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.

Comprehensive meta-QTL analysis for dissecting the genetic architecture of stripe rust resistance in bread wheat

BACKGROUND

Yellow or stripe rust, caused by the fungus Puccinia striiformis f. sp. tritici (Pst) is an important disease of wheat that threatens wheat production. Since developing resistant cultivars offers a viable solution for disease management, it is essential to understand the genetic basis of stripe rust resistance. In recent years, meta-QTL analysis of identified QTLs has gained popularity as a way to dissect the genetic architecture underpinning quantitative traits, including disease resistance.

RESULTS

Systematic meta-QTL analysis involving 505 QTLs from 101 linkage-based interval mapping studies was conducted for stripe rust resistance in wheat. For this purpose, publicly available high-quality genetic maps were used to create a consensus linkage map involving 138,574 markers. This map was used to project the QTLs and conduct meta-QTL analysis. A total of 67 important meta-QTLs (MQTLs) were identified which were refined to 29 high-confidence MQTLs. The confidence interval (CI) of MQTLs ranged from 0 to 11.68 cM with a mean of 1.97 cM. The mean physical CI of MQTLs was 24.01 Mb, ranging from 0.0749 to 216.23 Mb per MQTL. As many as 44 MQTLs colocalized with marker-trait associations or SNP peaks associated with stripe rust resistance in wheat. Some MQTLs also included the following major genes- Yr5, Yr7, Yr16, Yr26, Yr30, Yr43, Yr44, Yr64, YrCH52, and YrH52. Candidate gene mining in high-confidence MQTLs identified 1,562 gene models. Examining these gene models for differential expressions yielded 123 differentially expressed genes, including the 59 most promising CGs. We also studied how these genes were expressed in wheat tissues at different phases of development.

CONCLUSION

The most promising MQTLs identified in this study may facilitate marker-assisted breeding for stripe rust resistance in wheat. Information on markers flanking the MQTLs can be utilized in genomic selection models to increase the prediction accuracy for stripe rust resistance. The candidate genes identified can also be utilized for enhancing the wheat resistance against stripe rust after in vivo confirmation/validation using one or more of the following methods: gene cloning, reverse genetic methods, and omics approaches.

Recent advances on genome-wide association studies (GWAS) and genomic selection (GS); prospects for Fusarium head blight research in Durum wheat

PURPOSE

Wheat is an important cereal crop that is cultivated in different parts of the world. The biotic stresses are the major concerns in wheat-growing nations and are responsible for production loss globally. The change in climate dynamics makes the pathogen more virulent in foothills and tropical regions. There is growing concern about FHB in major wheat-growing nations, and until now, there has been no known potential source of resistance identified in wheat germplasm. The plant pathogen interaction activates the cascade of pathways, genes, TFs, and resistance genes. Pathogenesis-related genes' role in disease resistance is functionally validated in different plant systems. Similarly, Genomewide association Studies (GWAS) and Genomic selection (GS) are promising tools and have led to the discovery of resistance genes, genomic regions, and novel markers. Fusarium graminearum produces deoxynivalenol (DON) mycotoxins in wheat kernels, affecting wheat productivity globally. Modern technology now allows for detecting and managing DON toxin to reduce the risk to humans and animals. This review offers a comprehensive overview of the roles played by GWAS and Genomic selection (GS) in the identification of new genes, genetic variants, molecular markers and DON toxin management strategies.

METHODS

The review offers a comprehensive and in-depth analysis of the function of Fusarium graminearum virulence factors in Durum wheat. The role of GWAS and GS for Fusarium Head Blight (FHB) resistance has been well described. This paper provides a comprehensive description of the various statistical models that are used in GWAS and GS. In this review, we look at how different detection methods have been used to analyze and manage DON toxin exposure.

RESULTS

This review highlights the role of virulent genes in Fusarium disease establishment. The role of genome-based selection offers the identification of novel QTLs in resistant wheat germplasm. The role of GWAS and GS selection has minimized the use of population development through breeding technology. Here, we also emphasized the function of recent technological developments in minimizing the impact of DON toxins and their implications for food safety.

