeted population and its supplementation is recommended to improve maternal outcome.