Multi-locus genome-wide association studies (ML-GWAS) reveal novel genomic regions associated with seedling and adult plant stage leaf rust resistance in bread wheat (Triticum aestivum L.)

Leaf rust is one of the important diseases limiting global wheat production and productivity. To identify quantitative trait nucleotides (QTNs) or genomic regions associated with seedling and adult plant leaf rust resistance, multilocus genome-wide association studies (ML-GWAS) were performed on a panel of 400 diverse wheat genotypes using 35 K single-nucleotide polymorphism (SNP) genotyping assays and trait data of leaf rust resistance. Association analyses using six multi-locus GWAS models revealed a set of 201 significantly associated QTNs for seedling and 65 QTNs for adult plant resistance (APR), explaining 1.98-31.72% of the phenotypic variation for leaf rust. Among these QTNs, 51 reliable QTNs for seedling and 15 QTNs for APR were consistently detected in at least two GWAS models and were considered reliable QTNs. Three genomic regions were pleiotropic, each controlling two to three pathotype-specific seedling resistances to leaf rust. We also identified candidate genes, such as leucine-rich repeat receptor-like (LRR) protein kinases, P-loop containing nucleoside triphosphate hydrolase and serine-threonine/tyrosine-protein kinases (STPK), which have a role in pathogen recognition and disease resistance linked to the significantly associated genomic regions. The QTNs identified in this study can prove useful in wheat molecular breeding programs aimed at enhancing resistance to leaf rust and developing next-generation leaf rust-resistant varieties.

Design of a Device for Lower Limb Prophylaxis and Exercise

The problem of immobility of legs leading to a potentially life threatening condition including deep venous thrombosis (DVT) is well known. The reduced mobility of leg affects a large number of patients in a wide range of clinical scenarios spanning from swelling of the legs to pulmonary embolism. In normal human beings, an elegant system of venous return, both active and passive is responsible for prevention of deep venous thrombosis. The paper proposes a prophylaxis and exercise device that mimics the natural principles of venous return to promote the blood flow. The device is based on electromechanical actuation, and simultaneous alternating compression mechanism, that is compact and, suitably form fitted in design and additionally requires no specialised training for the usage. The device was tested on a healthy volunteer on two different days and findings support the efficacy of the prophylaxis and exercise device in significantly improving the blood flow rate in the lower limb. The prototype device is considered as a major step towards designing a clinically validated lower limb device.

Pediatric cerebral proliferative angiopathy presenting infratentorial hemorrhage

Cerebral proliferative angiopathies (CPAs) are distinct vascular malformations with varied clinical presentations and radiological findings from arteriovenous malformations (AVM) (Lasjaunias et al. in Stroke 39(3):878-85, 2008). They usually manifest with seizures if present supratentorial, headache, and progressive neurological deficits due to steal phenomenon or rarely with hemorrhage (Lasjaunias et al. in Stroke 39(3):878-85, 2008). Most of the patients are usually young females. Pediatric cases are extremely rare, with few cases reported till now. Here we report a child who presented with cerebellar bleed and diagnosed as CPA. The child was managed medically, and there was no change in caliber of the vessels after 18 months of follow-up. A short review of cases of CPA in pediatric age group presentations and management was undertaken in this case report.

Surgical Management and Outcomes of Aneurysms of Posterior Inferior Cerebellar Artery: Location-Based Approaches with Review of Literature

Background  Posterior inferior cerebellar artery (PICA) is a tortuous, variable, and uncommon site for aneurysms. Surgical management of PICA aneurysms involves careful selection of approach based on the location of the aneurysm and meticulous dissection of the neurovascular structures and perforators.

Materials and Methods  We did a retrospective review of all the PICA aneurysms operated at our institute in the past 10 years along with the site, presentation, and approach used for the same. Preoperative World Federation of Neurosurgical Society scores and follow-up modified Rankin scores (mRS) were also evaluated. During the same period, data for intervention cases of PICA aneurysm were also collected with follow-ups for a comparative analysis.

Results  A total of 20 patients with 21 PICA aneurysms were reviewed. All the reviewed cases presented with subarachnoid hemorrhage, and the most common location was the lateral medullary segment and vertebral artery (VA)–PICA junction. Midline approaches were used for distal PICA cases, with far-lateral approach reserved for anterior medullary/VA–PICA junction. No lower cranial nerve palsies were recorded at follow-up. Four cases needed cerebrospinal fluid diversion and two developed cerebellar infarcts. All cases were mRS 0 to 2 at follow-up.

Conclusion  Our series compares well with some of the larger surgical series of PICA aneurysms. This may be due to early referral patterns and early surgery (<24 hours) policy at our institution. Anatomical knowledge of PICA anatomy and sound perioperative management are keys to good outcomes in these cases.

"Tailored" far lateral approach to anterior foramen magnum meningiomas - The importance of condylar preservation

Introduction

Anterior and anterolaterally situated foramen magnum meningiomas are a technically complex subgroup of meningiomas. The need for an extensive exposure and bone work and their complex anatomy make them a difficult and challenging group of tumors to resect. The bone work has ranged from an extensive condylar resection to condylar preserving exposures. In this paper, we present our experience with condylar preserving or minimal condylar resection based approaches to these tumors.

Materials and Methods

All patients who underwent surgical resection of anterior and anterolaterally situated foramen magnum meningiomas were included in the analysis. The study period was more than 10 years from 2005 to 2015 at our institute; a tertiary referral centre in India. The records along with demographic profile, clinico-radiological features, surgical strategies, outcomes as well as mortality and morbidity were analysed.

Results

There were a total of 20 patients (9 males and 11 females) who were operated during the study period. The average age was 36.7 years. In 16 patients, gross-total or near-total resection could be achieved, four patients underwent subtotal resection. Eight patients had fresh morbidity in the form of new motor deficits, pseudomeningocele formation, worsening of the lower cranial nerve functions or post-operative adhesions leading to syrinx formation. The follow-up ranged from 6 months to 140 months.

Conclusion

Foramen magnum meningiomas are an eminently treatable group of tumors. Condylar preservation provides a good visualization, while helping to preserve joint stability and in avoiding instrumental stabilization.

An unusual site of metastasis from carcinoma of tongue - metastasis to lumbar vertebrae: A case report and review of literature

Background:

Carcinoma of tongue is a common site of oral cancer. It usually occurs at mean age of 61.1 years and is more common in males when compared with females. It commonly spreads directly and through lymphatics to the surrounding structures. It has a low incidence of hematogenous metastasis. Lung is the usual distant metastasis site for carcinoma of tongue and other head and neck cancers. Metastases to vertebrae are rare and very few cases have been reported.

Case Description:

We report a rare case of carcinoma of tongue spreading to lumbar vertebrae causing destruction of the body and thecal sac compression. A patient underwent posterior transpedicular approach, tumor decompression, and titanium cage placement. The patient had good relief of symptoms and could be mobilized on first postoperative day.

Conclusion:

Hematogenous spread to the spine is a rare phenomenon but should be kept in mind particularly in advanced stage of oral cancers.

Rare Cranial Nerve Schwannomas: A Retrospective Review of Nontrigeminal, Nonvestibular Cranial Nerve Schwannomas

Introduction:

Intracranial schwannomas arising from non-trigeminal and non-vestibular sources are extremely rare constituting <0.8% of all schwannomas. In this article, we have analyzed our experience in the management of these rare tumors over a 10-year period.

Material and Methods:

There were a total of 16 cases, with 11 of them undergoing microsurgical resection and 5 undergoing stereotactic radiosurgery (SRS).

Results:

There were no fresh neurological deficit in any of these patients and two patients underwent postoperative SRS for residual tumor. One patient died due to postoperative septicemia.

Conclusion:

Knowledge of these lesions along with their clinicoradiological profile is essential to maintain a high index of suspicion and understand the nuances of treatment.

Wolf in Sheep's clothing: Intracranial actinomycosis masquerading as en-plaque meningioma

Background:

Actinomycosis israeli is a gram-positive non-acid-fast bacterium and is the most common causative agent of actinomycosis. It usually presents as a brain abscess via a secondary spread from the cervicofacial region or lungs. However, presentation as an en-plaque lesion with bone involvement out of proportion to brain parenchyma is rare and needs to be acknowledged.

Case Description:

We report a case of intracranial en-plaque lesion in a 47-year-old female with restriction of mouth opening and right third nerve palsy for 1 year. Imaging showed hyperostosis of the maxilla, temporal base, sphenoid, and zygoma with dural thickening suggestive of a meningioma. Surgical decompression yielded a granulomatous lesion along with empirical antitubercular therapy. However, patient succumbed to the infection and final histopathology revealed actinomycosis infection.

Conclusion:

Adequate knowledge along with clinical suspicion are the pillars to treating this unfortunate disease. Cheek swelling with bone involvement should be actively sought as risk factors. This case presents a unique opportunity to identify the fox among the sheep by elucidating the characteristic imaging findings and intraoperative view of this rare entity.

Evaluation of 19,460 Wheat Accessions Conserved in the Indian National Genebank to Identify New Sources of Resistance to Rust and Spot Blotch Diseases

A comprehensive germplasm evaluation study of wheat accessions conserved in the Indian National Genebank was conducted to identify sources of rust and spot blotch resistance. Genebank accessions comprising three species of wheat-Triticum aestivum, T. durum and T. dicoccum were screened sequentially at multiple disease hotspots, during the 2011-14 crop seasons, carrying only resistant accessions to the next step of evaluation. Wheat accessions which were found to be resistant in the field were then assayed for seedling resistance and profiled using molecular markers. In the primary evaluation, 19,460 accessions were screened at Wellington (Tamil Nadu), a hotspot for wheat rusts. We identified 4925 accessions to be resistant and these were further evaluated at Gurdaspur (Punjab), a hotspot for stripe rust and at Cooch Behar (West Bengal), a hotspot for spot blotch. The second round evaluation identified 498 accessions potentially resistant to multiple rusts and 868 accessions potentially resistant to spot blotch. Evaluation of rust resistant accessions for seedling resistance against seven virulent pathotypes of three rusts under artificial epiphytotic conditions identified 137 accessions potentially resistant to multiple rusts. Molecular analysis to identify different combinations of genetic loci imparting resistance to leaf rust, stem rust, stripe rust and spot blotch using linked molecular markers, identified 45 wheat accessions containing known resistance genes against all three rusts as well as a QTL for spot blotch resistance. The resistant germplasm accessions, particularly against stripe rust, identified in this study can be excellent potential candidates to be employed for breeding resistance into the background of high yielding wheat cultivars through conventional or molecular breeding approaches, and are expected to contribute toward food security at national and global levels.

Successful treatment of primary cerebral mucormycosis: Role of microbiologist

Fungal brain abscess is rare with a rapidly progressive disease with fulminant course and invariably fatal outcome, unless diagnosed early and treated rapidly. We report a 56-year-old woman diagnosed to have fungal abscess who recovered completely following amphotericin B treatment. She presented with weakness of the right hand, deviation of mouth to left and aphasia for 2 days. Computed tomography of the brain revealed a left frontal capsuloganglionic hypodense lesion. Stereotactic biopsy was performed, and microbiological confirmation of non-septate fungal hyphae from pus from aspirate within 2 h helped initiate timely and appropriate treatment leading to cure. Histopathology and culture later confirmed mucormycosis.

Softworms: the design and control of non-pneumatic, 3D-printed, deformable robots

Robots that can easily interact with humans and move through natural environments are becoming increasingly essential as assistive devices in the home, office and hospital. These machines need to be safe, effective, and easy to control. One strategy towards accomplishing these goals is to build the robots using soft and flexible materials to make them much more approachable and less likely to damage their environment. A major challenge is that comparatively little is known about how best to design, fabricate and control deformable machines. Here we describe the design, fabrication and control of a novel soft robotic platform (Softworms) as a modular device for research, education and public outreach. These robots are inspired by recent neuromechanical studies of crawling and climbing by larval moths and butterflies (Lepidoptera, caterpillars). Unlike most soft robots currently under development, the Softworms do not rely on pneumatic or fluidic actuators but are electrically powered and actuated using either shape-memory alloy microcoils or motor tendons, and they can be modified to accept other muscle-like actuators such as electroactive polymers. The technology is extremely versatile, and different designs can be quickly and cheaply fabricated by casting elastomeric polymers or by direct 3D printing. Softworms can crawl, inch or roll, and they are steerable and even climb steep inclines. Softworms can be made in any shape but here we describe modular and monolithic designs requiring little assembly. These modules can be combined to make multi-limbed devices. We also describe two approaches for controlling such highly deformable structures using either model-free state transition-reward matrices or distributed, mechanically coupled oscillators. In addition to their value as a research platform, these robots can be developed for use in environmental, medical and space applications where cheap, lightweight and shape-changing deformable robots will provide new performance capabilities.

A pure non-gestational ovarian choriocarcinoma with delayed solitary brain metastases: Case report and review of the literature

Choriocarcinoma is the most malignant tumour of gestational trophoblastic origin. Most ovarian choriocarcinomas are gestational in origin and usually metastasize to the ovary from uterine or tubal choriocarcinoma. Non gestational choriocarcinoma (NGOC) of the ovary is exceedingly rare and usually seen along with other germ cell tumors. Non gestational choriocarcinoma has been found to be resistant to single-agent chemotherapy and has a worse prognosis than gestational choriocarcinoma. We are reporting long term follow up of published rare case of pure non gestational ovarian choriocarcinoma (NGOC) with concurrent metastases to the spleen and adrenal glands, who developed a delayed solitary brain metastases, two years after completion of primary treatment. Surgery along with triple agent chemotherapy and radiotherapy was found to give good remission in this aggressive disease.

A pure non-gestational ovarian choriocarcinoma with delayed solitary brain metastases: Case report and review of the literature

Choriocarcinoma is the most malignant tumour of gestational trophoblastic origin. Most ovarian choriocarcinomas are gestational in origin and usually metastasize to the ovary from uterine or tubal choriocarcinoma. Non gestational choriocarcinoma (NGOC) of the ovary is exceedingly rare and usually seen along with other germ cell tumors. Non gestational choriocarcinoma has been found to be resistant to single-agent chemotherapy and has a worse prognosis than gestational choriocarcinoma. We are reporting long term follow up of published rare case of pure non gestational ovarian choriocarcinoma (NGOC) with concurrent metastases to the spleen and adrenal glands, who developed a delayed solitary brain metastases, two years after completion of primary treatment. Surgery along with triple agent chemotherapy and radiotherapy was found to give good remission in this aggressive disease.

Machine learning methods for the classification of gliomas: Initial results using features extracted from MR spectroscopy

CONTEXT

With the advent of new imaging modalities, radiologists are faced with handling increasing volumes of data for diagnosis and treatment planning. The use of automated and intelligent systems is becoming essential in such a scenario. Machine learning, a branch of artificial intelligence, is increasingly being used in medical image analysis applications such as image segmentation, registration and computer-aided diagnosis and detection. Histopathological analysis is currently the gold standard for classification of brain tumors. The use of machine learning algorithms along with extraction of relevant features from magnetic resonance imaging (MRI) holds promise of replacing conventional invasive methods of tumor classification.

AIMS

The aim of the study is to classify gliomas into benign and malignant types using MRI data.

SETTINGS AND DESIGN

Retrospective data from 28 patients who were diagnosed with glioma were used for the analysis. WHO Grade II (low-grade astrocytoma) was classified as benign while Grade III (anaplastic astrocytoma) and Grade IV (glioblastoma multiforme) were classified as malignant.

METHODS AND MATERIALS

Features were extracted from MR spectroscopy. The classification was done using four machine learning algorithms: multilayer perceptrons, support vector machine, random forest and locally weighted learning.

RESULTS

Three of the four machine learning algorithms gave an area under ROC curve in excess of 0.80. Random forest gave the best performance in terms of AUC (0.911) while sensitivity was best for locally weighted learning (86.1%).

CONCLUSIONS

The performance of different machine learning algorithms in the classification of gliomas is promising. An even better performance may be expected by integrating features extracted from other MR sequences.